bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-based, synthesis-driven: setting the agenda for computational ecology
Authors: Poisot Timothée , Labrie Richard , Larson Erin , Rahlin Anastasia 
Published: June 2017

AbstractComputational thinking is the integration of algorithms, software, and data, to solve general questions in a field. Computation ecology has the potential to transform the way ecologists think about the integration of data and models. As the practice is gaining prominence as a way to conduct ecological research, it is important to reflect on what its agenda could be, and how it fits within the broader landscape of ecological research. In this contribution, we suggest areas in which empirical ecologists, modellers, and the emerging community of computational ecologists could engage in a constructive dialogue to build on one another’s expertise; specifically, about the need to make predictions from models actionable, about the best standards to represent ecological data, and about the proper ways to credit data collection and data reuse. We discuss how training can be amended to improve computational literacy.
In spoken word recognition the future predicts the past
Authors: Gwilliams Laura , Linzen Tal , Poeppel David , Marantz Alec 
Published: June 2017

AbstractSpeech is an inherently noisy and ambiguous signal. In order to fluently derive meaning, a listener must integrate contextual information to guide interpretations of the sensory input. While many studies have demonstrated the influence ofpriorcontext on speech perception, the neural mechanisms supporting the integration ofsubsequentcontext remain unknown. Using magnetoencephalography, we analysed responses to spoken words with a varyingly ambiguous onset phoneme, the identity of which is later disambiguated at the lexical uniqueness point1. Our findings suggest that primmary auditory cortex is sensitive to phonological ambiguity very early during processing — at just 50 ms after onset. Subphonemic detail is preserved in auditory cortex over long timescales, and re-evoked at subsequent phoneme positions. Commitments to phonological categories occur in parallel, resolving on the shorter time-scale of ~450 ms. These findings provide evidence that future input determines the perception of earlier speech sounds by maintaining sensory features until they can be integrated with top down lexical information.Significance statementThe perception of a speech sound is determined by its surrounding context, in the form of words, sentences, and other speech sounds. Often, such contextual information becomes availablelaterthan the sensory input. The present study is the first to unveil how the brain uses this subsequent information to aid speech comprehension. Concretely, we find that the auditory system supports prolonged access to the transient acoustic signal, while concurrently making guesses about the identity of the words being said. Such a processing strategy allows the content of the message to be accessed quickly, while also permitting re-analysis of the acoustic signal to minimise parsing mistakes.
Space, Time and Episodic Memory: the Hippocampus is all over the Cognitive Map
Authors: Ekstrom Arne D. , Ranganath Charan 
Published: June 2017

AbstractIn recent years, the field has reached an impasse between models suggesting that the hippocampus is fundamentally involved in spatial processing and models suggesting that the hippocampus automatically encodes all dimensions of experience in the service of memory. Here, we consider key conceptual issues that have impeded progress in our understanding of hippocampal function, and we review findings that establish the scope and limits of hippocampal involvement in navigation and memory. We argue that space and time serve as a primary scaffold to break up experiences into specific contexts, and to organize multimodal input that is to be associated within a context. However, the hippocampus is clearly capable of incorporating additional dimensions into the scaffold if they are determined to be relevant in the event-defined context. Conceiving of the hippocampal representation as constrained by immediate task demands—yet preferring axes that involve space and time—helps to reconcile an otherwise disparate set of findings on the core function of the hippocampus.
The rodent hippocampus as a bilateral structure: A review of hemispheric lateralization
Authors: Jordan Jake T. 
Published: June 2017

AbstractThe left and right rodent hippocampi exhibit striking lateralization in some of the very neural substrates considered to be critical for hippocampal cognitive function. Despite this, there is an overwhelming lack of consideration for hemispheric differences in studies of the rodent hippocampus. Asymmetries identified so far suggest that a bilateral model of the hippocampus will be essential for an understanding of this brain region, and perhaps of the brain more widely. Although hypotheses have been proposed to explain how the left and right hippocampi contribute to behavior and cognition, these hypotheses have either been refuted by more recent studies or have been limited in the scope of data they explain. Here, I will first review data on human and rodent hippocampal lateralization. The implications of these data suggest that considering the hippocampus as a bilateral structure with functional lateralization will be critical moving forward in understanding the function and mechanisms of this brain region. In exploring these implications, I will then propose a hypothesis of the hippocampus as a bilateral structure. This discrete-continuous (DC) hypothesis proposes that the left and right hippocampi contribute to spatial memory and navigation in a complementary manner. Specifically, the left hemisphere stores spatial information as discrete, salient locations and that the right hemisphere represents space continuously, contributing to route computation and flexible spatial navigation. Consideration of hippocampal lateralization in designing future studies may provide insight into the function of the hippocampus and resolve debates concerning its function.
Modeling of cytometry data in logarithmic space: when is a bimodal distribution not bimodal?
Authors: Erez Amir , Vogel Robert , Mugler Andrew , Belmonte Andrew , Altan-Bonnet Grégoire 
Published: June 2017

AbstractRecent efforts in systems immunology lead researchers to build quantitative models of cell activation and differentiation. One goal is to account for the distributions of proteins from single-cell measurements by flow cytometry or mass cytometry as a readout of biological regulation. In that context, large cell-to-cell variability is often observed in biological quantities. We show here that these readouts, viewed in logarithmic scale may result in two easily-distinguishable modes, while the underlying distribution (in linear scale) is unimodal. We introduce a simple mathematical test to highlight this mismatch. We then dissect the flow of influence of cell-to-cell variability proposing a graphical model which motivates higher-dimensional analysis of the data. Finally we show how acquiring additional biological information can be used to reduce uncertainty introduced by cell-to-cell variability, helping to clarify whether the data is uni- or bimodal. This communication has cautionary implications for manual and automatic gating strategies, as well as clustering and modeling of single-cell measurements.
Astrocytes release prostaglandin E2 to modify respiratory network activity
Authors: Forsberg David , Ringstedt Thomas , Herlenius Eric 
Published: June 2017

AbstractProstaglandin E2 (PGE2) released during hypercapnic challenge increases Ca2+oscillation frequency in the chemosensitive parafacial respiratory group (pFRG/RTN). Here, we demonstrate that pFRG/RTN astrocytes are the PGE2 source. Two distinct astrocyte subtypes were found using transgenic mice expressing GFP and MrgA1 receptors in astrocytes. Although most astrocytes appeared dormant during time-lapse calcium imaging, a subgroup displayed persistent, rhythmic oscillating calcium activity. These active astrocytes formed a subnetwork within the respiratory network distinct from the neuronal network. Activation of exogenous MrgA1 receptors expressed in astrocytes tripled their calcium oscillation frequency activity in both the preBötzinger complex and pFRG/RTN. However, neurons in the preBötC were unaffected, whereas neuronal calcium oscillatory frequency in pFRG/RTN doubled. Notably, astrocyte activation in pFRG/RTN triggered local PGE2 release and blunted the hypercapnic response. Thus, astrocytes play an active role in respiratory rhythm modulation, modifying respiratory-related behaviorthrough PGE2 release in the pFRG/RTN.
Reducing resistance allele formation in CRISPR gene drives
Authors: Champer Jackson , Liu Jingxian , Oh Suh Yeon , Reeves Riona , Luthra Anisha , Oakes Nathan , Clark Andrew G. , Messer Philipp W. 
Published: June 2017

ABSTRACTCRISPR gene drives can efficiently convert heterozygous cells with one copy of the drive allele into homozygotes, thereby enabling super-Mendelian inheritance. This mechanism could be used, for example, to rapidly disseminate a genetic payload through a population, promising novel strategies for the control of vector-borne diseases. However, all CRISPR gene drives tested have produced significant quantities of resistance alleles that cannot be converted to drive alleles and would likely prevent these drives from spreading in a natural population. In this study, we assessed three strategies for reducing resistance allele formation. First, we directly compared drives with thenanosandvasapromoters, which showed that thevasadrive produced high levels of resistance alleles in somatic cells. This was not observed in thenanosdrive. Another strategy was the addition of a second gRNA to the drive, which both significantly increased the drive conversion efficiency and reduced the formation rate of resistance alleles. Finally, to minimize maternal carryover of Cas9, we assessed the performance of an autosomal drive acting in the male germline, and found no subsequent formation of resistance alleles in embryos. Our results mark a step toward developing effective gene drives capable of functioning in natural populations and provide several possible avenues for further reduction of resistance rates.
Difficulty identifying universal high-efficacy locations for public access defibrillators
Authors: Somers Scott , LoGiudice Anthony 
Published: June 2017

PurposeThis paper reports on an investigation of spatial patterns of out-of-hospital cardiac arrest (OHCA) incidence in a large American city. The purpose of this paper is to identify neighborhoods and public occupancies with highest risk in order to develop an evidence-based strategy to promote cardiac health and improve survival.Design/methodology/approachTwo-tailed bivariate analysis was conducted using a Spearman correlation coefficient to check the covariance of census variables that were expected to relate to OHCA incidence. A principal component analysis was conducted on the remaining variables that statistically correlated with OHCA. Local indicators of spatial analysis was conducted to test the OHCA risk index and assess how well it predicts the observed OHCA incidence.FindingsClusters of OHCA events were found in neighborhoods with socially isolated older persons, as well as low-income minority populations. However, while past research has documented high-risk OHCA locations, these were not the case in this community.Originality/valueThe results highlight the importance of using local data to develop public health policies. Understanding neighborhood-level risks invariably guides resource allocation, service provision, and policy decisions to improve community public health and safety outcomes.
UK ambulance service complaints: a review of the literature
Authors: Brady Mike 
Published: June 2017

Purpose
Complaints are an integral element of the quality control and clinical governance process of UK ambulance services, and form a valid and reliable way of identifying areas of practice that require improvement. The purpose of this paper is to assess to what extent such complaints and their possible causes are researched; to identify any possible areas of practice requiring further investigation.

Design/methodology/approach
A computerised literature search was conducted using the online databases Science Direct, Cochrane library, and Web of Science, as well as specific searches of the Journal of Paramedic Practice and the International Journal of Paramedic Practice database. Online databases were searched for peer-reviewed full research articles between January 2012 and May 2016.

Findings
A total of 125 papers were identified and after further screening 90 articles were excluded. Additional screening using the critical appraisal skills programme (2014) criterions excluded a further 21 papers, leaving 14 studies for inclusion within the review.

Originality/value
This review found no specific research focussing on any causes of complaints made to UK ambulance services. Moreover, no research was identified specifically investigating the top three cited themes of complaints made in the last three years. More research is required both in researching those themes of complaints already known but also determining any other possible causes of complaints made. This review has evidenced that studies investigating response times improvement strategies, ambulance staff attitudes, and educational assessments of errors, all have findings which are meaningful and valid to determining the possible causes of complaints and possible improvement strategies. Ambulance services, commissioners, practitioners, and clinical academics should endeavour to research and share causes of complaints made to improve the quality of patient care.
Determinants of SME integration into global value chains
Authors: Kotturu Chandra Mouli V.V. , Mahanty Biswajit 
Published: June 2017

PurposeIn recent years, due to intense competition, small and medium-sized enterprises (SMEs) are unable to meet performance expectations and find difficulty in fulfilling the needs of the original equipment manufacturers (OEMs). Consequently, the growth of the SMEs has slowed down considerably. Constrained by their infrastructural resources, SMEs’ participation in global value chains (GVCs) has the potential to bring significant benefits, such as enhancing technological learning and innovation and generating positive contributions to the development of the SMEs. The purpose of this paper is to explore competitive priorities, key factors, and causal relationships influencing SMEs to enter GVCs.Design/methodology/approachIn this paper, the GVC framework is adopted and qualitative feedback loop analysis is used to identify the key factors influencing the competitive factors. A questionnaire survey was carried out with the automotive component manufacturers of a transnational corporation in India.FindingsThe survey in the automotive component manufacturing industry reveals product quality standards as the most important priority for joining global production networks, followed by price competitiveness, timely delivery, innovativeness, manufacturing flexibility, service, and dependability. The qualitative findings reveal continuous personnel training, capacity expansion, research development, and others as key factors influencing competitiveness.Practical implicationsTo retain SMEs’ role in economic development and to accelerate the growth of global production networks in India, thereby realizing opportunities from the emerging GVCs, support is needed for SMEs regarding the aspects identified in this study.Originality/valueThe study explores the dynamics of each competitive priority of SMEs in Indian automotive component manufacturing industry to enter the GVCs. No study has explored the dynamics of SMEs competitiveness to enter GVCs in the automotive manufacturing industry.
A longitudinal study into the effectiveness of the HPO Framework
Authors: de Waal André 
Published: June 2017

Purpose
The academic and management literature offers an abundance of techniques for helping organizations improve their performance. Generally, though, these techniques have not been subjected to rigorous, evidence-based evaluation or have been tested in practice over time. The purpose of this paper is to describe a longitudinal study into the effectiveness of the High Performance Organization (HPO) Framework at a social care and rehabilitation organization.

Design/methodology/approach
The HPO Framework was applied at LIMOR in the Netherlands. The longitudinal nature of the study consisted of conducting an “HPO diagnosis” twice at the organization, in 2012 and 2015. In the second diagnosis, the effectiveness of the interventions the organization undertook to address the recommendations originating from the first HPO diagnosis was also measured.

Findings
The study aimed to discover whether the HPO Framework was a suitable improvement technique with which to increase the performance of a social care and rehabilitation organization in a sustainable way. The results showed that it was used to ward off and contain the negative effects of external turbulent developments, and thereby helped LIMOR to perform better than comparable organizations.

Originality/value
As a longitudinal study of the workings and effects of the HPO Framework at a social care and rehabilitation organization, this study is the first of its kind. Moreover, it addresses two gaps in the current literature, by contributing longitudinal evidence to the body of knowledge on improvement techniques, specifically in the non-profit sector, and by adding insights on the practical workings of the HPO Framework in a non-profit context, specifically the social care and rehabilitation sector.
Cedratvirus lausannensis – digging into Pithoviridae diversity
Authors: Bertelli Claire , Mueller Linda , Thomas Vincent , Pillonel Trestan , Jacquier Nicolas , Greub Gilbert 
Published: June 2017

SummaryAmoeba‐infecting viruses have raised scientists’ interest due to their novel particle morphologies, their large genome size and their genomic content challenging previously established dogma. We report here the discovery and the characterization of Cedratvirus lausannensis, a novel member of the Megavirales, with a 0.75–1 µm long amphora‐shaped particle closed by two striped plugs. Among numerous host cell types tested, the virus replicates only in Acanthamoeba castellanii leading to host cell lysis within 24 h. C. lausannensis was resistant to ethanol, hydrogen peroxide and heating treatments. Like 30 000‐year‐old Pithovirus sibericum, C. lausannensis enters by phagocytosis, releases its genetic content by fusion of the internal membrane with the inclusion membrane and replicates in intracytoplasmic viral factories. The genome encodes 643 proteins that confirmed the grouping of C. lausannensis with Cedratvirus A11 as phylogenetically distant members of the family Pithoviridae. The 575,161 bp AT‐rich genome is essentially devoid of the numerous repeats harbored by Pithovirus, suggesting that these non‐coding repetitions might be due to a selfish element rather than particular characteristics of the Pithoviridae family. The discovery of C. lausannensis confirms the contemporary worldwide distribution of Pithoviridae members and the characterization of its genome paves the way to better understand their evolution.
Low‐abundant species facilitates specific spatial organization that promotes multispecies biofilm formation
Authors: Liu Wenzheng , Russel Jakob , Røder Henriette L. , Madsen Jonas S. , Burmølle Mette , Sørensen Søren J. 
Published: June 2017

SummaryMicroorganisms frequently co‐exist in matrix‐embedded multispecies biofilms. Within biofilms, interspecies interactions influence the spatial organization of member species, which likely play an important role in shaping the development, structure and function of these communities. Here, a reproducible four‐species biofilm, composed of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus, was established to study the importance of individual species spatial organization during multispecies biofilm development. We found that the growth of species that are poor biofilm formers, M. oxydans and P. amylolyticus, were highly enhanced when residing in the four‐species biofilm. Interestingly, the presence of the low‐abundant M. oxydans (0.5% of biomass volume) was observed to trigger changes in the composition of the four‐species community. The other three species were crucially needed for the successful inclusion of M. oxydans in the four‐species biofilm, where X. retroflexus was consistently positioned in the top layer of the mature four‐species biofilm. These findings suggest that low abundance key species can significantly impact the spatial organization and hereby stabilize the function and composition of complex microbiomes.
Loss of the ssrA genome island led to partial debromination in the PBDE respiring Dehalococcoides mccartyi strain GY50
Authors: Ding Chang , Rogers Matthew J. , Yang Kun‐Lin , He Jianzhong 
Published: June 2017

SummaryPolybrominated diphenyl ethers (PBDEs), chemicals commonly used as flame‐retardants in consumer products, are emerging persistent organic pollutants that are ubiquitous in the environment. In this study, we report a PBDE‐respiring isolate – Dehalococcoides mccartyi strain GY50, which debrominates the most toxic tetra‐ and penta‐BDE congeners (∼1.4 µM) to diphenyl ether within 12 days with hydrogen as the electron donor. The complete genome sequence revealed 26 reductive dehalogenase homologous genes (rdhAs), among which three genes (pbrA1, pbrA2 and pbrA3) were highly expressed during PBDE debromination. After 10 transfers of GY50 with trichloroethene or 2,4,6‐trichlorophenol as the electron acceptor instead of PBDEs, the ssrA‐specific genome island (ssrA‐GI) containing pbrA1 and pbrA2 was deleted from the genome of strain GY50, leading to two variants (strain GY52 with trichloroethene, strain GY55 with 2,4,6‐trichlorophenol) with identically impaired debromination capabilities (debromination of penta‐/tetra‐BDEs ceased at di‐BDE 15). Through analysis of Illumina paired‐end sequencing data, we identified read pairs that probably came from variants that contain ssrA‐GI deletions, indicating their possible presence in the original strain GY50 culture. The two variant strains provide real‐time examples on rapid evolution of organohalide‐respiring organisms. As PBDE‐respiring organisms, GY50‐like strains may serve as key players in detoxifying PBDEs in contaminated environments.