bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mathematical modeling of navigational decisions based on intensity versus directionality in Drosophila larval phototaxis
Authors: de Andres-Bragado Lucia , Mazza Christian , Senn Walter , Sprecher Simon G. 
Published: January 2018

AbstractOrganisms use environmental cues for directed navigation. Depending on the sensory modality and complexity of the involved sensory organs, different types of information may be processed. Understanding the basic logic behind navigational decisions critically depends on the complexity of the nervous system. Due to the comparably simple organization of the nervous system of the fruit fly larva, it stands as a powerful model to study decision-making processes that underlie directed navigation. Here, we formulate a stochastic method based on biased Markov chains to model the behavioral basis of negative phototaxis. We have quantitatively measured phototaxis in response to defined sensory inputs. We find that larvae make navigational decisions by taking into account both light intensities and its spatial gradients, and our model allows us to quantify how larvae minimize their exposure to light intensity and at the same time maximize their distance to the source of light. The response to the light field is a non-linear response and saturates above an intensity threshold. Our mathematical model simulates and predicts larval behavioral dynamics only using light intensity and directionality as input parameters. Moreover, it allows us to evaluate the relative importance of these two factors governing visual navigation. The model has been validated with experimental biological data yielding insight into the strategy that larvae use to achieve their goal with respect to the navigational cue of light, paving the way for future work to study the role of the different neuronal components in this mechanism.Author SummaryNavigational decision-making is a complex process during which the nervous system is able to decipher external input through molecular and cellular mechanisms to produce a spatially-coordinated behavioral output. Drosophila larvae provide an excellent model to understand these decision-making mechanisms as we can measure the behavioral output (larval navigation) in response to quantifiable external input (different light conditions). We have performed experiments to quantify larval light avoidance in order to subsequently design a mathematical model that quantitatively reproduces larval behavior. Our results allow us to characterize the relative importance of light intensity and directionality and yield insight into the neural algorithms used in the decision-making mechanism of larval phototaxis.
Navigating in vitro bioactivity data: investigating available resources using model compounds
Authors: Ilmjärv Sten , Augsburger Fiona , Bolleman Jerven Tjalling , Liechti Robin , Bridge Alan James , Sandström Jenny , Jaquet Vincent , Xenarios Ioannis , Krause Karl-Heinz 
Published: January 2018

ABSTRACTModern medicine and an increasingly complex environment contribute to exposure of humans to a large number of chemical compounds, that can potentially be toxic. Although widely used, compound testing in animals has important limitations. In vitro testing provides a promising alternative. However, because of the relative inaccessibility and fragmentation of available data, the in vitro approach largely underperforms its potential. The aim of this study is to investigate how available public online resources (tools and databases) support accessing and distribution of in vitro compound data. We examined 19 public online resources, mapped their features, and evaluated their usability with a set of four model compounds (aspirin, rosiglitazone, valproic acid, and tamoxifen). By investigating compound names and identifiers, we observed extensive variation and inconsistencies in available resources: the synonyms were different, compounds’ structural identifiers (InChI, InChIKey, SMILES and IUPAC systematic name) underperformed in omics databases, identification of compound related metadata (e.g. concentrations used in the experiments) from omics experiments was complex and none of the available resources clearly distinguished between in vivo and in vitro data. In addition, we estimated accessibility of selected public resources using computational queries. Only a few public resources provided access to compound-related data using semantic web technology. The general quality of experiment annotations created further difficulties in identifying data of interest. Therefore, we identified several standardized ontologies with potential to provide an increased accuracy for extensive data retrieval of in vitro compound data. Furthermore, using the examples of our model compounds, we provide recommendations on the use of ontologies by suggesting specific ontology terms to annotate in vitro experimental data when being published.
A host-pathogen interaction screen identifiesada2as a mediator ofCandida glabratadefences against reactive oxygen species
Authors: Kounatidis Ilias , Ames Lauren , Mistry Rupal , Ho Hsueh-lui , Haynes Ken , Ligoxygakis Petros 
Published: January 2018

AbstractCandida glabrata (C. glabrata) forms part of the normal human gut microbiota but can cause life-threatening invasive infections in immune-compromised individuals.C. glabratadisplays high resistance to common azole antifungals, which necessitates new treatments. In this investigation, we identified fiveC. glabratadeletion mutants (Δada2, Δbas1, Δhir3,Δino2andΔmet31) from a library of 196 transcription factor mutants that were unable to grow and activate an immune response inDrosophilalarvae. This highlighted the importance of these transcription factors inC. glabratainfectivity. Furtherex vivoinvestigation into these mutants revealed the requirement ofC. glabrata ADA2for oxidative stress tolerance. We confirmed this observationin vivowhereby growth of theC. glabrata Δada2strain was permitted only in flies with suppressed production of reactive oxygen species (ROS). Conversely, overexpression ofADA2promotedC. glabratareplication in infected wild type larvae resulting in larval killing. We propose thatADA2orchestrates the response ofC. glabrataagainst ROS-mediated immune defences during infection. With the need to find alternative antifungal treatment forC. glabratainfections, genes required for survival in the host environment, such asADA2, provide promising potential targets.
Adaptation decorrelates shape representations
Authors: Mattar Marcelo G. , Olkkonen Maria , Epstein Russell A. , Aguirre Geoffrey K. 
Published: January 2018

AbstractPerception and neural responses are modulated by sensory history. Visual adaptation, an example of such an effect, has been hypothesized to improve stimulus discrimination by decorrelating responses across a set of neural units. While a central theoretical model, behavioral and neural evidence for this theory is limited and inconclusive. Here, we use a parametric 3D shape-space to test whether adaptation decorrelates shape representations in humans. In a behavioral experiment with 20 subjects, we find that adaptation to a shape class improves discrimination of subsequently presented stimuli with similar features. In a BOLD fMRI experiment with 10 subjects we observe that adaptation to a shape class decorrelates the multivariate representations of subsequently presented stimuli with similar features in object-selective cortex. These results support the long-standing proposal that adaptation improves perceptual discrimination and decorrelates neural representations, offering insights into potential underlying mechanisms.
Ostreococcus tauri is a high-lipid content green algae that extrudes clustered lipid droplets
Authors: Smallwood Chuck R. , Chrisler William , Chen Jian-Hua , Patello Emma , Thomas Mathew , Boudreau Rosanne , Ekman Axel , Wang Hongfei , McDermott Gerry , Evans James E. 
Published: January 2018

AbstractLipid droplet biogenesis, accumulation and secretion is an important field of research spanning biofuel feedstock production in algae and yeast to plant-microbe symbiosis or human metabolic disorders and other diseases. Here we evaluate the critical elements that influence lipid accumulation in the highly simplified and smallest known eukaryote Ostreococcus tauri and identify several conditions that satisfy its classification as an oleaginous green alga. In addition, these experiments revealed the release of excess lipids in pea-pod like structures where many dense lipid droplets are clustered in a linear fashion surrounded by an enveloping membrane which contrasts with known mechanisms from other eukaryotes. These results highlight the potential for Ostreococcus tauri to probe the evolution of lipid droplet dynamics as an emerging model organism with a compacted eukaryotic genome and also to impact lipid feedstock bioproduction applications either directly or using synthetic biology.One Sentence SummaryThe smallest known eukaryote Ostreococcus tauri is oleaginous and sheds lipid droplets as pea-pod like membrane enclosed clusters.
Mutations in efflux pump Rv1258c (Tap) cause resistance to pyrazinamide and other drugs inM. tuberculosis
Authors: Liu Jiayun , Shi Wanliang , Zhang Shuo , Cassell Gail , Maslov Dmitry A. , Shur Kirill V. , Bekker Olga B. , Danilenko Valery N. , Hao Xiaoke , Zhang Ying 
Published: January 2018

AbstractAlthough drug resistance inM. tuberculosisis mainly caused by mutations in drug activating enzymes or drug targets, there is increasing interest in possible role of efflux in causing drug resistance. Previously, efflux genes are shown upregulated upon drug exposure or implicated in drug resistance in overexpression studies, but the role of mutations in efflux pumps identified in clinical isolates in causing drug resistance is unknown. Here we investigated the role of mutations in efflux pump Rv1258c (Tap) from clinical isolates in causing drug resistance inM. tuberculosisby constructing point mutations V219A, S292L in Rv1258c in the chromosome ofM. tuberculosisand assessed drug susceptibility of the constructed mutants. Interestingly, V219A, S292L point mutations caused clinically relevant drug resistance to pyrazinamide (PZA), isoniazid (INH), and streptomycin (SM), but not to other drugs inM. tuberculosis. While V219A point mutation conferred a low level resistance, the S292L mutation caused a higher level of resistance. Efflux inhibitor piperine inhibited INH and PZA resistance in the S292L mutant but not in the V219A mutant. S292L mutant had higher efflux activity for pyrazinoic acid (the active form of PZA) than the parent strain. We conclude that point mutations in the efflux pump Rv1258c in clinical isolates can confer clinically relevant drug resistance including PZA and could explain some previously unaccounted drug resistance in clinical strains. Future studies need to take efflux mutations into consideration for improved detection of drug resistance inM. tuberculosisand address their role in affecting treatment outcome in vivo.
CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language
Authors: Kotliar Michael , Kartashov Andrey V. , Barski Artem 
Published: January 2018

AbstractBackgroundMassive growth in the amount of research data and computational analysis has led to increased utilization of pipeline managers in biomedical computational research. However, each of more than 100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL.FindingsHere, we present CWL-Airflow, an extension for the Apache Airflow pipeline manager supporting CWL. CWL-Airflow utilizes CWL v1.0 specification and can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. A sample CWL pipeline for processing of ChIP-Seq data is provided.ConclusionsCWL-Airflow will provide users with the features of a fully-fledged pipeline manager and an ability to execute CWL workflows anywhere Airflow can run—from a laptop to cluster or cloud environment.AvailabilityCWL-Airflow is available under Apache license v.2 and can be downloaded from https://barski-lab.github.io/cwl-airflow, http://doi.org/10.5281/zenodo.2669582, RRID: SCR_017196.
Accurate analysis of genuine CRISPR editing events with ampliCan
Authors: Labun Kornel , Guo Xiaoge , Chavez Alejandro , Church George , Gagnon James , Valen Eivind 
Published: January 2018

AbstractWe present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental artifacts, event-specific normalization, off-target read detection and quantifies insertions, deletions, HDR repair as well as targeted base editing. It is scalable to thousands of amplicon sequencing-based experiments from any genome editing experiment, including CRISPR. It enables automated integration of controls and accounts for biases at every step of the analysis. We benchmarked ampliCan on both real and simulated datasets against other leading tools, demonstrating that it outperformed all in the face of common confounding factors.
Modifying assurance practices to meet the needs of integrated reporting
Authors: Maroun Warren 
Published: January 2018

PurposeTraditional methods of assurance outlined by current professional standards are risk-based models where the emphasis is on the veracity of published data rather than on the rigour of the interpretation or analysis of information provided to users. As such, they are not well suited for expressing an opinion on qualitative, subjective or forward-looking assessments typically included in integrated reports. In this context, the purpose of this paper is to describe an alternate approach to assurance and identifies the initial elements of an “interpretive assurance model”.Design/methodology/approachThe research is exploratory/interpretive. It relies on detailed interviews with experienced auditors and preparers to develop an initial approach for providing some level of assurance over an integrated report.FindingsThe research identifies elements of an interpretive assurance model which focusses on providing assurance on the interpretation and analysis of information included in an integrated report rather than on underlying data. These include an examination of the completeness of the explanation of the value creation process provided in an integrated report; the methods used to support management discussion and analysis; and the reasonability of the review process used to ensure the reliability of qualitative, subjective and forward-looking representations contained in an integrated report.Research limitations/implicationsThe study is conducted in a South African setting. While limiting the study to a single jurisdiction may be seen as a limitation, local preparers and auditors have had at least five years of experience with the application of an integrated reporting framework and are in a strong position to provide detailed insights.Practical implicationsAn interpretive assurance model shifts the focus from objective verification of data using defined test procedures to evaluation of the interpretation and analysis process used to prepare an integrated report. Application of the proposed model will require practitioners and auditing students to be trained extensively in qualitative analytical techniques. The inherent complexity of contemporary business models and the multi-dimensional focus of integrated reports will also result in changes in the composition of audit teams which are currently dominated by experts in financial reporting rather than integrated or strategic business management.Originality/valueThe paper is the first to offer a practical approach for providing assurance over an integrated report. It responds to calls form the International Integrated Reporting Council and International Auditing and Assurance Standards Board for more innovative assurance models for addressing the reporting needs of contemporary organisations.
Enabling an effective knowledge and information flow between the phases of building construction and facilities management
Authors: Tan Adeline Zhu Teng , Zaman Atiq , Sutrisna Monty 
Published: January 2018

Purpose
The purpose of this study is to investigate ways of transferring knowledge and information during the life-cycle phases of construction projects, particularly between the construction and occupancy phases, and to find an approach to minimise knowledge and information gaps during the handover process.

Design/methodology/approach
The study applied a qualitative approach involving a literature review and an archival analysis of information flow in the studied cases of a construction project, followed by a cross-cases analysis and expert interviews. Data on information flow were collected from three cases of building construction projects in Perth, Western Australia. In addition, a total of 18 local facilities management experts were interviewed to identify the key reasons of knowledge and information gaps and to propose an effective knowledge flow model.

Findings
The findings of this study indicated a significant knowledge and information gap, which exists during the handover process in construction projects in Western Australia. The findings of case analysis and expert interviews identified that the project handover guidelines were often ignored in construction projects in Western Australia, and the handover phase was not given the same priority as the design and construction phases by most of the project stakeholders, which led to information and knowledge gaps between the project construction and post-occupancy phases. The study conducted, integrated knowledge and information flow modelling to analyse the knowledge and information gaps followed by mapping the gaps against existing knowledge sharing frameworks (KSFs) before proposing an integrated knowledge sharing conceptual model to improve current practice and to enhance the information flow during the various phases of the construction project life cycle.

Research limitations/implications
The study is based on three cases in Perth, Western Australia, and thus the findings and recommendations are contextual. Whilst laying a good foundation to do so, further research is needed to investigate more cases in Western Australia and beyond to fully generalise the findings from this study.

Originality/value
The study contributes to improve the handover process and information flows in project life-cycle phases in Western Australia and develop an information flow model followed by bringing together existing KSFs, namely, the open communication channel (OCC), soft landing framework (SLF) and building information modelling (BIM), to propose an integrated knowledge sharing conceptual model. The methodology used here to analyse the information flow in a diagrammatic manner, the mapping of FM issues against the KSFs’ capabilities and a conceptual model to facilitate change in the industry’s silo mindset are the main contributions of this paper.
Export promotion programmes for assisting SMEs
Authors: Coudounaris Dafnis N. 
Published: January 2018

Purpose
This paper aims to shed light on how small- and medium-sized enterprises can use export promotion programmes (EPPs) to improve their performance. The proposed conceptual model focuses on the need that the mechanism of awareness and use of EPPs should play a more active strategic role in shaping the firm’s export performance.

Design/methodology/approach
A meta-analysis of the pertinent literature reveals 16 studies on EPPs.

Findings
This study reveals that there are 16 relationships which are important based on the meta-analytic correlations. The analysis of these relationships shows that EPPs, export performance, strategy, knowledge, commitment, capabilities, competitive advantage and experience are the mostly used constructs.

Originality/value
This investigation supports the view that the moderating effects of the improvement of trust relationship between partners, i.e. importers to exporter and public policymakers to exporter, and the mechanism of awareness and use of EPPs accelerate the firm’s export performance. EPPs explain 31.3 per cent of the variance in export performance indicating their catalytic role in the exports’ growth.
Interconnecting exporter types with export growth and decline patterns
Authors: Vissak Tiia , Lukason Oliver , Segovia-Vargas Maria-Jesus 
Published: January 2018

Purpose
This paper aims to find out if different exporter types dominate among matched mature Spanish and Estonian firms and whether these types are associated with specific export growth/decline patterns.

Design/methodology/approach
This study is based on firm-level data from the Estonian Business Register’s database of annual financial reports and SEPI Foundation’s survey on Spanish firms’ business strategies. From both countries, 242 firms were included and the period 2009-2013 was chosen.

Findings
Committed exporters (with 75 per cent or higher export shares) dominated in Estonia and experimental exporters (with export shares mostly below 10 per cent) in Spain. While in Estonia, the most frequent export growth/decline pattern encompassed four consecutive growth years, in Spain, it had two consecutive growth years and then two decline years. Spanish firms’ export growth/decline patterns were more random: 12 patterns of 16 fell within the range of a random walk assumption, while in Estonia, only 5 patterns were within the range. Contingency existed between exporter types and export growth/decline patterns only for the whole sample.

Originality/value
This paper studies if committed/aggressive/active exporters experience more export fluctuations than passive/experimental exporters, and how random export growth/decline patterns are.
“Thinking Outside the Camp”: Education Solutions for Syrian Refugees in Jordan
Authors: VON BAEYER SARAH LEBARON 
Published: January 2018

This paper presents a case study of a project on education solutions for Syrian refugees in Jordan conducted between 2015–2017. First, it describes how ReD's methodological approach provided a unique perspective to studies on refugees. By immersing a team in the day‐to‐day lives and settings that most Syrian refugees experience in Jordan—i.e., outside of camps and in people's actual homes—ReD led its client to “think outside the camp,” something that relief agencies and companies often fail to do due to the refugee camp model of humanitarian assistance that, ever since WWII, has dominated the approach to refugees. Second, as a result of its unique methodological approach, ReD uncovered important findings about social networks and technology use and access in Syrian refugees’ homes and communities that ultimately shaped the client's perspective on solution development. For example, ReD's team of ethnographers found that nearly all out‐of‐camp Syrian households had at least one Smartphone in their possession, if not two or more, and that digital devices served as important tools of communication and community‐building among people displaced by conflict. Consequently, ReD advised its client to tap into these pre‐existing social networks and mobile technologies in order to develop an education solution that best fit refugees’ “real‐life” practices. Ultimately, both ReD's methods and its findings led to a significant impact in how the client strategized on and developed their education solution, and can serve as a broader model for how to approach building services and/or products for displaced populations with access to basic mobile technologies.“The Jordanian educational/policy response to refugees is broken and will not easily be fixed or tinkered with. Solutions must work around this system.” (Education expert and activist working with vulnerable youth and school dropouts in Jordan)