bluuebunny/crossref_metadata_2025_split huggingface dataset:
GrandPrix: Scaling up the Bayesian GPLVM for single-cell data
Authors: Ahmed Sumon , Rattray Magnus , Boukouvalas Alexis 
Published: December 2017

AbstractMotivationThe Gaussian Process Latent Variable Model (GPLVM) is a popular approach for dimensionality reduction of single-cell data and has been used for pseudotime estimation with capture time information. However current implementations are computationally intensive and will not scale up to modern droplet-based single-cell datasets which routinely profile many tens of thousands of cells.ResultsWe provide an efficient implementation which allows scaling up this approach to modern single-cell datasets. We also generalize the application of pseudotime inference to cases where there are other sources of variation, such as branching dynamics. We apply our method on microarray, nCounter, RNA-seq, qPCR and droplet-based datasets from different organisms. The model converges an order of magnitude faster compared to existing methods whilst achieving similar levels of estimation accuracy. Further, we demonstrate the flexibility of our approach by extending the model to higher-dimensional latent spaces that can be used to simultaneously infer pseudotime and other structure such as branching. Thus, the model has the capability of producing meaningful biological insights about cell ordering as well as cell fate regulation.AvailabilitySoftware available at github.com/ManchesterBioinference/GrandPrix.
Metabolic traits predict the effects of warming on phytoplankton competition
Authors: Bestion Elvire , Garcia-Carreras Bernardo , Schaum Charlotte-Elisa , Pawar Samraat , Yvon-Durocher Gabriel 
Published: December 2017

ABSTRACTUnderstanding how changes in temperature affect interspecific competition is critical for predicting changes in ecological communities as the climate warms. Here we develop a simple theoretical model that links interspecific differences in metabolic traits, which capture the temperature-dependence of resource acquisition, to the outcome of pairwise competition in phytoplankton. We parameterised our model with metabolic traits derived from six species of freshwater phytoplankton and tested its ability to predict the outcome of competition in all pairwise combinations of the species in a factorial experiment, manipulating temperature and nutrient availability. The model correctly predicted the outcome of competition in 71% of the pairwise experiments. These results demonstrate that metabolic traits play a key role in determining how changes in temperature influence interspecific competition and lay the foundation for developing theory to predict the effects of warming in complex, multi-species communities.
Subject-independent decoding of affective states using functional near-infrared spectroscopy
Authors: Trambaiolli Lucas R. , Tossato Juliana , Cravo André M. , Biazoli Claudinei E. , Sato João R. 
Published: December 2017

AbstractAffective decoding is the inference of human emotional states using brain signal measurements. This approach is crucial to develop new therapeutic approaches for psychiatric rehabilitation, such as affective neurofeedback protocols. To reduce the training duration and optimize the clinical outputs, an ideal clinical neurofeedback could be trained using data from an independent group of volunteers before being used by new patients. Here, we investigated if this subject-independent design of affective decoding can be achieved using functional near-infrared spectroscopy (fNIRS) signals from frontal and occipital areas. For this purpose, a linear discriminant analysis classifier was first trained in a dataset (49 participants, 24.65±3.23 years) and then tested in a completely independent one (20 participants, 24.00±3.92 years). Significant balanced accuracies between classes were found for positive vs. negative (64.50 ± 12.03%, p<0.01) and negative vs. neutral (68.25 ± 12.97%, p<0.01) affective states discrimination during a reactive block consisting in viewing affective-loaded images. For an active block, in which volunteers were instructed to recollect personal affective experiences, significant accuracy was found for positive vs. neutral affect classification (71.25 ± 18.02%, p<0.01). In this last case, only three fNIRS channels were enough to discriminate between neutral and positive affective states. Although more research is needed, for example focusing on better combinations of features and classifiers, our results highlight fNIRS as a possible technique for subject-independent affective decoding, reaching significant classification accuracies of emotional states using only a few but biologically relevant features.
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
Authors: Iorio Francesco , Behan Fiona M , Gonçalves Emanuel , Bhosle Shriram G , Chen Elisabeth , Shepherd Rebecca , Beaver Charlotte , Ansari Rizwan , Pooley Rachel , Wilkinson Piers , Harper Sarah , Butler Adam P , Stronach Euan A , Saez-Rodriguez Julio , Yusa Kosuke , Garnett Mathew J 
Published: December 2017

AbstractBackground:Genome editing by CRISPR-Cas9 technology allows large-scale screening of gene essentiality in cancer. A confounding factor when interpreting CRISPR-Cas9 screens is the high false-positive rate in detecting essential genes within copy number amplified regions of the genome. We have developed the computational toolCRISPRcleanRwhich is capable of identifying and correcting gene-independent responses to CRISPR-Cas9 targeting. CRISPRcleanR uses an unsupervised approach based on the segmentation of single-guide RNA fold change values across the genome, without making any assumption about the copy number status of the targeted genes.ResultsApplying our method to existing and newly generated genome-wide essentiality profiles from 15 cancer cell lines, we demonstrate that CRISPRcleanR reduces false positives when calling essential genes, correcting biases within and outside of amplified regions, while maintaining true positive rates. Established cancer dependencies and essentiality signals of amplified cancer driver genes are detectable post-correction. CRISPRcleanR reports sgRNA fold changes and normalised read counts, is therefore compatible with downstream analysis tools, and works with multiple sgRNA libraries.ConclusionsCRISPRcleanR is a versatile open-source tool for the analysis of CRISPR-Cas9 knockout screens to identify essential genes.
Nestin in immature embryonic neurons regulates axon growth cone morphology and Semaphorin3a sensitivity
Authors: Bott C.J. , Johnson C. G. , Yap C.C. , Dwyer N.D. , Litwa K.A. , Winckler B. 
Published: December 2017

AbstractCorrect wiring in the neocortex requires that responses to an individual guidance cue vary among neurons in the same location, and within the same neuron over time. Nestin is an atypical intermediate filament expressed highly in neural progenitors and is thus used widely as a progenitor marker. Here we show a subpopulation of embryonic cortical neurons which transiently express nestin in their axons. Nestin expression is thus not restricted to neural progenitors but persists at lower levels in some newborn neurons for 2-3 days. We found that nestin-expressing neurons have smaller growth cones, suggesting that nestin affects cytoskeletal dynamics. Nestin, unlike other intermediate filament subtypes, regulates cdk5 kinase. Cdk5 activity is induced by the repulsive guidance cue Sema3a leading to growth cone collapse in vitro. Therefore, we tested whether nestin-expressing neurons showed altered responses to Sema3a. We find that nestin-expressing newborn neurons are more sensitive to Sema3a in a roscovitine-sensitive manner, whereas nestin knockdown results in lowered sensitivity to Sema3a. We propose that nestin functions in immature neurons to modulate cdk5 and thereby the Sema3a response. Thus, the transient expression of nestin could allow for temporal modulation of a neuron's response to Sema3a particularly during early axon guidance decisions.
Glucose facilitates Aβ oligomerization and tau phosphorylation in C. elegans model of Alzheimer’s disease
Authors: Ahmad Waqar 
Published: December 2017

AbstractFormation of Aβ plaques from peptide oligomers and development of neurofibrillary tangles from hyperphosphorylated tau are hallmarks of Alzheimer’s disease (AD). These markers of AD severity are further associated with impaired glucose metabolism. However, the exact role of glucose metabolism on disease progression has not been elucidated. In this study, the effects of glucose on Aβ and tau-mediated toxicity are investigated using a C. elegans model system. We find that addition of glucose or 2-deoxy-d-glucose (2DOG) to the growth medium delayed Aβ-associated paralysis, though it was unable to restore previously impaired acetylcholine neurotransmission in pre-existing Aβ-mediated pathology. Glucose also inhibited egg laying and hatching in the worms that express Aβ. The harmful effects of glucose were associated with an increase in toxic Aβ oligomers. Increased phosphorylation of tau is associated with formation of neurofibrillary tangles (NFTs) and increased severity of AD, but O-β-GlcNAcylation can inhibit phosphorylation of adjacent phosphorylation sites. We reasoned that high glucose levels might induce tau O-β-GlcNAcylation, thereby protecting against tau phosphorylation. Contrary to our expectation, glucose increased tau phosphorylation but not O-β-GlcNAcylation. Increasing O-β-GlcNAcylation, either with Thiamet-G (TMG) or by suppressing the O-GlcNAcase (oga-1) gene does interfere with and therefore reduce tau phosphorylation. Furthermore, reducing O-β-GlcNAcylation by suppressing O-GlcNAc transferase (ogt-1) gene causes an increase in tau phosphorylation. These results suggest that protective O-β-GlcNAcylation is not induced by glucose. Instead, as with vertebrates, we demonstrate that high levels of glucose exacerbate disease progression by promoting Aβ aggregation and tau hyperphosphorylation, resulting in disease symptoms of increased severity. The effects of glucose cannot be effectively managed by manipulating O-β-GlcNAcylation in the tau models of AD in C. elegans. Our observations suggest that glucose enrichment is unlikely to be an appropriate therapy to minimize AD progression.
The role of peripherality in students’ entrepreneurial learning
Authors: Kubberød Elin , Pettersen Inger Beate 
Published: December 2017

Purpose
The purpose of this paper is to expand on the entrepreneurial learning literature and situated learning theory to explore how students with different educational backgrounds learn to recognise opportunities at the periphery of an entrepreneurial practice. The authors theoretically outline factors that may influence students’ entrepreneurial learning, including co-participation and roles at the periphery, power relations in communities of practice (CoP), and emotional exposure. The authors make use of the concept legitimate peripheral participation and Politis’ entrepreneurial learning framework to explore empirically students’ entrepreneurial learning transformations and entrepreneurial learning outcomes.

Design/methodology/approach
The authors adopted a qualitative approach in research, used the focus group methodology and the critical incident technique in interviewing. The research investigated two groups of Norwegian master students that differed in educational background aiming to explore their experience with entrepreneurial learning in a three months long internship in American start-ups representing emerging CoPs.

Findings
The research identified important factors influencing students’ entry transitions into an entrepreneurial practice, highlighting the complexity in peripheral participation. By acknowledging and exploring the social dimensions in students’ learning, the authors demonstrate and exemplify how these influence students’ entrepreneurial learning trajectories, learning outcomes and ultimately their influence in students’ contributions to the practice community.

Originality/value
The research integrates the existing entrepreneurial learning literature and situated learning theory to identify various factors influencing entrepreneurial learning, contributing with novel insights about the role of peripherality in students’ entrepreneurial learning in situated practice.
Information seeking by geoscientists: an update on Bichteler and Ward (1989)
Authors: Alstad Knut , Hertzum Morten 
Published: December 2017

PurposeThe purpose of this paper is to investigate how often geoscientists use different information sources and how this pattern of source use balances their perceptions of the quality and ease of use of the information sources.Design/methodology/approachThe geoscientists at the Geological Survey of Norway were surveyed about their information-seeking behavior. The response rate was 70 percent.FindingsThe geoscientists primarily relied on web search and colleagues for information. These two information sources were perceived as easy to use, more so than bibliographic databases (GeoRef, Web of Science, and the library database). Bibliographic databases were used infrequently and perceived as yielding poorer quality results than consulting a colleague. The likelihood of using web search and colleagues to find information about a new topic was determined by the ease of using these sources. In contrast, the quality of the resulting information did not determine the frequency with which any of the information sources were used. The geoscientists who spent more time looking for information searched the web more often, had more reservations toward the quality of information obtained from colleagues, and read more journal articles and conference papers.Research limitations/implicationsGeoscientists’ use of an information source is self-reinforcing and unlikely to increase through improving its quality alone. It should be noted that the study is restricted to one geoscience organization.Originality/valueThe main reference about the information-seeking behavior of geoscientists is almost three decades old. This study provides an update.
Multinational enterprises, risk management, and the business and economics of peace
Authors: Oetzel Jennifer , Miklian Jason 
Published: December 2017

Purpose
The purpose of this paper is to reconceptualize how managers of multinational enterprises (MNEs) manage risk, particularly in fragile and/or conflict-affected areas of operation. The authors suggest that MNEs consider reducing risk at its source rather than trying to avoid or react to risks as they occur. By incorporating peacebuilding strategies, managers may not only reduce investment risk but also contribute to stability and prosperity in the communities where they operate, and gain a competitive advantage in doing so.

Design/methodology/approach
The authors show how firms can take a more holistic approach to working in conflict-affected areas. They do so by overlaying conceptualizations of risk with those of peacebuilding and then use case examples to illustrate how such actions work in practice.

Findings
Using a series of examples, the authors find that MNEs that incorporate peacebuilding frameworks in their risk calculations in complex settings tend to have a better understanding of local environments and how they affect firm operations and profitability. These same MNEs may hold a long-term advantage over international competitors that do not share the same understanding.

Originality/value
The authors argue that the study of relationships between international businesses and society in conflict-affected or fragile areas of operation is under-developed and tends to focus on negative (risk-aversion) aspects as opposed to positive (value-added) opportunities. This paper offers new ways in which these relationships can be reconceptualized. The authors’ main takeaway is that a peacebuilding approach does not require corporations to be arbitrators of peace at the expense of profit. Rather, it is instead a broader way to conceptualize and weigh risk when working in the world’s most challenging regions. This approach is more likely to be in the long-term interest of both the firm and the local society where the firm operates.
Influencing Fairtrade consumption through servant leadership: Bruce Crowther’s story
Authors: Samuel Anthony , White Gareth R.T. , Martin Helen , Rowling Martyn 
Published: December 2017

PurposeThis study aims to expand understanding of servant leadership beyond organisational boundaries by making an examination of its role in the establishment and growth of a social movement.Design/methodology/approachThis paper’s findings are developed from four sequential, semi-structured interviews and a narrated tour of Garstang with the founder of the Fairtrade Towns (FTT) movement. It follows a theoretical framework of servant leadership (SLship) from Spears (1996; 2009). Evidence is gathered through in-depth investigation of the activities of Bruce Crowther, the architect and driving force behind the FTT initiative.FindingsThe findings discovered how SLship operates in a social, place-based setting to influence Fairtrade consumption. The paper argues the success of the FTT movement is linked to Bruce Crowther’s leadership. The findings presented draw and expand upon Spears’ ten characteristics of SLship. Utilisation of this framework sees Crowther emerge as a servant leader operating at a community level to influence FT consumption via the FTT movement.Originality/valueThe paper makes a contribution to theory by identifying the novel characteristic of servant leaders that is exploring affinity and proffers it as an extension of Spears’ framework. It also provides valuable information about the impact and importance of SLship in the efficacious advance of ethical consumerism.
The Design of Powersplit Transmissions Using New Technologies of Hydrostatic Components
Authors: Göllner Wilhelm , Rahmfeld Robert , Hames Bernd 
Published: December 2017

In powersplit systems, which are state-of-the-art in tractor transmissions, the efficiency is of much higher importance than in most other vehicles. Key for high efficiency is to transmit only some power hydrostically and a high amount mechanically (Fig. 1 and 2) because the mechanical path has higher efficiency than the hydrostatic path. The hydrostatic path is needed to get an infinitely variable transmission.
The understanding of powerloss characteristics of hydrostatic components helps to choose between swashplate and bent axis components. Best total efficiencies of 97% are key arguments for using 45° bent axis technology. This is the reason for a dominant use of 45° bent axis in powersplit transmissions.
The search for further reduction in powerloss shows the weak volumetric efficiency at small displacements and high pressure levels. The compression loss is now a dominant subject for improvement. The paper will explain a new design for reduced compression loss, which can be applied to 45° bent axis units. The powerloss reduction will be shown for a powersplit transmission with 2 and 3 modes, which are state of the art today [7].
CFD Simulation and Experimental Investigation of Steady State Flow Force Reduction in a Hydraulic Spool Valve With Machined Back Angles
Authors: Jackson Randall S. , Belger Matthew M. , Cassaidy Kevin J. , Kokemoor Andrew R. 
Published: December 2017

As the force output of an electromagnetic actuator is limited, achieving reliable operation of a direct-acting solenoid valve at high pressures and flow rates can be challenging. The major performance obstacle is the hydrodynamic flow force acting on the spool as it moves between energized and de-energized states. With trends in the fluid power industry requiring valves to operate at higher pressures and volumetric flow rates, while minimizing electrical power consumption, methods to reduce hydrodynamic flow forces become critical in developing functional products.
This paper presents CFD simulation and correlating experimental results in using back angles to reduce the hydrodynamic flow forces in a direct-acting, solenoid operated, cartridge-style, directional control valve. Traditional methods of calculating flow forces are discussed and a brief summary of prior research is presented. A commercially available CFD package, Fluent, was used to numerically estimate the flow forces using a realizable k-ε turbulence closure model. A parametric analysis of flow, pressure, and spool stroke showed sensitivity to the metering edge geometry. A special fixture was created to isolate and directly measure the forces acting on the spool. The addition of a +60° back-angle showed the largest flow force reduction of 36% compared to a spool with no back angle.
An Approach to Visualize Lifetime Limiting Factors in the Cylinder Block/Valve Plate Gap in Axial Piston Pumps
Authors: Ivantysyn Roman , Shorbagy Ahmed , Weber Jürgen 
Published: December 2017

The lifetime of axial piston pumps is depending on the application and it’s overall robustness to external loads, but even in ideal conditions pumps will fail eventually. The analytics to this problem are known to pump manufacturers. Bearing and shaft calculations paired with FEM models are invaluable tools, however the main questions remain with the rotating kit – cylinder block, pistons, and slippers. If properly designed these parts should theoretically outlast the finite lifetime parts, such as roller bearings due to their hydrostatic and hydrodynamic bearings. In reality however failures still occur due to fatigue or other factors such as contamination or wear.
This paper describes an approach for the thermal analysis of the cylinder block / valve plate sealing interface. Using a state of the art test rig the temperature distribution, instantaneous gap height as well as particle wear have been analyzed across the entire operating range of an axial piston pump at the block / valve plate sealing interface. Simulations are done with cooperation of Purdue University by using their developed gap simulation model called Caspar FSTI. These simulations along with the measurements are used to locate potential lifetime reducing operating conditions and analyze them. The first results of the thermal behavior of this interface will be presented in this paper.
A Solution for an Electronically-Controlled Variable Delivery External Gear Pump
Authors: Tankasala Srinath , Vacca Andrea 
Published: December 2017

This paper describes an innovative design concept to enable electronic control of the flow delivered by external spur gear pumps. The basic principle used to obtain flow variation relies on a variable timing concept previously demonstrated by the author’s research team. This principle permits to vary the flow within a certain range, without introducing additional sources of power loss. Previous work proved the applicability of the proposed concept in a pressure compensated design of an external gear pump for high pressure applications. This concept took advantage of the pressure differential acting on the “slider”, which is an internal element performing the flow regulation.
In this paper, a solution that permits to achieve balance of the pressure forces acting on the slider is proposed. This solution reduces the actuation forces, thus enabling direct flow control actuation through an electronic control system. The proposed solution is cost effective, it consists of a limited number of parts, and it is suitable for pumps without pressure compensation, i.e. for low or intermediate pressures.
The paper details the aspects of the pump design, which was performed by using a multi-objective algorithm that maximizes the flow operating range and at the same time the pump. The optimum design could achieve a flow variation of about 32% in simulation and this was also demonstrated in actual experiments on a prototype realized at the author’s Research Center.
The proposed design can impact several of the current applications of external gear pumps, introducing the additional “flow on demand” capability.