bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of potential disease-associated microRNAs using structural perturbation method
Authors: Zeng Xiangxiang , Liu Li , Lü Linyuan , Zou Quan 
Published: November 2017

AbstractMotivationThe 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.ResultsThe 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. TheAUCvalues 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 Implementationhttps://github.com/lecea/SPM-code.gitContactlinyuan.lv@gmail.com,zouquan@nclab.net.Supplementary informationSupplementary data are available atBioinformaticsonline.
Task-dependent modulation of spinal and transcortical stretch reflexes linked to motor learning rate
Authors: Dimitriou Michael 
Published: November 2017

AbstractIt is generally believed that task-dependent control of body configuration (‘posture’) is achieved by adjusting voluntary motor activity and transcortical ‘long-latency’ reflexes. Spinal monosynaptic circuits are thought not to be engaged in such task-level control. Similarly, being in a state of motor learning has been strongly associated only with an upregulation of feedback responses at transcortical latencies and beyond. In two separate experiments, the current study examined the task-dependent modulation of stretch reflexes by perturbing the hand of human subjects while they were waiting for a ‘Go’ signal to move at the different stages of a classic kinematic learning task (visuomotor rotation). Although the subjects had to resist all haptic perturbations equally, the study leveraged that task-dependent feedback controllers may already be ’loaded’ at the movement anticipation stage. In addition to an upregulation of short- and long-latency reflex gains during early exposure to the visual distortion, I found a relative inhibition of reflex responses in the ‘washout’ stage (sensory realignment state). For more distal muscles (brachioradialis), this inhibition also extended to the monosynaptic reflex response (‘R1’). These R1 gains reflected individual motor learning performance in the visuomotor task. The results demonstrate that the system’s ‘control policy’ in visuomotor adaptation can also include inhibition of proprioceptive reflexes, and that aspects of this policy can affect monosynaptic spinal circuits. The latter finding suggests a novel form of state-related control, probably realized by independent control of fusimotor neurons, through which segmental circuits can tune to higher-level features of a sensorimotor task.Additional InformationConflict of interestThe author declares no conflict of interest.Author contributionsM.D. devised, designed and implemented the project, analyzed the data and wrote the manuscript. The author approves the final version of the manuscript and is fully accountable for all aspects of the work. The experiments were performed at the Department of Integrative Medical Biology, Umeå University, Sweden.FundingThis work was financially supported through grants awarded to M.D. by the Kempe Foundation, the local Foundation for Medical Research (“Insamlingsstiftelsen”) and the Swedish Research Council (project 2016-02237).
Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor
Authors: Bucca Giselda , Pothi Radhika , Hesketh Andrew , Möller-Levet Carla , Hodgson David A. , Laing Emma E. , Stewart Graham R. , Smith Colin P. 
Published: November 2017

AbstractStress-induced adaptations require multiple levels of regulation in all organisms to repair cellular damage. In the present study we evaluated the genome-wide transcriptional and translational changes following heat stress exposure in the soil-dwelling model actinomycete bacterium, Streptomyces coelicolor. The combined analysis revealed an unprecedented level of translational control of gene expression, deduced through polysome profiling, in addition to transcriptional changes. Our data show little correlation between the transcriptome and ‘translatome’; while an obvious downward trend in genome wide transcription was observed, polysome associated transcripts following heat-shock showed an opposite upward trend. A handful of key protein players, including the major molecular chaperones and proteases were highly induced at both the transcriptional and translational level following heat-shock, a phenomenon known as ‘potentiation’. Many other transcripts encoding cold-shock proteins, ABC-transporter systems, multiple transcription factors were more highly polysome-associated following heat stress; interestingly, these protein families were not induced at the transcriptional level and therefore were not previously identified as part of the stress response. Thus, stress coping mechanisms at the level of gene expression in this bacterium go well beyond the induction of a relatively small number of molecular chaperones and proteases in order to ensure cellular survival at non-physiological temperatures.
q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data
Authors: Bokulich Nicholas A. , Zhang Yilong , Dillon Matthew , Rideout Jai Ram , Bolyen Evan , Li Huilin , Albert Paul S. , Caporaso J. Gregory 
Published: November 2017

AbstractStudies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sectional and pre/post study designs. To support the needs of microbiome researchers performing longitudinal studies, we developed q2-longitudinal, a software plugin for the QIIME 2 microbiome analysis platform (https://qiime2.org). The q2-longitudinal plugin incorporates multiple methods for analysis of longitudinal and paired-sample data, including paired differences and distances, linear mixed effects models, microbial interdependence test, first differencing, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open source software released under a BSD-3-Clause license and is freely available, including for commercial use.
The temporal evolution of conceptual object representations revealed through models of behavior, semantics and deep neural networks
Authors: Bankson B. B. , Hebart M.N. , Groen I.I.A. , Baker C.I. 
Published: November 2017

AbstractVisual object representations are commonly thought to emerge rapidly, yet it has remained unclear to what extent early brain responses reflect purely low-level visual features of these objects and how strongly those features contribute to later categorical or conceptual representations. Here, we aimed to estimate a lower temporal bound for the emergence of conceptual representations by defining two criteria that characterize such representations: 1) conceptual object representations should generalize across different exemplars of the same object, and 2) these representations should reflect high-level behavioral judgments. To test these criteria, we compared magnetoencephalography (MEG) recordings between two groups of participants (n = 16 per group) exposed to different exemplar images of the same object concepts. Further, we disentangled low-level from high-level MEG responses by estimating the unique and shared contribution of models of behavioral judgments, semantics, and different layers of deep neural networks of visual object processing. We find that 1) both generalization across exemplars as well as generalization of object-related signals across time increase after 150 ms, peaking around 230 ms; 2) behavioral judgments explain the most unique variance in the response after 150 ms. Collectively, these results suggest a lower bound for the emergence of conceptual object representations around 150 ms following stimulus onset.
Quantitative relationships for radiation induced chromosome instability: data analysis
Authors: Eidelman Y.A. , Slanina S.V. , Pyatenko V.S. , Khvostunov I.K. , Andreev S.G. 
Published: November 2017

ABSTRACTThe experimental observations demonstrate that different cell lines reveal various shape of dynamic curves for radiation-induced chromosomal instability (RICI). We analyzed our own and published data on RICI for three cell lines, CHO-K1, V79 and TK6, on the basis of the mechanistic RICI model. We demonstrate that all three dynamic curves can be successfully described by the proposed model with partially cell line specific parameters.
Fatigue based design and life estimation of viscoelastic rotors
Authors: Roy Haraprasad , Khare Abhinav , Chandraker Saurabh , Dutt J.K. 
Published: November 2017

Purpose
High-speed rotor subjected to cyclic stress during operation may cause fatigue failure. Thus, the design of a rotor-shaft should involve the fatigue analysis for predicting safe life.

Design/methodology/approach
A damped rotor shaft with a centrally mounted disc, which is simulated as steam turbine rotor, is considered for fatigue analysis. The shaft is subjected to thermal load and axial torque. It is supported by two orthotropic flexible bearings at its two extreme ends. The bearings are modelled with two-element Voigt model along each orthogonal direction to consider the elastic damped behaviour. Finite element modelling is done through Rayleigh beam theory, where each element is also considered as a Voigt model. The mathematical model involves effect of external axial torque, softening and compressive action of the shaft due to thermal load by the high temperature steam.

Findings
This paper attempts to find dynamic stresses in a viscoelastic rotor-shaft subject to combined bending and torsional loading and is exposed to thermal environment during operation. The dynamic stress is then used to determine fatigue and also the life of rotors.

Research limitations/implications
Internal damping plays an important role in deciding dynamic behaviour of rotor shaft systems. Because of this, the rotor shaft becomes unstable after a certain spin speed. Thus, the design of the rotor based on fatigue analysis is limited to the stable zone.

Practical implications
For this purpose, equations of whirl motion of a viscoelastic rotor-shaft are first obtained after discretizing the continuum with finite beam elements and then the time domain solution of rotor displacement is used to find the bending stress and shear stress at various locations of the rotor. Location for the maximum stress decides the failure point. Safe rotor dimensions have been predicted by comparing dynamic stresses with the Soderberg diagram.

Originality/value
Design of rotor for safe life operation and prediction of stability could serve a good reference for designers.
In-flight icing risk prediction and management in consideration of wing stall
Authors: Pei Binbin , Xu Haojun , Xue Yuan , Chen Wei , Shen Anwei 
Published: November 2017

Purpose
The purpose of this work is to develop an in-flight icing risk assessment methodology by quantification of changing flight dynamic characteristics under icing conditions.

Design/methodology/approach
This paper develops an approach for the quantitative assessment of flight risk under icing conditions. Using the six degree-of-freedom simulation model, the icing effects model is used to obtain the extreme values of the key parameters relevant to fight safety, allowing calculation of accident probability based on extreme value theory. The risk portion of the flight risk index is designed to account for different levels of flight risk and to provide criteria to allow pilots’ decision-making. Numerical examples are carried out by a series of simulated elevator overshoots of various levels and different distributions of ice accretion to compare the risk index under different icing conditions.

Findings
Case results show that the proposed methodology is able to analyze conditions of different severity and distribution of icing and assess quantitatively how these different parameters affect flight safety.

Practical implications
The quantification of flight risk in icing conditions demonstrated here can be applied to provide an objective and intuitive instrument to facilitate decisions by the aircrew or air traffic controller, especially prior to the aircraft entering into areas with adverse meteorological conditions.

Originality/value
Existing flight risk assessments under icing conditions are typically guided by aerodynamic changes, ice accumulation process or the subjective feeling of the pilot. Here, it is proposed to use the probability of flight risk event to measure different icing intensity levels in a quantitative way. This quantitative metric combines the alteration of aerodynamic characteristics, flight dynamic characteristics and limitation of critical parameters, providing a new and comprehensive viewpoint to measure in-flight icing risk. This may be a promising and more reasonable way to assess the risk.
Modeling and control for ultra-low altitude cargo airdrop
Authors: Han Yanhua 
Published: November 2017

Purpose
The purpose of this paper is to model the aircraft-cargo’s coupling dynamics during ultra-low altitude heavy cargo airdrop and to design the aircraft’s robust flight control law counteracting its aerodynamic coefficients perturbation induced by ground effect and the disturbance from the sliding cargo inside.

Design/methodology/approach
Aircraft-cargo system coupling dynamics model in vertical plane is derived using the Kane method. Trimmed point is calculated when the cargo fixed in the cabin and then the approximate linearized motion equation of the aircraft upon it is derived. The robust stability and robust H∞ optimal disturbance restraint flight control law are designed countering the aircraft’s aerodynamic coefficients perturbation and the disturbance moment, respectively.

Findings
Numerical simulation shows the effectiveness of the proposed control law with elevator deflection as a unique control input.

Practical implications
The model derived and control law designed in the paper can be applied to heavy cargo airdrop integrated design and relevant parameters choice.

Originality/value
The dynamics model derived is closed, namely, the model can be called in numerical simulation free of assuming the values of parachute’s extraction force or cargo’s relative sliding acceleration or velocity as seen in many literatures. The modeling is simplified using Kane method rather than Newton’s laws. The robust control law proposed is effective in guaranteeing the aircraft’s flight stability and disturbance restraint performance in the presence of aerodynamic coefficients perturbation.
Action at a distance
Authors: Ekanayake Athula 
Published: November 2017

PurposeBy using Latour’s notion of “action at a distance” (Latour, 1987), the purpose of this paper is to examine the ways in which the government acts at a distance to achieve corporate governance of public sector banks, and the extent to which accounting enables such actions of the government.Design/methodology/approachThis study follows the qualitative research approach and adopts the case study research method. A major public sector bank in Sri Lanka was selected as the case organization for this study. Data were gathered from semi-structured interviews with organizational participants and document study.FindingsThe study provides evidence to suggest that inscriptions produced through four areas of accounting, namely external reporting, external auditing, management accounting and internal auditing, have the capacity to develop strong explanations enabling action at a distance and good corporate governance in the case organization. The study also provides evidence to show how the role of accounting in long-distance control and corporate governance in the case organization is influenced by various contextual factors. In particular, the study finds that undue government interference over the case organization to gain the long-distance control have resulted in deteriorating the level of corporate governance.Research limitations/implicationsThe findings support the literature that examines the accounting in its social context.Practical implicationsThe findings suggest that actors should be allowed to operate independently, particularly without political expedience and undue influences from pressure groups, which ensure effective utilization of accounting inscriptions by the actors in long-distance control as well as good corporate governance of public sector banks.Originality/valueAlthough research into accounting in public sector organizations has gained considerable importance in recent times, those studies examining public sector banks are still lacking. The paper aims to fill this gap.
Adherence to responsibility in organic dry food supply chains
Authors: Jacob-John Jubin 
Published: November 2017

Purpose
The purpose of this paper is to explore the sharing of sustainability and social responsibility-centric values along the export-oriented organic dry food supply chain (ODFSC) using an institutional lens.

Design/methodology/approach
To understand the perceptions of the shared ethos of the organic food industry along the entire supply chain, the research employed a multi-tier qualitative approach using semi-structured interviews and observations. The study focussed on supply chain actors including farmers and traders from the Indian sub-continent, and traders and retailers based in Europe and North America.

Findings
Isomorphism, brought about by the vertical channelling of consumer preferences and values resulted in a higher degree of responsibility within the industry. The responsibility-centric ethos of the supply chain affected the responsibility-orientation of the supply chain actors and their operations.

Research limitations/implications
The research focused mainly on the ODFSC actors in Kerala, a state in India, and this focus of the research could be a significant limitation in generalizing the findings to the rest of the emerging economy context because of cultural and educational differences.

Originality/value
Literature lacks in the studies of sharing of responsibility-centric values in supply chains through an institutional lens and this investigation contributes to the scant literature on isomorphism, shared values and responsible supply chain management.
An entrepreneurial learning approach to assessment of internships
Authors: Ramsgaard Michael Breum , Østergaard Sara Juul 
Published: November 2017

Purpose
The purpose of this paper is to investigate how using an entrepreneurial learning approach for assessment of internships could increase the reflected value of combining theory and practice articulated in students’ learning outcomes. Furthermore, the purpose was to investigate whether the applied approach led to enhanced perception of professional identity and new understandings of employability for students in the internship course.

Design/methodology/approach
A qualitative research design was the basis for investigation of the topics in focus. The data consisted of five focus groups, observation notes, and documentation from the exam situations. Two consecutive groups of students (2015 and 2016) participated in the study at a university of applied science in Denmark.

Findings
Results from the study provided evidence that students in internships collectively develop a comprehensive understanding of how to apply theory to practical settings. By working with an entrepreneurial learning approach in the professional practice, students reported an enhanced reflective understanding of learning outcomes and the theory-practice gap, developed an ability for opportunity identification, and established a grounded feeling of professional identity and employability.

Practical implications
The current pilot project serves as a full and context-rich case study that can inform educators about formative and summative assessment practices when designing internships courses. Furthermore, internship supervisors can get valuable insight into learning processes during an internship.

Originality/value
The suggested model for an entrepreneurial learning approach to assessment of internships provides a basis for further research within entrepreneurial learning and the application to design of assessment practices in this context.