bluuebunny/crossref_metadata_2025_split huggingface dataset:
Practical Fluorescence Reconstruction Microscopy for Large Samples and Low-Magnification Imaging
Authors: LaChance Julienne , Cohen Daniel J. 
Published: March 2020

AbstractFluorescence reconstruction microscopy (FRM) describes a class of techniques where transmitted light images are passed into a convolutional neural network that then outputs predicted epifluorescence images. This approach enables many benefits including reduced phototoxicity, freeing up of fluorescence channels, simplified sample preparation, and the ability to re-process legacy data for new insights. However, FRM can be complex to implement, and current FRM benchmarks are abstractions that are difficult to relate to how valuable or trustworthy a reconstruction is. Here, we relate the conventional benchmarks and demonstrations to practical and familiar cell biology analyses to demonstrate that FRM should be judged in context. We further demonstrate that it performs remarkably well even with lower-magnification microscopy data, as are often collected in screening and high content imaging. Specifically, we present promising results for nuclei, cell-cell junctions, and fine feature reconstruction; provide data-driven experimental design guidelines; and provide researcher-friendly code, complete sample data, and a researcher manual to enable more widespread adoption of FRM.
Dynamics of microbial competition, commensalism and cooperation and its implications for coculture and microbiome engineering
Authors: Xu Peng 
Published: March 2020

AbstractMicrobial consortium is a complex adaptive system with higher order dynamic characteristics that are not present by individual members. To accurately predict the social interactions, we formulate a set of unstructured kinetic models to quantitatively capture the dynamic interactions of multiple microbial species. By introducing an interaction coefficient, we analytically derived the steady state solutions for the interacting species and the substrate profile in the chemostat. We analyzed the stability of the possible co-existing states defined by competition, parasitism, amensalism, commensalism and cooperation. Our model predicts that only parasitism, commensalism and cooperation could lead to stable co-existing state. We also determined the optimal social interaction criteria of microbial coculture with sequential metabolic reactions compartmentalized into two distinct species. Coupled with Luedeking–Piret and Michaelis-Menten equations, accumulation of metabolic intermediates in one species and formation of end-product in another species could be derived and assessed. We discovered that parasitism consortia disfavor the bioconversion of intermediate to final product; and commensalism consortia could efficiently convert metabolic intermediates to final product and maintain metabolic homeostasis with a broad range of operational conditions (i.e., dilution rates); whereas cooperative consortia leads to highly nonlinear pattern of precursor accumulation and end-product formation. The underlying dynamics and emergent properties of microbial consortia may provide critical knowledge for us to engineer efficient bioconversion process, deliver effective gut therapeutics as well as elucidate probiotic-pathogen interactions in general.
A method for achieving complete microbial genomes and improving bins from metagenomics data
Authors: Lui Lauren M. , Nielsen Torben N. , Arkin Adam P. 
Published: March 2020

AbstractMetagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes (i.e., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Less than 100 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available athttps://github.com/lmlui/Jorg.
Nine Novel Cluster E Mycobacteriophages Isolated from Soil
Authors: Gaballa Joseph M. , Freise Amanda , Parker Jordan Moberg 
Published: March 2020

ABSTRACTNovel mycobacteriophages FireRed, MISSy, MPhalcon, Murica, Sassay, Terminus, Willez, YassJohnny, and Youngblood were isolated from soil samples on the hostMycobacterium smegmatis. Transmission electron microscopy revealed phage structures suggestive of theSiphoviridaefamily of phages. Phage genomes were sequenced and annotated, revealing that they belong to actinobacteriophage Cluster E. Here, we describe the features of these phage genomes and discuss their similarity to previously discovered cluster E phages.
A short review on analytical methods for a fully fourth-order nonlinear integral boundary value problem with fractal derivatives
Authors: He Ji-Huan 
Published: March 2020

Purpose
This paper aims to review some effective methods for fully fourth-order nonlinear integral boundary value problems with fractal derivatives.

Design/methodology/approach
Boundary value problems arise everywhere in engineering, hence two-scale thermodynamics and fractal calculus have been introduced. Some analytical methods are reviewed, mainly including the variational iteration method, the Ritz method, the homotopy perturbation method, the variational principle and the Taylor series method. An example is given to show the simple solution process and the high accuracy of the solution.

Findings
An elemental and heuristic explanation of fractal calculus is given, and the main solution process and merits of each reviewed method are elucidated. The fractal boundary value problem in a fractal space can be approximately converted into a classical one by the two-scale transform.

Originality/value
This paper can be served as a paradigm for various practical applications.
An integrated OEE framework for structured productivity improvement in a semiconductor manufacturing facility
Authors: Cheah Chew Keat , Prakash Joshua , Ong Kok Seng 
Published: March 2020

PurposeThe purpose of this paper is to introduce a practical integrated overall equipment effectiveness (OEE) framework that encompasses the core characteristics of OEE.Design/methodology/approachThe paper reviewed the backgrounds of OEE and improvement frameworks and explored the limitations. An integrated OEE framework was developed by synergizing the strengths of OEE and improvement frameworks to complement the shortcomings. This new framework underlies the OEE concepts and provides structural improvement steps. It was applied to systematically assist and guide OEE practitioners in a case study.FindingsThe review of OEE literature found that there is a lack of improvement frameworks with systematic steps specifically developed for OEE implementation. Conversely, a review on improvement frameworks of different methodologies revealed that they do not fully capitalize on the use of performance measures as benchmarks and improvement drivers. An integrated framework that incorporated the advantages of both OEE and conventional improvement frameworks was developed and validated through a case study over a period of 38 weeks. The OEE performance before the improvements was low (73.4 percent) due to high availability losses (76.5 percent). Both OEE and availability achieved the target of 76.5 percent and 80 percent, respectively, after using the framework for improvements.Research limitations/implicationsThe reviewed papers represent a sample of papers present in the literature and were selected based on relevancy. A greater number of papers incorporated into the literature review would certainly bring out a more comprehensive study.Practical implicationsThe proposed integrated OEE framework provides OEE practitioners with systematic directions and steps combined with benchmarking and loss prioritization features for effective improvement efforts. In addition, it provides overview for the practitioners to make better decisions in project management. This helps address the common issues of practitioners not sure of what the next improvement step is. A case study using the proposed framework at a semiconductor company had successfully achieved the OEE benchmarks and set target for conversion time.Originality/valueThis paper provides a new integrated OEE framework offering a systematic approach toward implementing OEE improvements.
Creditworthiness and access to finance of SMEs in Malaysia: do linkages with large firms matter?
Authors: Wasiuzzaman Shaista , Nurdin Nabila , Abdullah Aznur Hajar , Vinayan Gowrie 
Published: March 2020

PurposeThis study investigates the influence of inter-firm linkages between small and medium enterprises (SMEs) and large firms on the relationship between an SME's creditworthiness and its access to finance.Design/methodology/approachSurvey questionnaire was distributed to 456 SMEs in the manufacturing sector in the Selangor and Federal Territory of Kuala Lumpur regions and a total of 145 useable responses were gathered. Investigation into the possible differences in the effect of creditworthiness – and its dimensions – on access to finance for SMEs with and without linkages are examined using Partial Least Squares-Multi Group Analysis (PLS-MGA).FindingsIt is found that the relationship between creditworthiness and access to finance is significant for both SMEs with and without links to large firms. However, no significant difference is found in the effect of creditworthiness on access to finance for both types of SME. Further analysis on the five different dimensions of creditworthiness shows statistically significant differences between SMEs with links and those without for the dimensions of collateral and condition. This implies that alliances formed between SMEs and large firms do not have much of an influence on the overall creditworthiness but do influence the collateral and condition of the SME.Originality/valueThis study contributes to the understanding of the effects of interfirm linkages on SME creditworthiness and access to finance. To the authors' knowledge no such study has been conducted on links between SMEs and large firms, especially in a developing country such as Malaysia.
Pro-veganism on Instagram
Authors: Phua Joe , Jin S. Venus , Kim Jihoon (Jay) 
Published: March 2020

PurposeThrough two experiments, this study assessed source and message effects of Instagram-based pro-veganism messages.Design/methodology/approachExperiment 1 (N = 294) examined effects of organization (brand vs nonprofit) and message types (egoistic vs altruistic) on consumer responses to Instagram-based pro-veganism content. Experiment 2 (N = 288) examined effects of source type (celebrity vs noncelebrity) and message valence (positive vs negative) on consumer responses to Instagram-based pro-veganism content.FindingsResults demonstrated significant main effects of organization type, with consumers indicating more positive attitudes and higher credibility toward the brand. Significant main effects of message type were also found, with altruistic messages eliciting higher perceived information value than egoistic messages. Subjective norms had moderating effects on attitude toward the organization, while attitude toward veganism had moderating effects on perceived information value. Results also indicated significant main effects of message valence on perceived information value of pro-veganism Instagram posts and significant interaction effects of the two manipulated factors on intention to spread electronic word-of-mouth (eWOM) about pro-veganism.Originality/valueImplications for use of Instagram-based health marketing communication about veganism were discussed. Specifically, organizations looking to use social media to influence attitudes and behavioral intentions toward health issues should seek to reach their target audiences through selecting endorsers and messages that will optimally present the health issue in a relatable and engaging way.
β‐Glucan is a major growth substrate for human gut bacteria related to Coprococcus eutactus
Authors: Alessi Anna M. , Gray Victoria , Farquharson Freda M. , Flores‐López Adriana , Shaw Sophie , Stead David , Wegmann Udo , Shearman Claire , Gasson Mike , Collie‐Duguid Elaina S. R. , Flint Harry J. , Louis Petra 
Published: March 2020

SummaryA clone encoding carboxymethyl cellulase activity was isolated during functional screening of a human gut metagenomic library using Lactococcus lactis MG1363 as heterologous host. The insert carried a glycoside hydrolase family 9 (GH9) catalytic domain with sequence similarity to a gene from Coprococcus eutactus ART55/1. Genome surveys indicated a limited distribution of GH9 domains among dominant human colonic anaerobes. Genomes of C. eutactus‐related strains harboured two GH9‐encoding and four GH5‐encoding genes, but the strains did not appear to degrade cellulose. Instead, they grew well on β‐glucans and one of the strains also grew on galactomannan, galactan, glucomannan and starch. Coprococcus comes and Coprococcus catus strains did not harbour GH9 genes and were not able to grow on β‐glucans. Gene expression and proteomic analysis of C. eutactus ART55/1 grown on cellobiose, β‐glucan and lichenan revealed similar changes in expression in comparison to glucose. On β‐glucan and lichenan only, one of the four GH5 genes was strongly upregulated. Growth on glucomannan led to a transcriptional response of many genes, in particular a strong upregulation of glycoside hydrolases involved in mannan degradation. Thus, β‐glucans are a major growth substrate for species related to C. eutactus, with glucomannan and galactans alternative substrates for some strains.
Multiple Tools Are Needed for the Detection of Prenatal Alcohol Exposure: Findings From a Community Antenatal Setting
Authors: Stevens Suzanne , Anstice Nicola , Cooper Aimee , Goodman Lucy , Rogers Jennifer , Wouldes Trecia A. 
Published: March 2020

BackgroundAlthough the toxic effects of prenatal alcohol exposure (PAE) on children are well established, there is emerging evidence about the dynamics and associated demographics of drinking patterns across pregnancy, with risky drinking more likely to take place in the period before pregnancy awareness. This study investigated the use of complementary measurement tools in the understanding of alcohol use across pregnancy and reports on the rates and patterns of alcohol use in a community antenatal setting.MethodsData on alcohol consumption before and after awareness of pregnancy were collected via multiple measurement tools: anonymous lifestyle questionnaire, TWEAK (Tolerance, Worried, Eye‐opener, Amnesia, K/Cut down) screener questionnaire, and Substance Use Inventory interviews across multiple pregnancy timepoints. Additionally, phosphatidylethanol (PEth), a direct biomarker of alcohol metabolism, collected from newborns’ dried blood spot cards, was analyzed.ResultsThe TWEAK screener was more likely to identify risky drinking behavior than the lifestyle questionnaire. When pregnancy was unplanned, women were more likely to find out they are pregnant significantly later (p < 0.001) and consume alcohol at moderate–heavy levels (p = 0.03), prolonging the risk to the fetus. There was an association between maternal self‐reported alcohol use on the lifestyle questionnaire and Substance Use Inventory interviews, but no association between maternal reports of alcohol use and PEth results (p = 0.72). Women self‐reported moderate–heavy alcohol use in early pregnancy only and a positive PEth screen indicated PAE in late pregnancy, suggesting that these methods may identify different groups of women.ConclusionsMultiple measurement tools and methods are needed to identify PAE at different points across pregnancy. Prospective sensitive interviewing is better suited to detecting PAE in early pregnancy, but not later when social desirability bias is stronger, and the use of an objective biomarker, such a PEth, may be useful for identifying the risk of PAE in late pregnancy.
Risk factors of sepsis following pancreaticoduodenectomy based on inflammation markers and clinical characteristics
Authors: Zhang Haoyun , Meng Fanyu , Lu Shichun 
Published: March 2020

AbstractBackgroundSepsis is a common complication following pancreaticoduodenectomy (PD). The aim of this study was to evaluate the risk factors of sepsis based on serum inflammatory markers and clinical characteristics in patients who underwent PD.MethodsA total of 138 patients were enrolled in this study and all patients underwent curative PD. Logistic regression analysis was performed to identify risk factors for post‐operative sepsis. The patients' basic clinical features and inflammatory biomarkers including cytokines (IL‐1, IL‐2, IL‐6, IL‐8, IL‐10 and tumour necrosis factor‐α), procalcitonin, C‐reactive protein and peripheral neutrophil to lymphocyte ratio were analysed.ResultsOf 138 patients, 31 developed sepsis during hospitalization. Univariate logistic regression analysis showed that body mass index, blood transfusion, operative time, American Society of Anesthesiologists score and diabetes were significant predictors of sepsis among all clinical characteristic variables. IL‐2, IL‐6, IL‐10, procalcitonin and C‐reactive protein were significant predictors among all inflammation biomarkers. By including different variables, three different regression models were obtained. The full model including all predictors mentioned above showed a C‐index of 0.831 and blood transfusion showed no statistically significance in this model. The reduced model 1 including blood transfusion showed a C‐index of 0.809. Another reduced model which included pre‐operative and intra‐operative variables showed a C‐index of 0.814 and this model could be used for early sepsis risk estimation.ConclusionPre‐operative IL‐6 was an independent risk factor for sepsis following PD. The three different predictive models could help early sepsis estimation for patients underwent PD.
Environmental migrants, structural injustice, and moral responsibility
Authors: Dwyer James 
Published: March 2020

AbstractClimate change and environmental problems will force or induce millions of people to migrate. In this article, I describe environmental migration and articulate some of the ethical issues. To begin, I give an account of these migrants that overcomes misleading dichotomies. Then, I focus attention on two important ethical issues: justice and responsibility. Although we are all at risk of becoming environmental migrants, we are not equally at risk. Our risk depends on our temporal position, geographical location, social position, and the kind of society in which we live. We all contribute to environmental problems, but we do not contribute equally. About 11% of the world population is responsible for 50% of carbon emissions. These inequalities raise issues of justice because many of the people who are at high risk have contributed little to the problems. Since the issues of justice are relatively clear and compelling, I focus more attention on issues of responsibility. I use Iris Marion Young’s account of responsibility for structural injustice to address four key questions about moral responsibility and environmental migration.
DSGE models, detrending, and the method of moments
Authors: Mao Takongmo Charles Olivier 
Published: March 2020

AbstractOne important question in the DSGE literature is whether we should detrend data when estimating the parameters of a DSGE model using the moment method. It has been common in the literature to detrend data in the same way the model is detrended. Doing so works relatively well with linear models, in part because in such cases the information that disappears from the data is usually related to the parameters that also disappear from the detrended model. Unfortunately, in heavy non‐linear DSGE models, parameters rarely disappear from detrended models, but information does disappear from the detrended data. Using a simple real business cycle model, we show that both the moment method estimators of parameters and the estimated responses of endogenous variables to a technological shock can be seriously inaccurate when detrended data are used in the estimation process. Using a dynamic stochastic general equilibrium model and U.S. data, we show that detrending the data before estimating the parameters may result in a seriously misleading response of endogenous variables to monetary shocks. We suggest building the moment conditions using raw data, irrespective of the trend observed in the data.
A computational method based on Gustafson‐Kessel fuzzy clustering for a novel islanding detection for grid connected devices and sensors
Authors: Ponmudi B. , Balasubramanian G. 
Published: March 2020

AbstractFuzzy Clustering‐based (G‐K) Gustafson‐Kessel is used to create the fuzzy rule‐based classifier in a grid connected photovoltaic (PV) system where it is tested using specific features in a grid connected PV inverter for detecting islanding condition. It is detected when harmonic content of voltages at the Point of Common Coupling and inverter increases beyond a threshold value. If islanding is not detected, distribution lines are rendered unsafe. The present study uses G‐K fuzzy clustering to categorize islanding and nonislanding incidents. Two features based on Total Harmonic Distortion are extracted and used as inputs for the G‐K fuzzy clustering classifier. The proposed technique is tested using nonlinear loads and its performance is verified by simulation using MATLAB Simulink. A hardware test set‐up is developed to validate the proposed antiislanding technique and the results obtained are discussed.
The Moral Politics of Gendered Labour in Artisanal Mining in Sierra Leone
Authors: Rutherford Blair 
Published: March 2020

ABSTRACTDrawing on current anthropological approaches to labour, this article examines some of the moral politics mobilized around women and artisanal mining in policy‐inflected scholarship with reference to particular gold mining zones in Tonkolili district, Sierra Leone. In so doing, the article proposes that such a focus on labour not only allows one to appreciate how sentiments concerning (im)proper behaviour infuse wider policy proposals to amend social arrangements in regard to what is called ‘artisanal mining’, but it also offers insight into some of the enduring moral politics helping to constitute women as ‘family workers’ in the actual artisanal gold mining zones. The article suggests that examining the overlapping moral politics constituting women's labour practices provides a more supple understanding of the contested economic possibilities for women in this livelihood practice.