bluuebunny/crossref_metadata_2025_split huggingface dataset:
A System Dynamics Approach to Investigate The Effects of Disruption on The Supply Chain with A Mitigation Strategy
Authors: Abdullah MA , Hishamuddin H , Bazin Nen 
Published: December 2019

Abstract
In this paper, a system dynamics approach is used to simulate a three stages supply chain system experiencing supply disruption. The supply chain system consists of single supplier, manufacturer and retailer. The model is developed suggesting backlogged and inventory as the primary performance measure. The model is tested under three conditions, which are normal condition, disruption condition and disruption with a mitigation strategy. The main findings from the study are lead time changes on the entire system directly impact the inventory of the entire stages in the system. Furthermore, the disruption occurence produces an adverse effect on supply chain performance for a period longer than the actual period of the disruption and likewise, influence system performance. The study further identifies that by incorporating safety stock as a mitigation strategy in the event of a supply disruption, will significantly reduce the disruption impact. The proposed simulation model and experimental findings are important to assist management in their inventory and risk control decision-making in the event of disruptions.
The Development of SORREL Systematic Roselle Harvesting System for Efficient Transfer Process
Authors: Ali E A , Kamarudin K M , Me R Che , Sulaiman R , Alli H 
Published: December 2019

Abstract
Roselle (Hibiscus sabdariffa L.) belongs to the family of Malvaceae or Hibiscus the Malaysian national flower. In Malaysia, this plant is first introduced in the state of Terengganu as one of the alternatives to replace tobacco plants in sandy soils. Studies conducted on Roselle plantation in Malaysia identified too many repetitive steps in harvesting and deseeding process, as well as separating different grades of Roselle flowers and its logistics. The paper focuses on the improvement of harvesting and deseeding Roselle flowers, aiming to hybridize both processes into one effective process. The reason of developing such combination is to prevent frequent transferring of Roselle flowers to avoid damages, at the same time increasing the quality of harvest. This study also considers embedding few appropriate but simple technologies for systematic harvesting, making sure the Roselle flowers collected are in top quality and in best hygiene by user-friendly, ergonomic and safe to use processes.
Development of Robotic Rovers: A Review
Authors: Herman Nurul Aqilah , Ramli Roshahliza M , Adib Mohd Azrul Hisham Mohd , Widia Mirta 
Published: December 2019

Abstract
The robotic rover is defined as a small vehicle that can move over rough ground and it is initially used by NASA for space exploration. However, this type of rover is expensive, using complicated and complex materials and software as well as large in size. Robotic rover fills the gap without endangering personnel involves in life-threatening condition or scenario that human sometimes needs to deal with. It can be considered to be deployed in assisting safety authorities to collect information and insights as well as work lift in search and rescue operations. In this paper, the progress that has been made towards the development of robotic rover which has been done in previous years are reviewed, including the design, functions, specifications, and applications, to meet requirements in performing a variety of tasks including hazardous identification, site surveillance and monitoring. Subsequent to this, a few analyses on the design and development of the proposed robotic rover are also discussed. The ultimate aim is to come out with such rover that is portable, small in size and low cost, together with user-friendly functions and specifications for future potential applications.
Biogenic synthesis of magnetic iron oxide nanoparticles using inedible borassus flabellifer seed coat: characterization, antimicrobial, antioxidant activity and in vitro cytotoxicity analysis
Authors: Sandhya J , Kalaiselvam S 
Published: December 2019

Abstract
An environment friendly green synthesis of iron oxide nanoparticles using the seed coat extract of B.flabellifer was investigated. The nanoparticles were characterized using XRD, UV–vis spectroscopy, FTIR, TGA, SEM and EDS. The x-ray diffraction spectrum showed the formation of crystalline inverse spinel magnetite nanoparticles with crystallite size of 35 nm and the UV–vis absorption recorded characteristic peak at 352 nm for iron oxide nanoparticles. The surface functionalization of the nanoparticles was confirmed from the various functional group peaks present in the FTIR spectrum and the thermal decomposition of the synthesized nanoparticles from TGA. The morphological study using SEM showed the formation of hexagonal shaped, well dispersed nanoparticles. The cytocompatibilty of the iron oxide nanoparticles was studied using MTT assay and haemolytic analysis. The antimicrobial activity of the nanoparticles against E. coli, S. aureus, B.subtilis, Shigella, A.niger and Candida albicans were measured and the nanoparticles showed significant activity against all the microorganisms which increased with increase in the nanoparticle concentration. The free radical scavenging activity of the nanoparticles against DPPH, Hydrogen peroxide and hydroxyl radical was performed which showed efficient antioxidant activity.
BCdatabaser: on-the-fly reference database creation for (meta-)barcoding
Authors: Keller Alexander , Hohlfeld Sonja , Kolter Andreas , Schultz Jörg , Gemeinholzer Birgit , Ankenbrand Markus J 
Published: December 2019

Abstract

Summary
DNA barcoding and meta-barcoding have become irreplaceable in research and applications, where identification of taxa alone or within a mixture, respectively, becomes relevant. Pioneering studies were in the microbiological context, yet nowadays also plants and animals become targeted. Given the variety of markers used, formatting requirements for classifiers and constant growth of primary databases, there is a need for dedicated reference database creation. We developed a web and command-line interface to generate such on-the-fly for any applicable marker and taxonomic group with optional filtering, formatting and restriction specific for (meta-)barcoding purposes. Also, databases optionally receive a DOI, making them well-documented with meta-data, publicly sharable and citable.

Availability and implementation
source code: https://www.github.com/molbiodiv/bcdatabaser, webservice: https://bcdatabaser.molecular.eco, documentation: https://molbiodiv.github.io/bcdatabaser.
Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction
Authors: Li Jin , Zhang Sai , Liu Tao , Ning Chenxi , Zhang Zhuoxuan , Zhou Wei 
Published: December 2019

Abstract

Motivation
Predicting the association between microRNAs (miRNAs) and diseases plays an import role in identifying human disease-related miRNAs. As identification of miRNA-disease associations via biological experiments is time-consuming and expensive, computational methods are currently used as effective complements to determine the potential associations between disease and miRNA.

Results
We present a novel method of neural inductive matrix completion with graph convolutional network (NIMCGCN) for predicting miRNA-disease association. NIMCGCN first uses graph convolutional networks to learn miRNA and disease latent feature representations from the miRNA and disease similarity networks. Then, learned features were input into a novel neural inductive matrix completion (NIMC) model to generate an association matrix completion. The parameters of NIMCGCN were learned based on the known miRNA-disease association data in a supervised end-to-end way. We compared the proposed method with other state-of-the-art methods. The area under the receiver operating characteristic curve results showed that our method is significantly superior to existing methods. Furthermore, 50, 47 and 48 of the top 50 predicted miRNAs for three high-risk human diseases, namely, colon cancer, lymphoma and kidney cancer, were verified using experimental literature. Finally, 100% prediction accuracy was achieved when breast cancer was used as a case study to evaluate the ability of NIMCGCN for predicting a new disease without any known related miRNAs.

Availability and implementation
https://github.com/ljatynu/NIMCGCN/

Supplementary information
Supplementary data are available at Bioinformatics online.
Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets
Authors: Tintori Sophia C , Golden Patrick , Goldstein Bob 
Published: December 2019

Abstract

Summary
Differential Expression Gene Explorer (DrEdGE) is a web-based tool that guides genomicists through easily creating interactive online data visualizations, which colleagues can query according to their own conditions to discover genes, samples or patterns of interest. We demonstrate DrEdGE’s features with three example websites generated from publicly available datasets—human neuronal tissue, mouse embryonic tissue and Caenorhabditis elegans whole embryos. DrEdGE increases the utility of large genomics datasets by removing technical obstacles to independent exploration.

Availability and implementation
Freely available at http://dredge.bio.unc.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
Towards an integrative understanding of stamen–corolla tube modifications and floral architecture in Boraginaceae s.s. (Boraginales)
Authors: Jeiter Julius , Langecker Stella , Weigend Maximilian 
Published: December 2019

AbstractMorphological studies rarely address floral organ modifications or their integration into floral architecture and floral function. Boraginaceae show two prominent types of stamen–corolla tube modifications: faucal and basal scales. Both types, especially faucal scales, are widely used in classification. Here, the ontogeny and morphology of faucal and basal scales are studied in 29 species from eight tribes and all three subfamilies of Boraginaceae s.s. (=Boraginoideae sensu APG IV) using scanning electron microscopy. Integration into floral architecture is visualized with micro-computed tomography (µCT). Faucal and basal scales are present in 18 and 27 species, respectively. Both types of scales develop late in flower ontogeny, but with variable timing. Faucal scales are morphologically far more variable than basal scales. Faucal scales are located close to the anthers and sometimes are involved in anther cone formation. Basal scales cover either the gynoecial disc nectary or the entire ovary. The different scale morphologies identified here enclose complex internal spaces, but they show no obvious phylogenetic patterns. This probably indicates strong functional constraints and adaptive pressures. This is a first in-depth study of the morphology and development of stamen–corolla tube modifications in Boraginaceae s.s., demonstrating that in situ three-dimensional visualization of floral architecture with µCT provides unprecedented insights into the evolution and functional integration of stamen–corolla tube modifications in Boraginales.
Redeployment or robocalypse? Workers and automation in Ohio manufacturing SMEs
Authors: Waldman-Brown Anna 
Published: December 2019

AbstractA case study on small and medium metalworking firms in Ohio explores how US-based factory owners conceptualise automation and the impact that newly introduced technologies have on workers. The cost and risk of replacing entire production processes and the still-relevant capabilities of old equipment encourage the interviewed firms to complement rather than replace existing technologies and workers. An incremental, piecemeal strategy makes it less likely that companies will introduce more integrated automation systems that may presage fully-automated manufacturing.
Annotation and curation of the causality information in LncRNADisease
Authors: Jia Kaiwen , Gao Yuanxu , Shi Jiangcheng , Zhou Yuan , Zhou Yong , Cui Qinghua 
Published: December 2019

Abstract
Disease causative non-coding RNAs (ncRNAs) are of great importance in understanding a disease, for they directly contribute to the development or progress of a disease. Identifying the causative ncRNAs can provide vital implications for biomedical researches. In this work, we updated the long non-coding RNA disease database (LncRNADisease) with long non-coding RNA (lncRNA) causality information with manual annotations of the causal associations between lncRNAs/circular RNAs (circRNAs) and diseases by reviewing related publications. Of the total 11 568 experimental associations, 2297 out of 10 564 lncRNA-disease associations and 198 out of 1004 circRNA-disease associations were identified to be causal, whereas 635 lncRNAs and 126 circRNAs were identified to be causative for the development or progress of at least one disease. The updated information and functions of the database can offer great help to future researches involving lncRNA/circRNA-disease relationship. The latest LncRNADisease database is available at http://www.rnanut.net/lncrnadisease.
Physiological monitoring of the complex multimorbid heart failure patient – diabetes and monitoring glucose control
Authors: Seferović Petar M , Jhund Pardeep S 
Published: December 2019

AbstractHeart failure (HF) is a global epidemic, particularly affecting the elderly and/or frail patients often with comorbidities. Amongst the comorbidities, type 2 diabetes mellitus (T2DM) is highly prevalent and associated with higher morbidity and mortality. We review the detection and treatment of T2DM in HF and the need to balance the risk of hypoglycaemia and overall glycaemic control. Despite large attributable risks, T2DM is often underdiagnosed in HF. Therefore there is a need for systematic monitoring (screening) for undetected T2DM in HF patients. Given that patients with HF are at greater risk for developing T2DM compared with the general population, an emphasis also has to be placed on regular reassessment of glycaemic status during follow-up. Therefore, glucose-lowering therapies (e.g. sodium-glucose cotransporter-2 inhibitors, SGLT-2 inhibitors) with a known benefit for the prevention or delay of HF hospitalization could be considered early in the course of T2DM, to optimise treatment and reduce cardiovascular (CV) risk. Although intensive glycaemic control has been shown to effectively reduce the risk of microvascular complications in T2DM, these same trials have shown either no reduction in CV outcomes, or even an increase in mortality with tight glycaemic control (i.e. targeting HbA1c levels &lt;7.0%). More lenient glycaemic targets (e.g. HbA1c levels 7.0-8.0%) may be more appropriate for HF patients with T2DM. The 2016 ESC Guidelines for the diagnosis and treatment of HF proposed metformin as the first-line therapy, given its long-standing use and low risk of hypoglycaemia. More recently, several novel glucose lowering-medications have been introduced, including dipeptidyl peptidase-4 (DPP-4) inhibitors, glucagon-like peptide-1 receptor agonists (GLP-1 RA), and SGLT-2 inhibitors. The most consistent reduction in the risk of HF hospitalisation has been shown with the three SGLT-2 inhibitors (empagliflozin, canagliflozin and dapagliflozin) which now offer improved outcomes in patients with both HF and T2DM.
Self-consistent stick-slip recurrent behaviour of elastoplastic faults in intraplate environment: a Lagrangian solid mechanics approach
Authors: So Byung-Dal , Capitanio Fabio A 
Published: December 2019

SUMMARYOur understanding of the seismicity of continental interiors, far from plate margins, relies on the ability to account for behaviours across a broad range of time and spatial scales. Deformation rates around seismic faults range from the slip-on-fault during earthquakes to the long-term viscous deformation of surrounding lithosphere, thereby presenting a challenge to modelling techniques. The aim of this study was to test a new method to simulate seismic faults using a continuum approach, reconciling the deformation of viscoelastoplastic lithospheres over geological timescales. A von Mises yield criterion is adopted as a proxy for the frictional shear strength of a fault. In the elastoplastic fault models a rapid change in strength occurs after plastic yielding, to achieve stress–strain equilibrium, when the coseismic slip and slip velocity from the strain-rate response and size of the fault are calculated. The cumulative step-function shape of the slip and temporally partitioned slip velocity of the fault demonstrated self-consistent discrete fault motion. The implementation of elastoplastic faults successfully reproduced the conceptual models of seismic recurrence, that is strictly periodic and time- and slip-predictable. Elastoplastic faults that include a slip velocity strengthening and weakening with reduction of the time-step size during the slip stage generated yield patterns of coseismic stress changes in surrounding areas, which were similar to those calculated from actual earthquakes. A test of fault interaction captured the migration of stress between two faults under different spatial arrangements, reproducing realistic behaviours across time and spatial scales of faults in continental interiors.
Tranexamic acid and convulsive seizures after isolated coronary artery bypass surgery: the role of cardiopulmonary bypass and renal function
Authors: Hulde Nikolai , Zittermann Armin , Deutsch Marcus-Andre , von Dossow Vera , Gummert Jan F , Koster Andreas 
Published: December 2019

Abstract
In cardiac surgical patients, tranexamic acid (TXA) has been associated with an increased risk of convulsive seizure (CS). We aimed to investigate whether in patients undergoing isolated coronary artery bypass grafting (CABG) surgery the use of cardiopulmonary bypass (CPB) impacts the risk of CS. We studied 4198 propensity score matched patients. Patients who underwent CABG surgery without CPB, received a single bolus of 1 g TXA. Patients who underwent CABG with CPB, additionally received a TXA dose of 0.5 g in the CPB prime and an infusion of 0.2 g/h until the end of CPB. The risk of CS in the CPB group and the group without CPB was 0.7% and 0.6%, respectively (risk ratio 1.08, 95% confidence interval 0.51–2.30; P &gt; 0.99). Kidney function was significantly associated with the risk of CS (P = 0.005), the latter being highest in patients with glomerular filtration rates &lt;30 ml/min/1.73 m2 (2.2%) and lowest in those patients with values &gt;60 ml/min/1.73 m2 (0.4%). Our data in patients undergoing isolated CABG indicate no significant effect on CS risk by use of CPB when TXA doses of up to ∼2 g are given. However, caution regarding TXA administration is necessary in patients with renal impairment.
Trachoma Prevalence After Discontinuation of Mass Azithromycin Distribution
Authors: Godwin William , Prada Joaquin M , Emerson Paul , Hooper P J , Bakhtiari Ana , Deiner Michael , Porco Travis C , Mahmud Hamidah , Landskroner Emma , Hollingsworth T Déirdre , Medley Graham F , Pinsent Amy , Bailey Robin , Lietman Thomas M , Oldenburg Catherine E 
Published: December 2019

Abstract

Background
As the World Health Organization seeks to eliminate trachoma by 2020, countries are beginning to control the transmission of trachomatous inflammation–follicular (TF) and discontinue mass drug administration (MDA) with oral azithromycin. We evaluated the effect of MDA discontinuation on TF1–9 prevalence at the district level.

Methods
We extracted from the available data districts with an impact survey at the end of their program cycle that initiated discontinuation of MDA (TF1–9 prevalence &lt;5%), followed by a surveillance survey conducted to determine whether TF1–9 prevalence remained below the 5% threshold, warranting discontinuation of MDA. Two independent analyses were performed, 1 regression based and 1 simulation based, that assessed the change in TF1–9 from the impact survey to the surveillance survey.

Results
Of the 220 districts included, TF1–9 prevalence increased to &gt;5% from impact to surveillance survey in 9% of districts. Regression analysis indicated that impact survey TF1–9 prevalence was a significant predictor of surveillance survey TF1–9 prevalence. The proportion of simulations with &gt;5% TF1–9 prevalence in the surveillance survey was 2%, assuming the survey was conducted 4 years after MDA.

Conclusion
An increase in TF1–9 prevalence may represent disease resurgence but could also be due to measurement error. Improved diagnostic tests are crucial to elimination of TF1–9 as a public health problem.
Trained Immunity Confers Broad-Spectrum Protection Against Bacterial Infections
Authors: Ciarlo Eleonora , Heinonen Tytti , Théroude Charlotte , Asgari Fatemeh , Le Roy Didier , Netea Mihai G , Roger Thierry 
Published: December 2019

Abstract

Background
The innate immune system recalls a challenge to adapt to a secondary challenge, a phenomenon called trained immunity. Training involves cellular metabolic, epigenetic and functional reprogramming, but how broadly trained immunity protects from infections is unknown. For the first time, we addressed whether trained immunity provides protection in a large panel of preclinical models of infections.

Methods
Mice were trained and subjected to systemic infections, peritonitis, enteritis, and pneumonia induced by Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Citrobacter rodentium, and Pseudomonas aeruginosa. Bacteria, cytokines, leukocytes, and hematopoietic precursors were quantified in blood, bone marrow, and organs. The role of monocytes/macrophages, granulocytes, and interleukin 1 signaling was investigated using depletion or blocking approaches.

Results
Induction of trained immunity protected mice in all preclinical models, including when training and infection were initiated in distant organs. Trained immunity increased bone marrow hematopoietic progenitors, blood Ly6Chigh inflammatory monocytes and granulocytes, and sustained blood antimicrobial responses. Monocytes/macrophages and interleukin 1 signaling were required to protect trained mice from listeriosis. Trained mice were efficiently protected from peritonitis and listeriosis for up to 5 weeks.

Conclusions
Trained immunity confers broad-spectrum protection against lethal bacterial infections. These observations support the development of trained immunity-based strategies to improve host defenses.