bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalisation behaviour of predators toward warning signals displayed by harmful prey: answers from a videogame played by humans
Authors: Arias Mónica , Griffiths David , Joron Mathieu , Davey John , Martin Simon , Jiggins Chris , Nadeau Nicola , Llaurens Violaine 
Published: September 2018

AbstractThe persistence of several warning signals in sympatry is a puzzling evolutionary question because selection favours convergence of colour patterns among toxic species. Such convergence is shaped by predators’ reaction to similar but not identical stimulus,i.e.generalisation behaviour. However, studying generalisation behaviour in complex natural communities of predators is challenging, and is thus generally limited to simple variations of prey colour patterns. Here, we used humans as surrogate predators to investigate generalisation behaviours on two prey communities with different level of warning signals complexity. Humans’ generalisation capacities were estimated using a computer game simulating a simple (4 morphs) and a complex (10 morphs) community of defended (associated with a penalty) and palatable butterflies. Colour patterns used in the game are actually observed in natural populations of the defended butterfliesH. numata, and generalisation behaviour of natural predator’s communities on these colour patterns have previously been investigated in the wild, allowing direct comparison with human behaviour. We investigated human predation behaviour by recording attack rates on the different defended and palatable colour patterns, as well as player survival time (i.e. score). Phenotypic similarity among the different colour patterns was precisely quantified using a custom algorithm accounting for both colour and pattern variations (CPM method). By analysing attack behaviours of 491 game players, we found that learning was more efficient in the simple prey community. Additionally, profitable prey gained protection from sharing key visual features with unprofitable prey in both communities while learning, in accordance with natural predator behaviours. Moreover, other behaviours observed in natural predators, such as colour neophobia, were detected in humans and shaped morph vulnerability during the game. Similarities between our results in humans and the reaction of natural predator communities to the same colour patterns validate our video-game as a useful proxy to study predator behaviour. This experimental set-up can thus be compared to natural systems, enabling further investigations of generalisation on mimicry evolution.
Preferential sampling for presence/absence data and for fusion of presence/absence data with presence-only data
Authors: Gelfand Alan. E. , Shirota Shinichiro 
Published: September 2018

AbstractPresence/absence data and presence-only data are the two customary sources for learning about species distributions over a region. We present an ambitious agenda with regard to such data. We illuminate the fundamental modeling differences between the two types of data. Most simply, locations are considered as fixed under presence/absence data; locations are random under presence-only data. The definition of “probability of presence” is incompatible between the two. So, we take issue with modeling strategies in the literature which ignore this incom-patibility, which assume that presence/absence modeling can be induced from presence-only specifications and therefore, that fusion of presence-only and presence/absence data sources is routine.We argue that presence/absence data should be modeled at point level. That is, we need to specify a surface which provides the probability of presence at any location in the region. A realization from this surface is a binary map yielding the results of Bernoulli trials across all locations; this surface is only partially observed. Presence-only data should be modeled as a (partially observed) point pattern, arising from a random number of individuals at random locations, driven by specification of an intensity function. There is no notion of Bernoulli trials; events are associated with areas.We further argue that, with just presence/absence data, preferential sampling, using a shared process perspective, can improve our estimated presence/absence surface and prediction of presence. We also argue that preferential sampling can enable a probabilistically coherent fusion of the two data types.We illustrate with two real datasets, one presence/absence, one presence-only for invasive species presence in New England in the United States. We demonstrate that potential bias in sampling locations can affect inference with regard to presence/absence and show that in-ference can be improved with preferential sampling ideas. We also provide a probabilistically coherent fusion of the two datasets to again improve inference with regard to presence/absence.The importance of our work is to provide more careful modeling when studying species distributions. Ignoring incompatibility between data types and offering incoherent modeling specifications implies invalid inference; the community should benefit from this recognition.
Influenza A Virus Ribonucleoproteins Form Liquid Organelles at Endoplasmic Reticulum Exit Sites
Authors: Alenquer Marta , Vale-Costa Sílvia , Sousa Ana Laura , Etibor Temitope Akhigbe , Ferreira Filipe , João Amorim Maria 
Published: September 2018

ABSTRACTInfluenza A virus has an eight-partite RNA genome that during viral assembly forms a supramolecular complex containing one copy of each RNA. Genome assembly is a selective process driven by RNA-RNA interactions and is thought to lead to discrete punctate structures scattered through the cytosol. Here, we show that contrary to the accepted view, formation of these structures is not dependent on RNA-RNA interactions among distinct viral ribonucleoproteins (vRNPs), as they assemble in cells expressing only one vRNP type. We demonstrate that these viral inclusions display characteristics of liquid organelles, segregating from the cytosol without a delimitating membrane, dynamically exchanging material, deforming easily and adapting fast to hypotonic shock. We provide evidence that they develop close to the Endoplasmic Reticulum Exit Sites (ERES), being dependent on continuous ER-Golgi vesicular cycling. We show that viral inclusions do not promote escape to interferon response, and propose that they facilitate selected RNA-RNA interactions in a liquid environment of concentrated vRNPs.
Inspecting Morphological Features of Mosquito Wings for Identification with Image Recognition Tools
Authors: Haarlem Clinton , Vos Rutger 
Published: September 2018

AbstractMosquitoes are important disease vectors. Different mosquito genera are associated with different diseases at varying levels of specificity. Hence, quick and low-cost methods of identification, even if relatively coarse and to genus level, will be of use in assessing risk and informing mitigation measures. Here we assess the extent to which digital photographs of mosquito wings taken with common cell phone cameras and clip-on lenses can be used to discriminate among mosquito genera when fed into image feature extraction algorithms. Our results show that genera may be distinguished on the basis of features extracted using the SURF algorithm. However, we also found that the naïve features examined here require very standardized photography and that different phone cameras have different signatures that may need to be taken into account.
Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires
Authors: Laks Emma , Zahn Hans , Lai Daniel , McPherson Andrew , Steif Adi , Brimhall Jazmine , Biele Justina , Wang Beixi , Masud Tehmina , Grewal Diljot , Nielsen Cydney , Leung Samantha , Bojilova Viktoria , Smith Maia , Golovko Oleg , Poon Steven , Eirew Peter , Kabeer Farhia , de Algara Teresa Ruiz , Lee So Ra , Taghiyar M. Jafar , Huebner Curtis , Ngo Jessica , Chan Tim , Vatrt-Watts Spencer , Walters Pascale , Abrar Nafis , Chan Sophia , Wiens Matt , Martin Lauren , Scott R. Wilder , Underhill Michael T. , Chavez Elizabeth , Steidl Christian , Costa Daniel Da , Ma Yusanne , Coope Robin J. N. , Corbett Richard , Pleasance Stephen , Moore Richard , Mungall Andy J. ,   IMAXT Consortium, Marra Marco A. , Hansen Carl , Shah Sohrab P. , Aparicio Samuel 
Published: September 2018

SummaryEssential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing approach implemented on commodity hardware (DLP+) coupled with a cloud-based computational platform, we define a resource of 40,000 single-cell genomes characterized by their genome states, across a wide range of tissue types and conditions. We show that shallow sequencing across thousands of genomes permits reconstruction of clonal genomes to single nucleotide resolution through aggregation analysis of cells sharing higher order genome structure. From large-scale population analysis over thousands of cells, we identify rare cells exhibiting mitotic mis-segregation of whole chromosomes. We observe that tissue derived scWGS libraries exhibit lower rates of whole chromosome anueploidy than cell lines, and loss of p53 results in a shift in event type, but not overall prevalence in breast epithelium. Finally, we demonstrate that the replication states of genomes can be identified, allowing the number and proportion of replicating cells, as well as the chromosomal pattern of replication to be unambiguously identified in single-cell genome sequencing experiments. The combined annotated resource and approach provide a re-implementable large scale platform for studying lineages and tissue heterogeneity.
Efect of Sec61 interaction with Mpd1 on Endoplasmic Reticulum- Associated Degradation
Authors: Pereira Fábio , Rettel Mandy , Stein Frank , Savitski Mikhail M. , Collinson Ian , Römisch Karin 
Published: September 2018

AbstractProteins that misfold in the endoplasmic reticulum (ER) are transported back to the cytosol for ER-associated degradation (ERAD). The Sec61 channel is one of the candidates for the retrograde transport conduit. Channel opening from the ER lumen must be triggered by ERAD factors and substrates. Here we identified new lumenal interaction partners of Sec61 by chemical crosslinking and mass spectrometry. In addition to known Sec61 interactors we detected ERAD factors including Cue1, Ubc6, Ubc7, Asi3, and Mpd1. We show that the CPY* ERAD factor Mpd1 binds to the lumenal Sec61 hinge region. Deletion of the Mpd1 binding site reduced the interaction between both proteins and caused an ERAD defect specific for CPY* without affecting protein import into the ER or ERAD of other substrates. Our data suggest that Mpd1 binding to Sec61 is a prerequisite for CPY* ERAD and confirm a role of Sec61 in ERAD of misfolded secretory proteins.
Neural basis of learning guided by sensory confidence and reward value
Authors: Lak Armin , Okun Michael , Moss Morgane , Gurnani Harsha , Farrell Karolina , Wells Miles J , Reddy Charu Bai , Kepecs Adam , Harris Kenneth D , Carandini Matteo 
Published: September 2018

SummaryMaking efficient decisions requires combining present sensory evidence with previous reward values, and learning from the resulting outcome. To establish the underlying neural processes, we trained mice in a task that probed such decisions. Mouse choices conformed to a reinforcement learning model that estimates predicted value (reward value times sensory confidence) and prediction error (outcome minus predicted value). Predicted value was encoded in the pre-outcome activity of prelimbic frontal neurons and midbrain dopamine neurons. Prediction error was encoded in the post-outcome activity of dopamine neurons, which reflected not only reward value but also sensory confidence. Manipulations of these signals spared ongoing choices but profoundly affected subsequent learning. Learning depended on the pre-outcome activity of prelimbic neurons, but not dopamine neurons. Learning also depended on the post-outcome activity of dopamine neurons, but not prelimbic neurons. These results reveal the distinct roles of frontal and dopamine neurons in learning under uncertainty.
Association of HLA class I type with prevalence and outcome of patients with acute myeloid leukemia and mutated nucleophosmin
Authors: Kuželová Kateřina , Brodská Barbora , Schetelig Johannes , Röllig Christoph , Ráčil Zdeněk , Walz Juliane Stickel , Helbig Grzegorz , Fuchs Ota , Vraná Milena , Pecherková Pavla , Šálek Cyril , Mayer Jiří 
Published: September 2018

AbstractAcute myeloid leukemia with mutated nucleophosmin (NPMc+ AML) forms a distinct AML subgroup with better prognosis which can potentially be associated with immune response against the mutated nucleophosmin (NPM). As the T-cell-mediated immunity involves antigen presentation on HLA class I molecules, we hypothesized that individuals with suitable HLA type could be less prone to develop NPMc+ AML. We compared HLA class I distribution in NPMc+ AML patient cohort (398 patients from 5 centers) with the HLA allele frequencies of the caucasian population and found HLA-A*02, B*07, B*40 and C*07 underrepresented in the NPMc+ AML group. Presence of B*07 or C*07:01 antigen was associated with better survival in patients without concomitantFLT3internal tandem duplication. Candidate NPM-derived immunopeptides were found for B*40 and B*07 using prediction software tools. Our findings suggest that a T-cell-mediated immune response could actually explain better prognosis of NPMc+ patients and provide a rationale for attempts to explore the importance of immunosuppressive mechanisms in this AML subgroup.
Politicians’ use of Facebook during elections
Authors: Bronstein Jenny , Aharony Noa , Bar-Ilan Judit 
Published: September 2018

PurposeThe purpose of this paper is to understand the use of Facebook by Israeli party leaders during an election period by examining four elements: the type of Aristotelian language of persuasion; the level of online engagement measured by three different types of feedback: likes, comments and shares; the use of personalization elements as engagement strategies; and the vividness features used in the post (text, photographs and video).Design/methodology/approachAll of the posts from the Facebook pages of ten Israeli party leaders were collected for 45 days prior to the 2015 general elections. The number of posts, likes, comments and shares in each post were captured and the data were analyzed looking for elements of Aristotelian persuasion and of online engagement with the users.FindingsThe dominance of pathos was a salient element in the data demonstrating the politicians’ need to create an affective alliance with the public and it was the element that resulted in a higher number of likes, shares and comments. Only a few relationships were found and these do not point to a clear relationship between multimedia use and social media engagement. The interactive, open and free nature of social networking sites contributes to their development as a new type of political podia that allow politicians to produce a different kind of political communication. Instead of using these sites as platforms to disseminate their ideas, plans and strategies, politicians focus their interactions with the audience on the creation and maintenance of affective alliances.Originality/valueThe study contributes to the existing literature on the subject by examining four characteristics of the politicians’ personal profiles on social networks simultaneously while most of the past studies have focused on only one or two of these characteristics.
Mental health services for people with intellectual disability in Ireland: evidence, barriers and opportunities
Authors: Ramsay Hugh , Dodd Philip 
Published: September 2018

Purpose
The purpose of this paper is to outline the historical background and policy context of mental health services for people with intellectual disability (ID) in Ireland. It then considers recent implementation and lessons from the Irish experience.

Design/methodology/approach
The policy background and research literature relevant to the development of mental health services for people with ID in Ireland was reviewed and discussed.

Findings
Mental health services in Ireland remain in a state of change, moving towards the implementation of specialist multi-disciplinary teams in the community, alongside previous models of care and service.

Research limitations/implications
This paper summarises recent advances and research regarding mental health services for people with ID in Ireland.

Practical implications
The paper illustrates the process of delivering changes to mental health services with practical implications for mental health services internationally.

Originality/value
This is the first paper in many years to summarise the development of mental health services for people with ID in Ireland. There has been considerable recent change and it is therefore important to provide a useful reference for the current status of services.
The cooperation mechanisms of trade associations
Authors: Brache Jose 
Published: September 2018

PurposeThe purpose of this paper is to propose a conceptual model that portrays how contextual factors and behavioural cooperation mechanisms influence the effect of trade associations on the export performance of small and medium enterprises (SMEs) in a Latin American emerging economy.Design/methodology/approachThe author draws on multiple streams of literature including: co-location, networks, cooperation and export performance to suggest a series of solid theoretical insights to the literature on SMEs’ export performance, networks and co-location in the Latin American context.FindingsContextual factors and behavioural cooperation mechanisms influence the effect of trade associations on export performance determining the final sign of such effect. Trust plays a role within all proposed mechanisms, but is not as fundamental as previously characterised in studies on the export performance of SMEs. Cooperation might exist, prevail, and exert a positive impact on SMEs’ export performance even in the absence of trust.Originality/valueThis paper contributes to the literature on SMEs’ export performance, networks and co-location in the Latin American context by presenting a theoretical model that enfolds co-location, networks, trade associations and cooperation effects on SMEs’ export performance under the same foundation. It creates the categories of “contextual factors” and “behavioural cooperation mechanisms” to differentiate the elements that weight on the relationship between firms and trade associations, thus facilitating or hindering export performance. It guides policy makers and company managers on where to focus when incentivizing conduct towards a more productive export performance in Latin America and other emerging economies.
The effect of negative work outcomes and values on the perceived likelihood of employee dishonest behaviour
Authors: Jaakson Krista , Vadi Maaja , Baumane-Vītoliņa Ilona 
Published: September 2018

Purpose
Employee dishonesty is problematic for businesses in general, particularly for retailers. The purpose of this paper is to empirically analyse selected factors associated with the perceived likelihood of dishonest behaviour among retail employees. Specifically, the role of three negative work outcomes – insufficient pay, boredom, and perceived injustice – is investigated, as well as the effect of individual values and espoused organisational values.

Design/methodology/approach
The sample consisted of 784 retail employees from six retail organisations located in Estonia and Latvia. A survey questionnaire that used manipulated scenarios of work outcomes and organisational values was administered.

Findings
The study concludes that perceived injustice produces more dishonesty than other negative work outcomes (insufficient pay and boredom), whereas boredom was a surprisingly strong trigger for the perceived likelihood of dishonest behaviour. Individual ethical values determined the perceived likelihood of dishonest behaviour as hypothesised while sensation-seeking values did not. Espoused organisational values had no significant effect on the perceived likelihood of dishonest behaviour.

Practical implications
The results imply that the breach of distributional and procedural justice simultaneously associates most with employee dishonesty, and retail employee selection is the key to curbing dishonest behaviour in the workplace.

Originality/value
The paper makes a contribution to behavioural ethics literature by studying dishonest employee behaviour in the post-communist context while addressing various forms of dishonest behaviour, in addition to stealing. Also, the effect of espoused organisational values has been scarcely studied before.
Model for BPM implementation assessment: evidence from companies in Indonesia
Authors: E.R. Mahendrawathi , Hanggara Buce Trias , Astuti Hanim Maria 
Published: September 2018

Purpose
Enterprise resource planning (ERP) implementation commonly fails to recognize the need to treat it as a business process automation that must be managed and monitored continuously. Moreover, many studies on business process management (BPM) assessment focus on snapshots of different areas of BPM and not on the different stages of the lifecycle. The purpose of this paper is to propose a model that combines the BPM lifecycle, program/project implementation framework, principles of good practice, maturity and critical practices to assess how companies implementing ERP apply different BPM practices, as well as which areas are lacking and why.

Design/methodology/approach
The relevant literature was examined to develop the model for the study. Case studies of three companies in Indonesia were then conducted. The state of BPM implementation in each case was assessed through interviews, document reviews and observations.

Findings
This study found that three leading companies in Indonesia, implementing ERP for more than five years, obtained high scores for BPM implementation. They perform well in terms of process identification, implementation, monitoring and control, but are weak in process discovery and re-design, mainly because they do not optimally use specific tools for process modeling and there is a lack of process governance. The studies also pinpoint potential linkages between competition intensity and the nature of the industry with the need for good BPM.

Research limitations/implications
The model has only been tested in three cases in different industries and therefore the results, while providing good insights, cannot be generalized. More detailed assessment of certain BPM practices is needed. Furthermore, the assessment for each stage of BPM implementation was made at a single time, potentially yielding less detailed results than by assessing each stage of the BPM lifecycle.

Practical implications
The companies implementing ERP began with business process definition, but employ different process governance. The model developed here can be useful for leaders and teams to identify weak areas of practice within the stage of the BPM lifecycle; it can be used as an assessment tool for companies currently conducting BPM projects or programs including ERP implementation. It can also provide a roadmap for companies intending to conduct BPM programs.

Originality/value
Most of the BPM literature focuses on specific aspects. This study proposes a different perspective by providing a model to assess BPM implementation in each stage of its lifecycle and at the same time considers practical aspects of implementation, principles of good practice, maturity factors and critical practices.