bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological machine learning combined with bacterial population genomics reveals common and rare allelic variants of genes to cause disease
Authors: Bandoy DJ Darwin R. , Weimer Bart C. 
Published: August 2019

AbstractHighly dimensional data generated from bacterial whole genome sequencing is providing unprecedented scale of information that requires appropriate statistical frameworks of analysis to infer biological function from bacterial genomic populations. Application of genome wide association study (GWAS) methods is an emerging approach with bacterial population genomics that yields a list of genes associated with a phenotype with an undefined importance among the candidates in the list. Here, we validate the combination of GWAS, machine learning, and pathogenic bacterial population genomics as a novel scheme to identify SNPs and rank allelic variants to determine associations for accurate estimation of disease phenotype. This approach parsed a dataset of 1.2 million SNPs that resulted in a ranked importance of associated alleles of Campylobacter jejuni porA using multiple spatial locations over a 30-year period. We validated this approach using previously proven laboratory experimental alleles from an in vivo guinea pig abortion model. This approach, termed BioML, defined intestinal and extraintestinal groups that have differential allelic variants that cause abortion. Divergent variants containing indels that defeated gene callers were rescued using biological context and knowledge that resulted in defining rare and divergent variants that were maintained in the population over two continents and 30 years. This study defines the capability of machine learning coupled to GWAS and population genomics to simultaneously identify and rank alleles to define their role in abortion, and more broadly infectious disease.
Development of the Mouse and Human Cochlea at Single Cell Resolution
Authors: Yu Kevin Shengyang , Frumm Stacey M. , Park Jason S. , Lee Katharine , Wong Daniel M. , Byrnes Lauren , Knox Sarah M. , Sneddon Julie B. , Tward Aaron D. 
Published: August 2019

SummaryHearing loss is a common and disabling condition, yet our understanding of the physiologic workings of the inner ear has been limited by longstanding difficulty characterizing the function and characteristics of the many diverse, fragile, and rare cell types in the cochlea. Using single-cell RNA-sequencing and a novel clustering algorithm, CellFindR, we created a developmental map of the mouse and human cochlea, identifying multiple previously undescribed cell types, progenitor populations, and predicted lineage relationships. We additionally associated the expression of known hearing loss genes to the cell types and developmental timepoints in which they are expressed. This work will serve as a resource for understanding the molecular basis of hearing and designing therapeutic approaches for hearing restoration.
Assessment of a western blot signal for the Bcnt/Cfdp1, a tentative component of Srcap chromatin remodeling complex; trial to overcome off-target problems
Authors: Iwashita Shintaro , Suzuki Takehiro , Kiriyama Yoshimitsu , Dohmae Naoshi , Ohka Yoshiharu , Song Si-Young , Nakashima Kentaro 
Published: August 2019

AbstractThe BCNT (Bucentaur) protein family is characterized by a conserved amino acid sequence at the C-terminus (BCNT-C domain) and plays an essential role in gene expression and chromosomal maintenance in fungi, fly, and chicken. The mammalian Bucentaur/Craniofacial developmental protein 1 (Bcnt/Cfdp1) is also a tentative component of the Srcap (SNF2-Related CBP Activator Protein) chromatin remodeling complex, but little is known about its properties, partly because there are few suitable antibodies to detect the endogenous protein. We used multiple anti-Bcnt/Cfdp1 antibodies against unrelated immunogens derived from BCNT-C domain and mouse-specific N-terminal peptide. To assign western blot signals and evaluate these antibodies, we utilized a stem cell line from mutant embryos of mouse Bcnt/Cfdp1, whose mRNA expression levels were reduced to 75% of the parental cells. In western blotting of these mutant and parental cell extracts with the anti-Bcnt/Cfdp1 antibodies, mouse Bcnt/Cfdp1 was detected as a doublet of approximately 45 kDa. LC-MS/MS analysis of the corresponding doublet for the Flag-tagged mouse Bcnt/Cfdp1 constitutively expressed in T-REx 293 cell (a HEK293 derivative) exhibited that the upper band was much more phosphorylated than the lower band and that there was preferential Ser phosphorylation in the WESF motif in the BCNT-C domain. Western blot with these validated antibodies indicated a preferential expression of Bcnt/Cfdp1 in the early stages of brain development in mouse and rat, which is consistent with the expression of Bcnt/Cfdp1 mRNA. This article describes the evaluation of anti-Bcnt/Cfdp1 antibodies, including a scheme to prepare a potential negative control for western blot, and discusses immune-cross reactions with off-target proteins, particularly immunoreaction probabilities.
A universal reporter cell line for bioactivity evaluation of engineered cytokine products
Authors: Mock Jacqueline , Pellegrino Christian , Neri Dario 
Published: August 2019

ABSTRACTEngineered cytokine products represent a growing class of therapeutic proteins which need to be tested for biological activity at various stages of pharmaceutical development. In most cases, dedicated biological assays are established for different products, in a process that can be time-consuming and cumbersome. Here we describe the development and implementation of a universal cell-based reporter system for various classes of immunomodulatory proteins. The novel system capitalizes on the fact that the signaling of various types of pro-inflammatory agents (e.g., cytokines, chemokines, Toll-like receptor agonists) may involve transcriptional activation by NF-κB. Using viral transduction, we generated stably-transformed cell lines of B or T lymphocyte origin and compared the new reporter cell lines with conventional bioassays. The experimental findings with various interleukins and with members of the TNF superfamily revealed that the newly-developed “universal” bioassay method yielded bioactivity data which were comparable to the ones obtained with dedicated conventional methods. The engineered cell lines with reporters for NF-κB were tested with several antibody-cytokine fusions and may be generally useful for the characterization of novel immunomodulatory products. The newly developed methodology also revealed a mechanism for cytokine potentiation, based on the antibody-mediated clustering of TNF superfamily members on tumor-associated extracellular matrix components.
Social network analysis and the implications for Pontocaspian biodiversity conservation in Romania and Ukraine: A comparative study
Authors: Gogaladze Aleksandre , Raes Niels , Biesmeijer Koos , Ionescu Camelia , Pavel Bianca , Son Mikhail O. , Gozak Natalia , Anistratenko Vitaliy , Wesselingh Frank P. 
Published: August 2019

AbstractRomania and Ukraine share the Black Sea coastline, the Danube Delta and associated habitats, which harbor the unique Pontocaspian biodiversity. Pontocaspian biota represents endemic aquatic taxa adapted to the brackish (anomalohaline) conditions, which evolved in the Caspian and Black Sea basins. Currently, this biota is diminishing both in the numbers of species and their abundance because of human activities. Consequently, its future persistence strongly depends on the adequacy of conservation measures. Romania and Ukraine have a common responsibility to effectively address the conservation of this biota. The socio-political and legal conservation frameworks, however, differ in the two countries - Romania is a member of the European Union (EU), thus complying with the EU environmental policy, whereas Ukraine is an EU-associated country. This may result in differences in the social network structure of stakeholder institutions with different implications for Pontocaspian biodiversity conservation. Here, we study the structure and implications of the social network of stakeholder organizations involved in conservation of Pontocaspian biodiversity in Romania, and compare it to Ukraine. We apply a mix of qualitative and quantitative social network analysis methods to combine the content and context of the interactions with relational measures. We show that the social networks of stakeholder organizations in Romania and Ukraine are very different. Structurally, in Romanian network there is a room for improvement through e.g. more involvement of governmental and non-governmental organizations and increased motivation of central stakeholders to initiate conservation action, whereas Ukrainian network is close to optimal. Regardless, both networks translate into sub-optimal conservation action and the road to optimal conservation is different. We end with sketching implications and recommendations for improved national and cross-border conservation efforts.
A Bayesian framework for the detection of diffusive heterogeneity
Authors: Cass Julie A. , Williams C. David , Theriot Julie 
Published: August 2019

AbstractCells are crowded and spatially heterogeneous, complicating the transport of organelles, proteins and other substrates. One aspect of this complex physical environment, the mobility of passively transported substrates, can be quantitatively characterized by the diffusion coefficient: a descriptor of how rapidly substrates will diffuse in the cell, dependent on their size and effective local viscosity. The spatial dependence of diffusivity is challenging to quantitatively characterize, because temporally and spatially finite observations offer limited information about a spatially varying stochastic process. We present a Bayesian framework that estimates diffusion coefficients from single particle trajectories, and predicts our ability to distinguish differences in diffusion coefficient estimates, conditional on how much they differ and the amount of data collected. This framework is packaged into a public software repository, including a tutorial Jupyter notebook demonstrating implementation of our method for diffusivity estimation, analysis of sources of uncertainty estimation, and visualization of all results. This estimation and uncertainty analysis allows our framework to be used as a guide in experimental design of diffusivity assays.
Short-term effects of GPS collars on the activity, behavior, and adrenal response of scimitar-horned oryx (Oryx dammah)
Authors: Stabach Jared A. , Cunningham Stephanie A. , Connette Grant , Mota Joel L. , Reed Dolores , Byron Michael , Songer Melissa , Wacher Tim , Mertes Katherine , Brown Janine L. , Comizzoli Pierre , Newby John , Monfort Steven , Leimgruber Peter 
Published: August 2019

AbstractGPS collars have revolutionized the field of animal ecology, providing detailed information on animal movement and the habitats necessary for species survival. GPS collars also have the potential to cause adverse effects ranging from mild irritation to severe tissue damage, reduced fitness, and death. The impact of GPS collars on the behavior, stress, or activity, however, have rarely been tested on study species prior to release. The objective of our study was to provide a comprehensive assessment of the short-term effects of GPS collars fitted on scimitar-horned oryx (Oryx dammah), an extinct-in-the-wild antelope once widely distributed across Sahelian grasslands in North Africa. We conducted behavioral observations, assessed fecal glucocorticoid metabolites (FGM), and evaluated high-resolution data from tri-axial accelerometers. Using a series of non-standard regression models, we illustrate clear but short-term effects to animals fitted with GPS collars. Behavioral observations highlighted a significant increase in the amount of headshaking from pre-treatment levels, returning below baseline levels during the post-treatment period (>3 days post-collaring). Similarly, FGM concentrations (i.e., stress hormones) increased after GPS collars were fitted on animals but returned to pre-collaring levels within 5 days of collaring. Lastly, tri-axial accelerometers, collecting data at eight positions per second, indicated a > 480 percent increase in the amount of hourly headshaking immediately after collaring. This post-collaring increase in headshaking was estimated to decline in magnitude within 4 hours after GPS collar fitting. These effects constitute a handling and/or habituation response (model dependent), with animals showing short-term responses in activity, behavior, and stress that dissipated within several hours to several days of being fitted with GPS collars. Importantly, none of our analyses indicated any long-term effects that would have more pressing animal welfare concerns.
Integrated single-cell transcriptomics and chromatin accessibility analysis reveals novel regulators of mammary epithelial cell identity
Authors: Pervolarakis Nicholas , Nguyen Quy H. , Gutierrez Guadalupe , Sun Peng , Jhutty Darisha , Zheng Grace XY , Nemec Corey M , Dai Xing , Watanabe Kazuhide , Kessenbrock Kai 
Published: August 2019

ABSTRACTThe mammary epithelial cell (MEC) system is a bi-layered ductal epithelial network consisting of luminal and basal cells, which is maintained by a lineage of stem and progenitor cell populations. Here, we used integrated single-cell transcriptomics and chromatin accessibility analysis to reconstruct the cell types of the mouse MEC system and their underlying gene regulatory features in an unbiased manner. We define previously unrealized differentiation states within the secretory type of luminal cells, which can be divided into distinct clusters of progenitor and mature secretory cells. By integrating single-cell transcriptomics and chromatin accessibility landscapes, we identified novel cis- and trans-regulatory elements that are differentially activated in the specific epithelial cell types and our newly defined luminal differentiation states. Our work provides an unprecedented resource to reveal novel cis/trans regulatory elements associated with MEC identity and differentiation that will serve as a valuable reference to determine how the chromatin accessibility landscape changes during breast cancer.
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions
Authors: Sidore Angus M. , Plesa Calin , Samson Joyce A. , Kosuri Sriram 
Published: August 2019

AbstractMultiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here we improve DropSynth, a low-cost, multiplexed method which builds gene libraries by compartmentalizing and assembling microarray-derived oligos in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction, and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.
Feature intersection for agent-based customer churn prediction
Authors: N. Sandhya , Samuel Philip , Chacko Mariamma 
Published: August 2019

Purpose
Telecommunication has a decisive role in the development of technology in the current era. The number of mobile users with multiple SIM cards is increasing every second. Hence, telecommunication is a significant area in which big data technologies are needed. Competition among the telecommunication companies is high due to customer churn. Customer retention in telecom companies is one of the major problems. The paper aims to discuss this issue.

Design/methodology/approach
The authors recommend an Intersection-Randomized Algorithm (IRA) using MapReduce functions to avoid data duplication in the mobile user call data of telecommunication service providers. The authors use the agent-based model (ABM) to predict the complex mobile user behaviour to prevent customer churn with a particular telecommunication service provider.

Findings
The agent-based model increases the prediction accuracy due to the dynamic nature of agents. ABM suggests rules based on mobile user variable features using multiple agents.

Research limitations/implications
The authors have not considered the microscopic behaviour of the customer churn based on complex user behaviour.

Practical implications
This paper shows the effectiveness of the IRA along with the agent-based model to predict the mobile user churn behaviour. The advantage of this proposed model is as follows: the user churn prediction system is straightforward, cost-effective, flexible and distributed with good business profit.

Originality/value
This paper shows the customer churn prediction of complex human behaviour in an effective and flexible manner in a distributed environment using Intersection-Randomized MapReduce Algorithm using agent-based model.
Identification of operational demand in law enforcement agencies
Authors: Basilio Marcio Pereira , Pereira Valdecy , Brum Gabrielle 
Published: August 2019

Purpose
The purpose of this paper is to develop a methodology for knowledge discovery in emergency response service databases based on police occurrence reports, generating information to help law enforcement agencies plan actions to investigate and combat criminal activities.

Design/methodology/approach
The developed model employs a methodology for knowledge discovery involving text mining techniques and uses latent Dirichlet allocation (LDA) with collapsed Gibbs sampling to obtain topics related to crime.

Findings
The method used in this study enabled identification of the most common crimes that occurred in the period from 1 January to 31 December of 2016. An analysis of the identified topics reaffirmed that crimes do not occur in a linear manner in a given locality. In this study, 40 per cent of the crimes identified in integrated public safety area 5, or AISP 5 (the historic centre of the city of RJ), had no correlation with AISP 19 (Copacabana – RJ), and 33 per cent of the crimes in AISP 19 were not identified in AISP 5.

Research limitations/implications
The collected data represent the social dynamics of neighbourhoods in the central and southern zones of the city of Rio de Janeiro during the specific period from January 2013 to December 2016. This limitation implies that the results cannot be generalised to areas with different characteristics.

Practical implications
The developed methodology contributes in a complementary manner to the identification of criminal practices and their characteristics based on police occurrence reports stored in emergency response databases. The generated knowledge enables law enforcement experts to assess, reformulate and construct differentiated strategies for combating crimes in a given locality.

Social implications
The production of knowledge from the emergency service database contributes to the government integrating information with other databases, thus enabling the improvement of strategies to combat local crime. The proposed model contributes to research on big data, on the innovation aspect and on decision support, for it breaks with a paradigm of analysis of criminal information.

Originality/value
The originality of the study lies in the integration of text mining techniques and LDA to detect crimes in a given locality on the basis of the criminal occurrence reports stored in emergency response service databases.
A systematic literature review on Wikidata
Authors: Mora-Cantallops Marçal , Sánchez-Alonso Salvador , García-Barriocanal Elena 
Published: August 2019

PurposeThe purpose of this paper is to review the current status of research on Wikidata and, in particular, of articles that either describe applications of Wikidata or provide empirical evidence, in order to uncover the topics of interest, the fields that are benefiting from its applications and which researchers and institutions are leading the work.Design/methodology/approachA systematic literature review is conducted to identify and review how Wikidata is being dealt with in academic research articles and the applications that are proposed. A rigorous and systematic process is implemented, aiming not only to summarize existing studies and research on the topic, but also to include an element of analytical criticism and a perspective on gaps and future research.FindingsDespite Wikidata’s potential and the notable rise in research activity, the field is still in the early stages of study. Most research is published in conferences, highlighting such immaturity, and provides little empirical evidence of real use cases. Only a few disciplines currently benefit from Wikidata’s applications and do so with a significant gap between research and practice. Studies are dominated by European researchers, mirroring Wikidata’s content distribution and limiting its Worldwide applications.Originality/valueThe results collect and summarize existing Wikidata research articles published in the major international journals and conferences, delivering a meticulous summary of all the available empirical research on the topic which is representative of the state of the art at this time, complemented by a discussion of identified gaps and future work.
Social enterprise marketing: review of literature and future research agenda
Authors: Bandyopadhyay Chinmoy , Ray Subhasis 
Published: August 2019

PurposeThe purpose of this paper is to review existing literature on marketing in social enterprises (SEs). It identifies major trends and issues and highlights gaps in the existing knowledge base on social enterprise marketing (SEM).Design/methodology/approachRelevant articles on SEM were searched, following the PRISMA framework, in online databases using keywords and phrases like “marketing in social enterprises,” “marketing strategy/practice in social enterprises,” “social enterprise marketing” and “business practices in social enterprises.” After screening and checking for eligibility, 47 significant articles published in 21 peer-reviewed journals during 1995–2018 were selected for review.FindingsThe findings suggest that marketing in SEs has different issues and challenges when compared to marketing practices adopted by conventional business organizations. They are forced to address the varied expectations of the stakeholders in a resource-constrained situation, which creates problems for them. The review also highlights the fact that resource constraints, legacy mindset, and lack of marketing skills limit the impact of marketing practices in SEs. To address these issues, many social entrepreneurs survive through cost-effective marketing techniques.Originality/valueTo the authors’ knowledge, this is the first effort to identify and analyze extant literature in SEM. The resultant themes and research gaps highlight the current status of SEM literature. The paper can help SEs to understand and plan their marketing activities for better impact and profitability. Future research can draw on the findings of this review.