bluuebunny/crossref_metadata_2025_split huggingface dataset:
Horizontal transfer and gene loss shaped the evolution of alpha-amylases in bilaterians
Authors: Desiderato Andrea , Barbeitos Marcos , Gilbert Clément , Da Lage Jean-Luc 
Published: June 2019

AbstractThe subfamily GH13_1 of alpha-amylases is typical of Fungi, but it is also found in some unicellular eukaryotes (e.g. Amoebozoa, choanoflagellates) and non-bilaterian Metazoa. Since a previous study in 2007, GH13_1 amylases were considered ancestral to the Unikonts, including animals, except Bilateria, such that it was thought to have been lost in the ancestor of this clade. The only alpha-amylases known to be present in Bilateria so far belong to the GH13_15 and 24 subfamilies (commonly called bilaterian alpha-amylases) and were likely acquired by horizontal transfer from a proteobacterium. The taxonomic scope of Eukaryota genomes in databases has been greatly increased ever since 2007. We have surveyed GH13_1 sequences in recent data from ca. 1600 bilaterian species, 60 non-bilaterian animals and also in unicellular eukaryotes. As expected, we found a number of those sequences in non-bilaterians: Anthozoa (Cnidaria) and in sponges, confirming the previous observations, but none in jellyfishes and in Ctenophora. Our main and unexpected finding is that such fungal (also called Dictyo-type) amylases were also consistently retrieved in several bilaterian phyla: hemichordates (deuterostomes), brachiopods and related phyla, some molluscs and some annelids (protostomes). We discuss evolutionary hypotheses possibly explaining the scattered distribution of GH13_1 across bilaterians, namely, the retention of the ancestral gene in those phyla only and/or horizontal transfers from non-bilaterian donors.
SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection
Authors: Yang Yuchen , Li Gang , Qian Huijun , Wilhelmsen Kirk C. , Shen Yin , Li Yun 
Published: June 2019

AbstractBatch effect correction has been recognized to be indispensable when integrating single-cell RNA sequencing (scRNA-seq) data from multiple batches. State-of-the-art methods ignore single-cell cluster label information, but such information can improve effectiveness of batch effect correction, particularly under realistic scenarios where biological differences are not orthogonal to batch effects. To address this issue, we propose SMNN for batch effect correction of scRNA-seq data via supervised mutual nearest neighbor detection. Our extensive evaluations in simulated and real datasets show that SMNN provides improved merging within the corresponding cell types across batches, leading to reduced differentiation across batches over MNN, Seurat v3, and LIGER. Furthermore, SMNN retains more cell type-specific features, partially manifested by differentially expressed genes identified between cell types after SMNN correction being biologically more relevant, with precision improving by up to 841%.Key PointsBatch effect correction has been recognized to be critical when integrating scRNA-seq data from multiple batches due to systematic differences in time points, generating laboratory and/or handling technician(s), experimental protocol, and/or sequencing platform.Existing batch effect correction methods that leverages information from mutual nearest neighbors across batches (for example, implemented in SC3 or Seurat) ignore cell type information and suffer from potentially mismatching single cells from different cell types across batches, which would lead to undesired correction results, especially under the scenario where variation from batch effects is non-negligible compared with biological effects.To address this critical issue, here we present SMNN, a supervised machine learning method that first takes cluster/cell-type label information from users or inferred from scRNA-seq clustering, and then searches mutual nearest neighbors within each cell type instead of global searching.Our SMNN method shows clear advantages over three state-of-the-art batch effect correction methods and can better mix cells of the same cell type across batches and more effectively recover cell-type specific features, in both simulations and real datasets.
The Kaufman oculocerebrofacial syndrome protein Ube3b regulates synapse number by ubiquitinating Ppp3cc
Authors: Ambrozkiewicz Mateusz C. , Ripamonti Silvia , Borisova Ekaterina , Schwark Manuela , Schaub Theres , Altas Bekir , Yilmaz Rüstem , Piepkorn Lars , Horan Stephen , Jahn Olaf , Dere Ekrem , Rosário Marta , Borck Guntram , Ehrenreich Hannelore , Willig Katrin , Rhee JeongSeop , Tarabykin Victor , Kawabe Hiroshi 
Published: June 2019

ABSTRACTKaufman oculocerebrofacial syndrome (KOS) is a severe autosomal recessive disorder characterized by intellectual disability, developmental delays, microcephaly and characteristic dysmorphisms. Biallelic mutations ofUBE3B, encoding for a ubiquitin ligase E3B are causative for KOS. In this report, we characterize neuronal functions of its murine orthologUbe3b. We show that Ube3b regulates dendritic branching in a cell-autonomous manner. Moreover,Ube3bknockout (KO) neurons exhibit increased density and aberrant morphology of dendritic spines, altered synaptic physiology and changes in hippocampal circuit activity. Dorsal forebrain-specificUbe3bKO animals show impaired spatial learning and alterations in social interactions. We further demonstrate that Ube3b ubiquitinates the catalytic γ-subunit of calcineurin (Ppp3cc), the overexpression of which phenocopies the loss ofUbe3bwith regard to dendritic spine density. This work provides insights into the molecular pathologies underlying intellectual disability-like phenotypes in a genetic mouse model for KOS.
Bisphenol A promotes stress granule assembly and modulates the integrated stress response
Authors: Fay Marta M. , Columbo Daniella , Cotter Cecelia , Friend Chandler , Henry Shawna , Hoppe Megan , Karabelas Paulina , Lamy Corbyn , Lawell Miranda , Monteith Sarah , Noyes Christina , Salerno Paige , Wu Jingyi , Zhang Hedan Mindy , Anderson Paul J. , Kedersha Nancy , Ivanov Pavel , Farny Natalie G. 
Published: June 2019

AbstractBisphenol-A (BPA) is a ubiquitous precursor of polycarbonate plastics that is found in the blood and serum of >92% of Americans. While BPA has been well documented to act as a weak estrogen receptor (ER) agonist, its effects on cellular stress are unclear. Here, we demonstrate that high-dose BPA causes stress granules (SGs) in human cells. A common estrogen derivative, β-estradiol, does not trigger SGs, indicating the mechanism of SG induction is not via the ER pathway. We also tested other structurally related environmental contaminants including the common BPA substitutes BPS and BPF, the industrial chemical 4-nonylphenol (4-NP) and structurally related compounds 4-EP and 4-VP, and the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D). The variable results from these related compounds suggest that structural homology is not a reliable predictor of the capacity of a compound to cause SGs. Also, we demonstrate that BPA acts primarily through the PERK pathway to generate canonical SGs. Finally, we show that chronic exposure to a low physiologically relevant dose of BPA disrupts SG assembly by inhibiting SGs upon additional acute stress. Our work identifies additional effects of BPA beyond endocrine disruption that may have consequences for human health.
Length-weight relationships for 17 fish species in the Luanhe River Estuary, Bohai Sea, northern China
Authors: Min Xu , Xiao-Jing Song , Yun-Ling Zhang 
Published: June 2019

AbstractLength-weight regressions (LWR, W = a × Lb) of 17 coastal fish species from the Luanhe River Estuary in northern China are presented in this study. A total of 7354 samples from 11 families were measured and weighed. The slope (b) values for LWR ranged from 2.572 in Acanthogobius ommaturus to 3.6581 in Engraulis japonicus. The median value was 3.114 in Platycephalus indicus, although 50% of the values ranged between 2.9451 to 3.2965 for the entire data set.
Identification and characterization of novel filament-forming proteins in cyanobacteria
Authors: Springstein Benjamin L. , Woehle Christian , Weissenbach Julia , Helbig Andreas O. , Dagan Tal , Stucken Karina 
Published: June 2019

AbstractFilament-forming proteins in bacteria function in stabilization and localization of proteinaceous complexes and replicons; hence they are instrumental for myriad cellular processes such as cell division and growth. Here we present two novel filament-forming proteins in cyanobacteria. Surveying cyanobacterial genomes for coiled-coil-rich proteins (CCRPs) that are predicted as putative filament-forming proteins, we observed a higher proportion of CCRPs in filamentous cyanobacteria in comparison to unicellular cyanobacteria. Using our predictions, we identified nine protein families with putative intermediate filament (IF) properties. Polymerization assays revealed four proteins that formed polymersin vitroand three proteins that formed polymersin vivo. Fm7001 fromFischerella muscicolaPCC 7414 polymerizedin vitroand formed filamentsin vivoin several organisms. Additionally, we identified a tetratricopeptide repeat protein - All4981 - inAnabaenasp. PCC 7120 that polymerized into filamentsin vitroandin vivo. All4981 interacts with known cytoskeletal proteins and is indispensable forAnabaenaviability. Although it did not form filamentsin vitro, Syc2039 fromSynechococcus elongatusPCC 7942 assembled into filamentsin vivoand a Δsyc2039mutant was characterized by an impaired cytokinesis. Our results expand the repertoire of known prokaryotic filament-forming CCRPs and demonstrate that cyanobacterial CCRPs are involved in cell morphology, motility, cytokinesis and colony integrity.
Internet of things architectures: do organizational strategies matters?
Authors: Vishwakarma Niraj Kumar , Singh Rohit Kumar , Sharma R.R.K. 
Published: June 2019

PurposeThe technology used by an organization is significantly influenced by the organization’s preferred competitive capabilities. The Internet of things (IoT) is an important technology, which is implemented by most prominent business organizations. The purpose of this paper is to investigate the relationship between an organization’s strategies and the IoT architectures implemented by the organization.Design/methodology/approachThis study has been carried out on primary data collected with the help of a structured questionnaire. The data have been analyzed by statistical techniques like cluster analysis and discriminant analysis through SPSS.FindingsThe empirical investigation of data revealed that there is a relationship between organizational strategy and IoT architectures. The three-layered architecture of the IoT is most suitable for caretakers; the three-, four- or five- layered architectures are suitable for marketeers; whereas innovators find it more suitable to use five- or more-layered architecture of the IoT. This paper draws the conclusion based on maximum likelihood rather than using statistical analyses like ANOVA. The idea behind using the maximum likelihood estimate is that there are many subjective parameters in deciding the architectures of the IoT. These subjective parameters are difficult to quantify, so it is not possible to apply ANOVA on these parameters.Research limitations/implicationsThis study considers three organizational strategies; the relationship between other organizational strategies and IoT architecture will be studied in future.Practical implicationsThis study offers multiple opportunities to practitioners and consulting firms of the IoT to adopt a suitable IoT architecture according to the organizational strategy. This study equips IoT development engineers to select suitable technology for data capturing, data transmission, and data management and access for an IoT architecture.Originality/valueAlthough a lot of work has already been done on the architecture of IoT for different industries and businesses, to the best of our knowledge, this is the first study that relates organizational strategies to IoT architectures. This study applies to all the major industry types.
Time to take corporate innovation initiatives
Authors: Yang Ruiju , Zhu Wei , Marinova Dora , Wei Jiuchang 
Published: June 2019

PurposeA bad safety accident at a manufacturing company usually results in casualties and economic losses. The company affected by such an accident must deal with pressure from multiple stakeholder groups. Employees, in particular, play a key role in pushing the affected company to develop strategies to improve occupational safety and health. The purpose of this paper is to seek answers to two questions: does a safety accident affect employee behavior in terms of giving up prospects to develop a career at the affected company? If yes, could innovation initiatives adopted by the company help moderate the negative consequences from a safety accident?Design/methodology/approachBy investigating 120 safety accidents reported by publicly listed Chinese manufacturing companies between 2009 and 2016, the authors conduct an empirical study using regression-based statistical hypotheses testing to describe the companies’ responses and prospects for their employees.FindingsThe results show that the magnitude of the accident and the accident being caused by an employee error positively affect the turnover of employees. Furthermore, technical innovation initiatives, such as spending on R&D, by the accident-affected companies increase the positive effect of the accident magnitude on employee turnover. On the contrary, management innovation initiatives, such as corporate social responsibility activities, weaken the impact of the accident magnitude and employee error on employee turnover.Originality/valueThis study contributes to knowledge development by adding a crisis perspective in human resource management research. It helps to better understand the impact of safety accidents on employee behavior and the response taken by companies through innovation initiatives.
The importance and the adaptation of internal resources as a competitive advantage for the internationalization of food companies
Authors: Pigatto Gessuir , Santini Pigatto Giuliana Aparecida , Satolo Eduardo Guilherme , Negreti Amanda dos Santos 
Published: June 2019

Purpose
The purpose of this paper is to analyze how Brazilian food companies in the State of São Paulo determine the importance of and the need to adapt their internal resources as a competitive advantage for internationalization.

Design/methodology/approach
From a resource-based view (RBV), 35 different factors grouped into four categories were identified and presented to 24 companies. The data were analyzed through a gray relational analysis to establish all factors’ order of importance.

Findings
Factors linked to human and organizational resources present greater adaptability and allow companies competitive and sustainable advantages but have not yet been explored thoroughly. Identifying and adapting internal resources do not guarantee achieving competitive and sustainable advantages, as the access to international market is also a consequence of commercial agreements developed by countries and economic blocks.

Practical implications
The analysis highlights the fragility of competitiveness among the companies analyzed in exporting products with commodity characteristics, with none or little differentiation. Such products are traded mainly through trading companies, which allow the access of the same market to internal competitors and other countries. Thus, any lapse promoted by the company may be enough for it to lose its competitiveness and, hence, market space.

Originality/value
This paper stands out in the field of strategic management, specifically in the research on RBV, exportation and competitiveness, by making use of the theory of gray correlation system in an innovative and original way.
Calculation of flow in incompressible regenerative turbo-machines with bucket form blades based on the geometry of flow path
Authors: Nejadali Jafar 
Published: June 2019

Purpose
Regenerative flow pumps are dynamic machines with the ability to develop high heads at low flow rates. Simplicity, compactness, stable features and low manufacturing costs make them interesting for many applications in industries. The purpose of this study is to present a new method for calculating the flow through regenerative pumps with bucket form blades to predict the performance curves by a cheap and easy-to-use way.

Design/methodology/approach
The analysis was carried out based on the geometric shape of a fluid particle trajectory in a regenerative turbomachine. The fluid particle path was assumed to be a helix wrapped into a torus. Loss models were considered and the results of predictions were compared with computational fluid dynamics (CFD) data.

Findings
The overall trend of performance curves resulted from presented model looked consistent with CFD data. However, there were slight differences in high and low flow coefficients. The results showed that the predicted geometric shape of the flow path with the presented model (a helix wrapped into a torus) was not consistent with CFD results at high flow coefficients. Due to the complexity and turbulence of the fluid flow and errors in the calculation of losses, as well as slip factor, there was a discrepancy between the results of the presented model and numerical simulation, especially in high and low flow coefficients.

Originality/value
The analysis was carried out based on the geometric shape of a fluid particle trajectory in a regenerative turbomachine with bucket form blades. The fluid particle path was assumed to be a helix wrapped into a torus.
Identity deception detection: requirements and a model
Authors: van der Walt Estee , Eloff Jan 
Published: June 2019

Purpose
This paper aims to describe requirements for a model that can assist in identity deception detection (IDD) on social media platforms (SMPs). The model that was discovered demonstrates the usefulness of the requirements. The aim of the model is to identify humans lying about their identity on SMPs.

Design/methodology/approach
The requirements of a model for IDD will be determined through a literature study combined with a study that identifies currently available identity related metadata on SMPs. This metadata refers to the attributes that describe a user account on an SMP. The aim is to restrict IDD to be only based on these types of attributes, as opposed to or combined with the contents of a single or multiple communications.

Findings
Data science experiments were conducted and in particular supervised machine learning models were discovered that indeed detects identity deception on SMPs with an area under the receiver operator characteristics curve (ROC-AUC) of 75.5 per cent.

Originality/value
SMPs allow any user to easily communicate with their friends or the general public at large. People can now be targeted at great scale, most often for malicious purposes. The reality is that many of these cyber-attacks involve some form of identity deception, where the attackers lie about who they are. Much focus to date has been on the identification of non-human deceptive accounts. This paper focuses on deceptive human accounts that target vulnerable individuals on SMPs.
Fabrication of 3D printed garments using flat patterns and motifs
Authors: Kang Minjoo , Kim Sungmin 
Published: June 2019

Purpose
The purpose of this paper is to encourage the generation of 3D printed garments by developing a new software to open new potential of whole garment production in the fashion field.

Design/methodology/approach
The authors developed a 3D printed garment design software using flat patterns and design motifs, to allow fast and easy generation of a 3D printed garment. Users can generate motif-based design easily using various user interfaces.

Findings
A 3D printed garment could be printed not only by expensive SLS type printers but also by affordable FDM type printers with a simple assembly process using the software developed in this study.

Originality/value
Newly developed 3D printed garment design software enables the users to generate 3D printed garments easily using flat patterns and design motifs, without having to go through a complex and arduous 3D modeling process using commercial CAD systems.
Examining relationships among process quality, outcome quality, delight, satisfaction and behavioural intentions in fitness centres in Malaysia
Authors: Foroughi Behzad , Iranmanesh Mohammad , Gholipour Hassan F. , Hyun Sunghyup Sean 
Published: June 2019

Purpose
The purpose of this paper is to investigate the effects of process and outcome quality on fitness members’ delight and satisfaction. Furthermore, the relationships between delight, satisfaction and behavioural intention are investigated.

Design/methodology/approach
Data were obtained from a survey of 379 members of fitness centres in Malaysia and analysed using the partial least squares technique.

Findings
The results indicated that process quality and outcome quality had a significant effect on customer delight and satisfaction. Furthermore, customer delight influenced customers’ satisfaction and behavioural intentions.

Practical implications
The findings of this study will help fitness centre managers to understand the importance of outcome quality and delight in addition to process quality and satisfaction in shaping the members’ behavioural intentions, thereby allowing them to differentiate their service from their customers.

Originality/value
This study is the first attempt to investigate the importance of outcome quality and customer delight in the fitness industry.
Conceptualizing professional and public interest in the context of Turkey’s health care reforms
Authors: Agartan Tuba I. 
Published: June 2019

PurposeThe purpose of this paper is to investigate physicians’ response to reforms in Turkey on the basis of their experience of the changes in the daily work environment. It aims to bridge the gap between health policy and sociology of professions literatures to explain why some public-sector physicians have opposed the recent reforms.Design/methodology/approachThe research adopts a qualitative methodology including semi-structured interviews and content analysis. The fieldwork involves collecting information through written documents and interviews with 23 physicians working in public tertiary hospitals in one large city.FindingsPhysicians’ response combines a concern with material interests, previously conceptualized in terms of erosion of autonomy, with anxiety over damage to their professional image and social status. The particular reform discourse adopted by policymakers disrupts the existing constructions of harmony in the professional discourse between the public and professional interests, and between social value and material interests.Research limitations/implicationsOne major limitation of this paper is its exploratory nature and analysis based on one case study. Future studies that adopt a cross-country comparative approach could help addressing concerns of limited generalizability.Originality/valueEarlier social science literature on health reforms has explained physicians’ opposition in terms of protecting their professional self-interest and fighting against any regulation that could limit their income or autonomy. The paper adopts a broader definition of interests that goes beyond this materialist conception and includes subjective ideas about interests such as values and beliefs about how they serve the public interest. This definition allows us to unpack the relationship between interest and autonomy.