bluuebunny/crossref_metadata_2025 huggingface dataset:
No Significant Effect of Maternal Perception of the Food Environment on Reproductive Success or Pup Outcomes in C57BL/6J Mice
Authors: Gibbs Victoria K. , Schwartz Tonia S. , Johnson Maria S. , Patki Amit , Nagy Tim R. , George Brandon J. , Allison David B.
Published: February 2018

Objective

Prior work concerning maternal perception of the food environment suggests that perceived disparities in food resources resulted in reduced pup mass and dam reproductive success. This study attempted to replicate this result with increased sample size and additional measures.

Methods

Female C57BL/6J mice (n = 160; 3 weeks old) were randomly assigned to either subject or peer and were pair housed in partitioned cages with olfactory and visual contact. After a 6‐week maturation period on an energy‐rich cafeteria diet, cages were randomly assigned to Control (subject and peer fed pelleted diet) or Treatment (subject fed pellets, peer fed cafeteria diet), and subjects were bred. After weaning, one pup from each sex per litter was reared to 5 months.

Results

Treatment did not affect the number of births, pup size at birth, or the proportion of pups surviving to weaning (P > 0.09). Treatment did not affect dam body or fat mass at parturition (P > 0.22), but these measures were higher in some Treatment dams at weaning (P < 0.05). Smaller female pups were weaned from Treatment dams pregnant on the first breeding attempt (P = 0.01), but no other pup effects were observed (P > 0.07).

Conclusions

Exposure to food‐environment disparity in this study did not replicate previous findings or affect pup growth after weaning.
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

Objectives

International 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.

Method

Bibliographic 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.

Results

Twenty‐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.

Conclusion

The 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

Background

Optimized 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.

Methods

Paired 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).

Results

BCT 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.

Conclusions

Optimized 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

The 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.
Moon’s Magnetic Field May Magnetize Iron That Hits Its Surface
Authors: Witman Sarah
Published: February 2018

Scientists are using satellite data to study large impact basins on the surface of the Moon that contain magnetic anomalies.
Application of protein crystallization methodologies to enhance the solubility, stability and monodispersity of proteins
Authors: Zhou Ren-Bin , Lu Xiao-Li , Dong Chen , Ahmad Fiaz , Zhang Chen-Yan , Yin Da-Chuan
Published: February 2018

Application of protein crystallization methodologies to screen optimal solution formulations for proteins prone to aggregation.
Facile one-pot nanocatalysts encapsulation of palladium–NHC complexes for aqueous Suzuki–Miyaura couplings
Authors: Chen Chao , Zheng Qing , Ni Shengliang , Wang Hangxiang
Published: February 2018

Pd–NHC loaded nanocatalysts (NCs) were readily constructed by a facile one-pot self-assembly approach. These nanoparticles exhibited excellent catalytic activity in aqueous Suzuki–Miyaura couplings.
Selective growth of chirality-enriched semiconducting carbon nanotubes by using bimetallic catalysts from salt precursors
Authors: Zhao Xiulan , Yang Feng , Chen Junhan , Ding Li , Liu Xiyan , Yao Fengrui , Li Meihui , Zhang Daqi , Zhang Zeyao , Liu Xu , Yang Juan , Liu Kaihui , Li Yan
Published: February 2018

The controllable growth of 96% semiconducting SWNTs including 62% (14, 4) tubes was realized by using W–Co bimetallic catalysts.
3D silver nanoparticles with multilayer graphene oxide as a spacer for surface enhanced Raman spectroscopy analysis
Authors: Li Zhen , Jiang Shouzhen , Huo Yanyan , Ning Tingyin , Liu Aihua , Zhang Chao , He Yuan , Wang Minghong , Li Chonghui , Man Baoyuan
Published: February 2018

We explore the variation of SERS performance towards two different Ag NP layers using multilayer GO as a spacer.
UV and pH-responsive supra-amphiphiles driven by combined interactions for controlled self-assembly behaviors
Authors: Li Shangyang , Hao Aiyou , Shen Jian , Shang Ningzhao , Wang Chun
Published: February 2018

In order to fabricate a novel supra-amphiphile with multiple stimulus properties, we developed the strategy of introducing a bi-functional linker to bridge the hydrophilic and hydrophobic building blocks together, by utilizing more than one kind of interaction.
Tuning the dimensions and structures of nitrogen-doped carbon nanomaterials derived from sacrificial g-C3N4/metal–organic frameworks for enhanced electrocatalytic oxygen reduction
Authors: Wang Ruwen , Yan Tingting , Han Lupeng , Chen Guorong , Li Hongrui , Zhang Jianping , Shi Liyi , Zhang Dengsong
Published: February 2018

A facile strategy for tuning the dimensions and structures of nitrogen-doped carbon nanomaterials as ORR catalysts has been demonstrated.
Cobalt-doped Zn2GeO4 nanorods assembled into hollow spheres as high-performance anode materials for lithium-ion batteries
Authors: Lu Jiaxue , Li Deli , Li Li , Chai Yao , Li Meng , Yang Shun , Liang Jun
Published: February 2018

The synthesis of novel Co doped Zn2GeO4 hollow micro-spheres and the enhanced electrochemical performance for lithium-ion batteries.
Highly efficient white light-emitting diodes with a bi-component emitting layer based on blue and yellow thermally activated delayed fluorescence emitters
Authors: Chen Yongzhen , Li Shengyong , Hu Taiping , Wei Xiaofang , Li Zhiyi , Liu Yanwei , Liu Jianjun , Wang Ruifang , Yi Yuanping , Zhao Cuihua , Wang Ying , Wang Pengfei
Published: February 2018

A white LED with a bi-component light emitting layer is reported providing white light emission with a CIE of (0.38, 0.40), a CRI of 71, and a maximum EQE of 12.5%. These are among the best for bi-component based devices.
Reception and detection of a wide‐band OFDM signal in a Doppler spreading channel
Authors: Ma Lili , Jiang Wei , Xiang Haige
Published: February 2018

This study focuses on the reception strategy and the detection method of a wideband orthogonal frequency‐division multiplexing (OFDM) signal, which is passing through a Doppler channel. Most prior works regarded the Doppler effect as a reason of interchannel interference due to its destruction of the subcarrier orthogonality. Distinguishing from those works, the authors point out that the wideband OFDM signal is still an OFDM signal with subcarrier orthogonality after passing the channel with single Doppler scaling factor. Thus, the received OFDM signal passing the Doppler spreading channel is a linear superposition of a set of transmitted OFDM signals associated with different parameters. To make full use of the diversity gain offered by the superposition, the authors propose a strategy of diversity reception and a belief propagation detection method for the received wideband OFDM signal. The simulation results show that the proposed strategy improves the performance obviously with increase of the diversity order in a Doppler spreading channel. It offers different options for system demands. Furthermore, the proposed detection method can offer an acceptable performance even it combined with the conventional sampling process. It makes the conventional structure replacing the common resampling structure possible in a wideband OFDM system.
Individual channel estimation for amplify‐and‐forward relay networks using in‐band superimposed training
Authors: Dou Gaoqi , He Xianwen , Deng Ran , Gao Jun , Wang Qingbo
Published: February 2018

In amplify‐and‐forward relay networks, accurate channel estimation of individual links is essential for coherent reception and optimal design. To acquire the channel state information of individual links, a novel in‐band superimposed training is proposed, where relay superimposes its own training sequence directly on top of the information‐bearing received data. As a result, the training sequences from the source and relay nodes are independent of each other, thus making it more flexible and robust in relay‐training design. However, the proposed training scheme induces extra data interference that degrades the estimation performance. The authors first adopted the detected symbols to mitigate the data‐induced interference during channel estimation. However, the estimation performance is degraded by the symbol detection error and relay propagated noise. To resolve this problem, the interference nulling at the relay is proposed, where some special frequency components of the received data are nulled prior to training superimposition. As a result, both the data‐induced interference and relay propagated noise are totally removed during channel estimation. Simulation results are provided to assess the performance of the proposed schemes.
High‐efficiency wireless power transfer system for 3D, unstationary free‐positioning and multi‐object charging
Authors: Zhang Wei , Zhang Tengyuan , Guo Qiuquan , Shao Lingmin , Zhang Naibo , Jin Xiangliang , Yang Jun
Published: February 2018

Wireless power transfer (WPT) has become increasingly widespread in recent years, ranging from electric vehicles, portable consumer electronics, and implantable biomedical devices to flexible/stretchable electronics. The authors here present a WPT system based on the maximum efficiency design principle. Utilising the properties of Helmholtz coils, a near‐uniform 3D volume electromagnetic field is generated making it possible to transfer power to multiple devices simultaneously with no requirement of orientation and/or alignment. The system can also provide continuous wireless power to multiple devices even when they are moving, with an efficiency of up to 87%. An automatic frequency tracing technique was developed to compensate for the resonant frequency shifting issue encountered when the number of loadings changes. Meanwhile, a multi‐load decoupling control system was also developed, such that each secondary coil receives consistent energy without being affected by the addition or removal of another receiving coil(s). As a proof of concept, the authors successfully charged various numbers of mobile phones simultaneously and transmitted power to single/multiple moving devices wirelessly.
Non‐cooperative and cooperative optimisation of battery energy storage system for energy management in multi‐microgrid
Authors: Liu Xiaofeng , Gao Bingtuan , Zhu Zhenyu , Tang Yi
Published: February 2018

Multi‐microgrid is an integrated system of microgrids, distributed generations, and battery energy storage system (BESS). As the significant equipment in microgrid, BESS can perform multitasking, such as load management and peak shaving. This study mainly focuses on the energy consumption scheduling of multi‐microgrid considering the optimisation of BESS capacity. Energy management with BESS optimisation is studied by considering the cost of distributed generations, cost of BESS, and bidirectional energy trading. The optimisation problem is tackled from two different aspects: an individual‐oriented optimisation and a coalition‐based optimisation. In the first approach, each microgrid is optimised individually with a non‐cooperative game; while in the second approach, the joint optimisation of all microgrids is formulated through cooperation among multi‐microgrids. In order to achieve the optimal energy consumption strategy and BESS capacity, distributed algorithms for two formulations are presented, which combine particle swarm optimisation and interior point method. Simulation results show that both approaches can contribute to peak shaving and reducing the daily cost of multi‐microgrid.
Power coordinated control method with frequency support capability for hybrid single/three‐phase microgrid
Authors: Zhou Xiaoping , Chen Yandong , Zhou Leming , Luo An , Guerrero Josep M. , Wu Wenhua , Yang Ling , Tan Wenjuan
Published: February 2018

Due to the intermittent output power of distributed generations (DGs) and the variability of loads, voltage fluctuation and three‐phase power imbalance easily occur when hybrid single/three‐phase microgrid operates in islanded mode. To address these issues, the power exchange unit (PEU) and energy storage unit (ESU) are added into hybrid single/three‐phase microgrid, and a power coordinated control method with frequency support capability is proposed for hybrid single/three‐phase microgrid in this study. PEU is connected with three single‐phase microgrids to coordinate power exchange among three phases and provide frequency support for hybrid microgrid. Meanwhile, a power coordinated control method based on the droop control is proposed for PEU to alleviate three‐phase power imbalance and reduce voltage fluctuation of hybrid microgrid. Besides, ESU is injected into the DC‐link to buffer the system power fluctuation when DGs or loads suddenly change. The hierarchical control method is proposed for ESU to stabilise the DC‐link voltage and reasonably allocate the net exchanged power of PEU. Considering the collaboration between PEU and ESU, the state of charge of ESU is proposed to adjust the power transmission coefficient of PEU. The validity of the proposed control method has been verified by simulation and experiment.
Adaptive primary droop control for islanded operation of hybrid AC–DC MGs
Authors: Mortezapour Vahid , Lesani Hamid
Published: February 2018

This study is dedicated to establish an adaptive primary droop control of interlinking converter (IC) for the islanded operation of hybrid AC–DC microgrids (MGs). In this practise, the amount of transferred power through the IC is controlled such that all of the resources in both AC and DC MGs are in equal loading per cents. To do so, two different notions are contemplated. In the first one, the IC is controlled such that the aforementioned control objective is satisfied for all possible values of transmission lines impedance angles. To this end, a new algorithm is developed within which the IC estimates the impedance angle based on the local measurements in AC MG and then adapts itself. In the second outlook, the uncertainties in association with the renewable energy resources are considered and their effects are explored on IC performance. To lessen the negative impacts of uncertainties and fluctuating power generation of renewable resources, the control of IC is updated based on the instantaneous power generation in AC and DC MGs. Accordingly, the main control objective is effectively pursued. Performance of the proposed adaptive droop control is evaluated on a test MG. Results are discussed in depth.
Visual tracking via ensemble autoencoder
Authors: Dai Bo , Hou Zhiqiang , Yu Wangsheng , Zhu Feng , Wang Xin , Jin Zefenfen
Published: February 2018

The authors present a novel online visual tracking algorithm via ensemble autoencoder (AE). In contrast to other existing deep model based trackers, the proposed algorithm is based on the theory that the image resolution has an influence on vision procedures. When the authors employ a deep neural network to represent the object, the resolution is corresponding to the network size. The authors apply a small network to represent the pattern in a relatively lower resolution and search the object in a relatively larger area of the neighbourhood. After roughly estimating the location of the object, the authors apply a large network, which can provide more detailed information, to estimate the state of the object more accurately. Thus, the authors employ a small AE mainly for position searching and a larger one mainly for scale estimating. When tracking an object, the two networks interact to operate under the framework of particle filtering. Extensive experiments on the benchmark dataset show that the proposed algorithm performs favourably compared with some state‐of‐the‐art methods.
Leveraging synergy of SDWN and multi‐layer resource management for 5G networks
Authors: Derakhshani Mahsa , Parsaeefard Saeedeh , Le‐Ngoc Tho , Leon‐Garcia Alberto
Published: February 2018

Fifth‐generation (5G) networks are envisioned to predispose flexible edge‐to‐core infrastructure to offer diverse applications. Convergence of software‐defined networking, software‐defined radio, and virtualisation on the concept of software‐defined wireless networking (SDWN) is a promising approach to support such dynamic networks. The principal technique behind the 5G‐SDWN framework is the separation of control and data planes that allows the abstraction of resources as transmission parameters of users. In such environment, resource management plays a critical role to achieve efficiency and reliability. The authors introduce a converged multi‐layer resource management (CML‐RM) framework for SDWN‐enabled 5G networks that involve a functional model and an optimisation framework. In such framework, the key questions are if 5G‐SDWN can be leveraged to enable CML‐RM over the portfolio of resources, and reciprocally, if CML‐RM can effectively provide performance enhancement and reliability for 5G‐SDWN. The authors tackle these questions by proposing a flexible protocol structure for 5G‐SDWN, which can handle all the required functionalities in a more cross‐layer manner. They demonstrate how the proposed general framework of CML‐RM can control the end‐user quality of experience. Moreover, for two scenarios of 5G‐SDWN, they investigate the effects of joint user‐association and resource allocation via CML‐RM to improve performance in virtualised networks.
Eliminating cross interference between multiple receivers to achieve targeted power distribution for a multi‐frequency multi‐load MCR WPT system
Authors: Liu Fuxin , Yang Yong , Ding Ze , Chen Xuling , Kennel Ralph M.
Published: February 2018

Simultaneous non‐contact energy transmission for multiple loads with separate receiving coils is a remarkable advantage of magnetically coupled resonant (MCR) wireless power transfer (WPT). A novel multi‐frequency driver configuration for MCR WPT system with multiple loads is proposed, where the receiving resonant tanks are severally tuned at different resonant frequencies to make the loads selective. A methodology of adjusting the resonant frequency of the transmitter is presented to satisfy diverse energy requirements of specific loads. However, the cross interference from non‐targeted frequencies inherently exerts an influence between multiple receivers, and thus makes power allocation non‐constrained through multi‐coupling channels, which increase the difficulty of power control and parameters design. In order to reduce and further eliminate the influences of the cross interference and realise targeted power distribution for selective loads, three types of parallel and series resonant compensation circuits are introduced into receivers. By flexibly utilising the impedance characteristics of parallel and series resonant networks, the proposed compensation circuits are proved to be effective, significantly reducing the cross interference and exclusively delivering power to the selective loads corresponding to pre‐tuned resonant frequencies. Finally, the experimental results from a prototype have confirmed the effectiveness of the proposed methods.
Low‐temperature synthesis of high‐purity Ti2 AlC powder by microwave sintering
Authors: Zhou Weibing , Li Kang , Zhu Jiaoqun , Tian Shouqin , Zhu Da‐Ming
Published: February 2018

In this work, Ti2 AlC powders of high purity were prepared successfully by a facile microwave sintering technique which can reduce the sintering temperature from 1300 to 850°C obviously. This was probably because of the fact that the microwave field can decrease the activation energy of the particle surface, and improve ionic conductivity and the grain surface migration of charged vacancies. In addition, the purity of Ti2 AlC powders can be controlled by adjusting the molar ratio of Ti/Al/C/TiC as a precursor. It was interestingly found that Ti2 AlC powders with the highest purity of 96.6% were obtained at the molar ratio of Ti/Al/C/TiC = 1.5:1.0:0.5:0.45. This was probably attributed to the addition of TiC which favoured the formation of Ti2 AlC. However, excess TiC would influence the reaction path in the Ti–Al–C system and thus reduce the purity of Ti2 AlC. Therefore, this work can provide a facile method to synthesise other MAX powders.
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

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

This 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

Motivation

RNA 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.

Results

We 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<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 implementation

The ISOP method has been implemented as a R package and is available at https://github.com/nghiavtr/ISOP under a GPL-3 license.

Supplementary information

Supplementary 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

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

Ruminants 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.

Background

Sequencing 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.

Results

Here 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.

Conclusion

TAG.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

The 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

Gene 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

Light-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 Summary

Glaser 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

We 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.
Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum
Authors: Kim Wonyong , Miguel-Rojas Cristina , Wang Jie , Townsend Jeffrey P , Trail Frances
Published: February 2018

Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecia, the sexual fruiting bodies of Fusarium graminearum. We have identified 547 lncRNAs whose expression was developmental stage-specific, with about 40% of which peaked during the development of asci, the sac-like structures containing meiospores. A large fraction of the lncRNAs were found to be antisense to mRNAs, forming 300 sense–antisense pairs. Although small RNAs (sRNAs) were produced from these overlapping loci, most of the antisense lncRNAs appeared not to be involved in gene silencing pathways. Genome-wide analysis of sRNA clusters identified many silenced loci at the meiotic stage. However, we found transcriptionally-active sRNA clusters, many of which were associated with lncRNAs. Also, we observed that many antisense lncRNAs and their respective sense transcripts were induced in parallel as the perithecia matured. To identify regulatory components for lncRNA expression, we analyzed mutants defective in the nonsense-mediated decay (NMD) pathway. A subset of the lncRNAs appeared to be targeted by the NMD before the perithecia formation, suggesting a suppressive role of the NMD in lncRNA expression during vegetative stage. This research provides fundamental genomic resources that will spur further investigations on developmental lncRNAs that may play important roles in shaping the fungal fruiting bodies.
YAP1 oncogene is a context-specific driver for pancreatic ductal adenocarcinoma
Authors: Tu Bo , Yao Jun , Ferri-Borgogno Sammy , Zhao Jun , Chen Shujuan , Wang Qiuyun , Yan Liang , Zhou Xin , Zhu Cihui , Bang Seungmin , Chang Qing , Bristow Christopher A. , Kang Ya’an , Zheng Hongwu , Wang Huamin , Fleming Jason B. , Kim Michael , Heffernan Timothy P. , Draetta Giulio F. , Pan Duojia , Maitra Anirban , Yao Wantong , Gupta Sonal , Ying Haoqiang
Published: February 2018

Abstract

Transcriptomic profiling classifies pancreatic ductal adenocarcinoma (PDAC) into several molecular subtypes with distinctive histological and clinical characteristics. However, little is known about the molecular mechanisms that define each subtype and their correlation with clinical outcome. Mutant KRAS is the most prominent driver in PDAC, present in over 90% of tumors, but the dependence of tumors on oncogenic KRAS signaling varies between subtypes. In particular, squamous subtype are relatively independent of oncogenic KRAS signaling and typically display much more aggressive clinical behavior versus progenitor subtype. Here, we identified that YAP1 activation is enriched in the squamous subtype and associated with poor prognosis. Activation of YAP1 in progenitor subtype cancer cells profoundly enhanced malignant phenotypes and transformed progenitor subtype cells into squamous subtype. Conversely, depletion of YAP1 specifically suppressed tumorigenicity of squamous subtype PDAC cells. Mechanistically, we uncovered a significant positive correlation between WNT5A expression and the YAP1 activity in human PDAC, and demonstrated that WNT5A overexpression led to YAP1 activation and recapitulated YAP1-dependent but Kras-independent phenotype of tumor progression and maintenance. Thus, our study identifies YAP1 oncogene as a major driver of squamous subtype PDAC and uncovers the role of WNT5A in driving PDAC malignancy through activation of the YAP pathway.
Optimized breath detection algorithm in Electrical Impedance Tomography
Authors: Khodadad D. , Nordebo S. , Müller B. , Waldmann A. , Yerworth R. , Becher T. , Frerichs I. , Sophocleous L. , van Kaam A. , Miedema M. , Seifnaraghi N. , Bayford R.
Published: February 2018

Objective

This paper define a method for optimizing the breath delineation algorithms used in Electrical Impedance Tomography (EIT). In lung EIT the identification of the breath phases is central for generating tidal impedance variation images, subsequent data analysis and clinical evaluation. The optimisation of these algorithms is particularly important in neonatal care since the existing breath detectors developed for adults may give insufficient reliability in neonates due to their very irregular breathing pattern.

Approach

Our approach is generic in the sense that it relies on the definition of a gold standard and the associated definition of detector sensitivity and specificity, an optimisation criterion and a set of detector parameters to be investigated. The gold standard has been defined by 11 clinicians with previous experience with EIT and the performance of our approach is described and validated using a neonatal EIT dataset acquired within the EU-funded CRADL project.

Main results

Three different algorithms are proposed that are improving the breath detector performance by adding conditions on 1) maximum tidal breath rate obtained from zero-crossings of the EIT breathing signal, 2) minimum tidal impedance amplitude and 3) minimum tidal breath rate obtained from Time-Frequency (TF) analysis.

Significance

Based on the gold standard, the most crucial parameters of the proposed algorithms are optimised by using a simple exhaustive search and a weighted metric defined in connection with the Receiver Operating Characterics (ROC). This provides a practical way to achieve any desirable trade-off between the sensitivity and the specificity of the detectors.