bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating species interactions as a driver of phytophagous insect divergence
Authors: de Medeiros Bruno A. S. , Farrell Brian D. 
Published: November 2019

AbstractPlants and their specialized flower visitors provide valuable insights into the evolutionary consequences of species interactions. In particular, antagonistic interactions between insects and plants have often been invoked as a major driver of diversification. Here we use a tropical community of palms and their specialized insect flower visitors to test whether antagonisms lead to higher population divergence. Interactions between palms and the insects visiting their flowers range from brood pollination to florivory and commensalism, with the latter being species that feed on decaying and presumably undefended plant tissues. We test the role of insect-host interactions in the early stages of diversification of nine species of beetles sharing host plants and geographical ranges by delimiting cryptic species and then using models of genetic isolation by environment. The degree to which insect populations are structured by the genetic divergence of plant populations varies. A hierarchical model reveals that this variation is largely uncorrelated with the kind of interaction, showing that antagonistic interactions are not associated with higher genetic differentiation. More general aspects of host use that affect plant-associated insects regardless of the outcomes of their interactions, such as sensory biases, are likely more general drivers of insect population divergence.
Minimal Barriers to Invasion During Human Colorectal Tumor Growth
Authors: Ryser Marc D. , Mallo Diego , Hall Allison , Hardman Timothy , King Lorraine M. , Sorribes Inmaculada C. , Maley Carlo C. , Marks Jeffrey R. , Hwang E. Shelley , Shibata Darryl 
Published: November 2019

ABSTRACTIntra-tumoral heterogeneity (ITH) could represent clonal evolution where subclones with greater fitness confer more malignant phenotypes and invasion constitutes an evolutionary bottleneck. Alternatively, ITH could represent branching evolution with invasion of multiple subclones. The two models respectively predict a hierarchy of subclones arranged by phenotype, or multiple subclones with shared phenotypes. We delineated these modes of invasion by merging ancestral, topographic, and phenotypic information from 12 human colorectal tumors (11 carcinomas, 1 adenoma) obtained through saturation microdissection of 325 small tumor regions. The majority of subclones (29/46, 60%) shared superficial and invasive phenotypes. Of 11 carcinomas, 9 showed evidence of multiclonal invasion, and invasive and metastatic subclones arose early along the ancestral trees. Early multiclonal invasion in the majority of these tumors indicates the expansion of co-evolving subclones with similar malignant potential in absence of late bottlenecks, and suggests that barriers to invasion are minimal during colorectal cancer growth.
SharpTNI: Counting and Sampling Parsimonious Transmission Networks under a Weak Bottleneck
Authors: Sashittal Palash , El-Kebir Mohammed 
Published: November 2019

AbstractBackgroundTechnological advances in genomic sequencing are facilitating the reconstruction of transmission histories during outbreaks in the fight against infectious diseases. However, accurate disease transmission inference using this data is hindered by a number of challenges due to within-host pathogen diversity and weak transmission bottlenecks, where multiple genetically-distinct pathogenic strains co-transmit.ResultsWe formulate a combinatorial optimization problem for transmission network inference under a weak bottleneck from a given timed phylogeny and establish hardness results. We present SharpTNI, a method to approximately count and almost uniformly sample from the solution space. Using simulated data, we show that SharpTNI accurately quantifies and uniformly samples from the solution space of parsimonious transmission networks, scaling to large datasets. We demonstrate that SharpTNI identifies co-transmissions during the 2014 Ebola outbreak that are corroborated by epidemiological information collected by previous studies.ConclusionsAccounting for weak transmission bottlenecks is crucial for accurate inference of transmission histories during outbreaks. SharpTNI is a parsimony-based method to reconstruct transmission networks for diseases with long incubation times and large inocula given timed phylogenies. The model and theoretical work of this paper pave the way for novel maximum likelihood methods to co-estimate timed phylogenies and transmission networks under a weak bottleneck.
Transcriptomic Profiling of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Over Time
Authors: Lidgerwood Grace E. , Senabouth Anne , Smith-Anttila Casey J.A. , Gnanasambandapillai Vikkitharan , Kaczorowski Dominik C. , Amann-Zalcenstein Daniela , Fletcher Erica L. , Naik Shalin H. , Hewitt Alex W. , Powell Joseph E. , Pébay Alice 
Published: November 2019

AbstractHuman pluripotent stem cell (hPSC)-derived progenies are immature versions of cells, presenting a potential limitation to the accurate modelling of disease associated with maturity or age. Hence, it is important to characterise how closely cells used in culture resemble their native counterparts. In order to select appropriate points in time for RPE cultures to reflect native counterparts, we characterised the transcriptomic profiles of hPSC-derived retinal pigment epithelium (RPE) cells from 1- and 12-month cultures. We differentiated the human embryonic stem cell line H9 into RPE cells, performed single cell RNA-sequencing of a total of 16,576 cells, and analysed the resulting data to assess the molecular changes of RPE cells across these two culture time points. Our results indicate the stability of the RPE transcriptomic signature, with no evidence of an epithelial – mesenchymal transition, and with maturing populations of RPE observed with time in culture. Assessment of gene ontology pathways revealed that as cultures age, RPE cells upregulate expression of genes involved in metal binding and antioxidant functions. This might reflect an increased ability to handle oxidative stress as cells mature. Comparison with native human RPE data confirmed a maturing transcriptional profile of RPE cells in culture. These results suggest that in vitro long-term culture of RPE cells allow the modelling of specific phenotypes observed in native mature tissue. Our work highlights the transcriptional landscape of hPSC-derived RPE as they age in culture, which provides a reference for native and patient-samples to be benchmarked against.
Neural Gene Network Constructor: A Neural Based Model for Reconstructing Gene Regulatory Network
Authors: Zhang Zhang , Wang Lifei , Wang Shuo , Tao Ruyi , Xiao Jingshu , Mou Muyun , Cai Jun , Zhang Jiang 
Published: November 2019

SummaryReconstructing gene regulatory networks (GRNs) and inferring the gene dynamics are important to understand the behavior and the fate of the normal and abnormal cells. Gene regulatory networks could be reconstructed by experimental methods or from gene expression data. Recent advances in Single Cell RNA sequencing technology and the computational method to reconstruct trajectory have generated huge scRNA-seq data tagged with additional time labels. Here, we present a deep learning model “Neural Gene Network Constructor” (NGNC), for inferring gene regulatory network and reconstructing the gene dynamics simultaneously from time series gene expression data. NGNC is a model-free heterogenous model, which can reconstruct any network structure and non-linear dynamics. It consists of two parts: a network generator which incorporating gumbel softmax technique to generate candidate network structure, and a dynamics learner which adopting multiple feedforward neural networks to predict the dynamics. We compare our model with other well-known frameworks on the data set generated by GeneNetWeaver, and achieve the state of the arts results both on network reconstruction and dynamics learning.
A widely-distributed HIV-1 provirus elimination assay to evaluate latency-reversing agents in vitro
Authors: Matsuda Kouki , Islam Saiful , Takada Toru , Tsuchiya Kiyoto , Yang Tan Benjy Jek , Hattori Shin-ichiro , Katsuya Hiroo , Kitagawa Kosaku , Kim Kwang Su , Matsuo Misaki , Delino Nicole S. , Gatanaga Hiroyuki , Yoshimura Kazuhisa , Matsushita Shuzo , Mitsuya Hiroaki , Iwami Shingo , Satou Yorifumi , Maeda Kenji 
Published: November 2019

ABSTRACTPersistence of HIV-1 latent reservoir cells during antiretroviral therapy is a major obstacle for curing HIV-1. Latency-reversing agents (LRAs) are under development to reactivate and eradicate latently infected cells; however, there are few useful models for evaluating LRA activity in vitro. Here, we established a long-term cell culture system harboring thousands of different HIV-1-infected cell clones with a wide distribution of HIV-1 provirus similar to that observed in vivo. A combination of an LRA and antiretroviral therapy (ART) significantly reduced viral rebound upon treatment interruption. Experimental investigation and mathematical modeling demonstrated that addition of LRA to ART induced latency-reversing effect and contributed to the eradication of replication competent HIV-1. The widely distributed intact provirus elimination (WIPE) assay will be useful for optimizing therapeutics against HIV-1 latency and investigating mechanistic insights into the clonal selection of heterogeneous HIV-1-infected cells.
Protein prenylation and Hsp40 in thermotolerance ofPlasmodium falciparummalaria parasites
Authors: Mathews Emily S. , Jezewski Andrew J. , Odom John Audrey R. 
Published: November 2019

AbstractDuring its complex life cycle, the malaria parasite survives dramatic changes in environmental temperature. Protein prenylation is required during asexual replication ofPlasmodium falciparum, and heat shock protein 40 (HSP40; PF3D7_1437900) is post-translationally modified with a 15-carbon farnesyl isoprenyl group. In other organisms, farnesylation of Hsp40 orthologs controls its localization and function, including temperature stress survival. In this work, we find that plastidial isopentenyl pyrophosphate (IPP) synthesis and protein farnesylation are required for malaria parasite survival after cold and heat shock. Furthermore, loss of HSP40 farnesylation alters its membrane attachment and interaction with proteins involved in crucial biological processes, such as glycolysis and cytoskeletal organization. Together, this work reveals that farnesylation of HSP40 inP. falciparumis a novel essential function of plastidial isoprenoid biosynthesis. We propose a model by which farnesyl-HSP40 promotes parasite thermotolerance and facilitates vesicular trafficking through its interaction with client proteins.
Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection
Authors: Curran Emma V. , Stankowski Sean , Pardo-Diaz Carolina , Salazar Camilo , Linares Mauricio , Nadeau Nicola J. 
Published: November 2019

AbstractHybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterfliesHeliconius eratoandH. melpomene, which are distantly related Müllerian mimics that show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in the roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping-by-sequencing also revealed weaker population structure inH. melpomene, suggesting the hybrid zones may have evolved differently in each species; which may also contribute to the patterns of phenotypic divergence in this system Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role.
Cell lineage-dependent chiral actomyosin flows drive cellular rearrangements in early development
Authors: Pimpale Lokesh , Middelkoop Teije C. , Mietke Alexander , Grill Stephan W. 
Published: November 2019

ABSTRACTProper positioning of cells is important for many aspects of embryonic development, tissue homeostasis, and regeneration. A simple mechanism by which cell positions can be specified is via orienting the cell division axis. This axis is specified at the onset of cytokinesis, but can be reoriented as cytokinesis proceeds. Rotatory actomyosin flows have been implied in specifying and reorienting the cell division axis in certain cases, but how general such reorientation events are, and how they are controlled, remains unclear. In this study, we set out to address these questions by investigating earlyCaenorhabditis elegansdevelopment. In particular, we determined which of the early embryonic cell divisions exhibit chiral counter-rotating actomyosin flows, and which do not. We follow the first nine divisions of the early embryo, and discover that chiral counter-rotating flows arise systematically in the early AB lineage, but not in early P/EMS lineage cell divisions. Combining our experiments with thin film active chiral fluid theory we identify specific properties of the actomyosin cortex in the symmetric AB lineage divisions that favor chiral counter-rotating actomyosin flows of the two halves of the dividing cell. Finally, we show that these counter-rotations are the driving force of both the AB lineage spindle skew and cell reorientation events. In conclusion, we here have shed light on the physical basis of lineage-specific actomyosin-based processes that drive chiral morphogenesis during development.
Tfam knockdown results in reduction of mtDNA copy number, OXPHOS deficiency and abnormalities in zebrafish embryos
Authors: Otten Auke BC , Kamps Rick , Lindsey Patrick , Gerards Mike , Pendeville-Samain Hélène , Muller Marc , van Tienen Florence HJ , Smeets Hubert JM 
Published: November 2019

ABSTRACTHigh mitochondrial DNA (mtDNA) copy numbers are essential for oogenesis and embryogenesis and correlate with fertility of oocytes and viability of embryos. To understand the pathology and mechanisms associated with low mtDNA copy numbers, we knocked down mitochondrial transcription factor A (Tfam), a regulator of mtDNA replication, during early zebrafish development. Reduction ofTfamusing a splice-modifying morpholino (MO) resulted in a 42%±4% decrease in mtDNA copy number in embryos at 4 days post fertilization. Morphant embryos displayed abnormal development of the eye, brain, heart and muscle, as well as a 50%±11% decrease in ATP production. Transcriptome analysis revealed a decrease in protein-encoding transcripts from the heavy strand of the mtDNA. In addition, various RNA translation pathways were increased, indicating an upregulation of nuclear and mitochondria-related translation. The developmental defects observed were supported by a decreased expression of pathways related to eye development and haematopoiesis. The increase in mRNA translation might serve as a compensation mechanism, but appears insufficient during prolonged periods of mtDNA depletion, highlighting the importance of high mtDNA copy numbers for early development in zebrafish.SUMMARY STATEMENTThe first tuneable zebrafish model used to characterize the effect of a reduced mtDNA copy number and resulting OXPHOS deficiency on zebrafish embryonic development.
Considering the local and the translocal
Authors: Dalmer Nicole K. 
Published: November 2019

PurposeInstitutional ethnography is a method of inquiry that brings attention to people’s everyday work while simultaneously highlighting broader sites of administration and governance that may be organising that work. The purpose of this paper is to argue that the integration of institutional ethnography in health information practice research represents an important shift in the way that Library and Information Science professionals and researchers study and understand these practices.Design/methodology/approachThis paper first explores the key tenets and conceptual underpinnings of Dorothy Smith’s institutional ethnography, illuminating the importance of moving between translocal and the local contexts and identifying ruling relations. Drawing from a library and information science study that combined interviews and textual analyses to examine the social organisation of family caregivers’ health-related information work, the paper then explores the affordances of starting in the local particularities and then moving outwards to the translocal.FindingsThe paper concludes with an overall assessment of what institutional ethnography can contribute to investigations of health information practices. By pushing from the local to the translocal, institutional ethnography enables a questioning of existing library and information science conceptualisations of context and of reappraising the everyday-life information seeking work/non-work dichotomy. Ultimately, in considering both the local and the translocal, institutional ethnography casts a wider net on understanding individuals’ health information practices.Originality/valueWith only two retrieved studies that combine institutional ethnography with the study of health information practices, this paper offers health information practice researchers a new method of inquiry in which to reframe the application of methods used.
Advancing service design research with design science research
Authors: Teixeira Jorge Grenha , Patrício Lia , Tuunanen Tuure 
Published: November 2019

Purpose
Service design is a multidisciplinary approach that is key to service innovation, as it brings new service ideas to life. In this context, the development of new service design methods and models for creating new service futures is an important stream of service design research. Such developments can benefit from a systematized research methodology that builds on existing knowledge and robustly evaluates the suitability of research contributions. To address this challenge, the purpose of this paper is to present design science research (DSR), an established methodology from the information systems field, and examine how it can be useful for service design research by supporting the development of new artifacts, such as service design constructs, methods and models.

Design/methodology/approach
This paper presents DSR and related literature and shows how DSR can support service design research through a step-by-step approach. A methodology to develop prescriptive-driven solutions for classes of problems, DSR can support service design research in developing rigorous and relevant research. One illustrative example of a service design research effort using the DSR approach is presented.

Findings
Building on DSR’s robust methodological background, this paper discusses how DSR can support service design research, namely, through the development of new methods and models, and how DSR can be adapted to leverage service design research participatory, iterative, human-centric and creative approach.

Originality/value
This paper provides an overview of DSR and proposes it as a methodology to conduct service design research, offering step-by-step guidance on the application of DSR in service design research and discussing how it can be adapted according to the specific characteristics of service design research and drive future research.
Predictability of HK-REITs returns using artificial neural network
Authors: Loo Wei Kang 
Published: November 2019

Purpose
The purpose of this paper is to determine if artificial neural network (ANN) works better than linear regression in predicting Hong Kong real estate investment trusts’ (REITs) excess return.

Design/methodology/approach
Both ANN and the regression were applied in this study to forecast the Hong Kong REITs’ (HK-REITs) return using the capital asset pricing model and Fama and French’s three-factor models. Each result was further split into annual time series as a measure to investigate the consistency of the performance across time.

Findings
ANN had produced a better forecasting results than the regression based on their trading performance. However, the forecasting performance varied across individual REITs and time periods.

Practical implications
ANN should be considered for use when one were to attempt forecasting the HK-REITs excess returns. However, the trading performance should be always compared with buy and hold strategy prior to make any investment decisions.

Originality/value
This paper tested the predicting power of ANN on the HK-REITs and the consistency of its predicting power.
Organizational commitment: exploring the role of identity
Authors: Afshari Leila , Young Suzanne , Gibson Paul , Karimi Leila 
Published: November 2019

Purpose
The purpose of this paper is to enhance the understanding of how identification process is associated with development of organizational commitment.

Design/methodology/approach
A mixed-method approach incorporating surveys and interviews was employed. Data were obtained from a manufacturing organization in Australia. A clustering method was employed to identify commitment profiles. Respondents belonging to the clusters representing commitment profiles associated with desirable organizational outcomes were identified for the qualitative stage of the research.

Findings
The results showed that both organizational identity and professional/occupational identity are positively linked to the development of organizational commitment. An in-depth analysis of the qualitative data demonstrated that engagement of personal/individual level of self in identification process enhances the development of organizational commitment.

Practical implications
The findings suggest that human resource managers can build an effective identification process by strengthening feelings of organizational identity and creating a positive organizational image.

Originality/value
To the best of the author’s knowledge, this study is the first to employ a mixed-method approach to explore the relationship between organizational commitment and identification process. A mixed-method approach, on the one hand, enabled us to build on the existing objectivist commitment literature and explore commitment profiles, and on the other hand, it allowed us to provide a more complete and contextual portrayal of organizational commitment and identification process through qualitative interpretive strategies.