bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving delivery performance by using simulation, FMEA, and FTA
Authors: Hutabarat Rosiana , Sen Rimo Tan Hauw , Meilani  , Andika Aditya
Published: March 2020

Delivery performance is one of the indications of enterprise’s success to provide products to customers. In this research, simulation is done to measure the delivery performance and all the processes included in delivery process. In fact, every process has their own risks could delay delivery process that the delivery performance is reduced. The methods used to identify the risks and the causes are Failure Mode and Effects Analysis (FMEA) and Fault Tree Analysis (FTA). Risks analysis is done with the help of Pareto diagrams and scatter plot to determine the risks need to be corrected immediately. The proposed improvements are integrating the systems in form of e-cargo ready and implementing bar-coding. After the proposed e-cargo ready applied and being simulated, the delivery performance in terms of average total time reduced by 29,398%.
Temperature distribution in friction stir spot welding of aluminium alloy based on finite element analysis
Authors: Armansyah  , Chie Ho Hwi , Saedon Juri , Adenan Shahriman
Published: March 2020

Friction stir spot welding (FSSW) as the solid-state welding has been expanded to be used in various materials and many applications. The significant issue in FSSW is the existence of porosity or wormholes, leads to welding failure. One reason is due to imperfect heat generation leads to temperature distribution during FSSW effect to uncertain weldment formation. This is mainly influenced by improper parameters selection. In this study, the temperature distribution in the weld zones is investigated using finite element analysis via computer numerical simulation of Altair Hyperworks software with respect to parameters i.e. spindle speed, tool plunge depth, and tool dwell time. In the simulation, tool plunge depth and tool dwell time is set constant, but spindle speed was varied from 1400, 1500, and 1600 rpm respectively. Based on the results found that at a spindle speed of 1400 rpm was produced max temperature in the weld zone at 540 °C. Meanwhile, at 1500 rpm increased the temperature at 596 °C. At 1600 rpm reached its highest temperature at 650 °C. The results show that increasing tool rotational speed, at a constant tool plunge depth and constant tool dwell time will increase the amount of temperature distribution in the weld-zones. It is concluded that the suitable temperature distribution required in FSSW is 540 °C represented the solid-state joining process provided by spindle speed of 1400 rpm.
Feed-forward back-propagation (FFBP) algorithm for property prediction in friction stir spot welding of aluminium alloy
Authors: Armansyah  , Chie Ho Hwi , Saedon Juri , Adenan Shahriman
Published: March 2020

Facing the issue of cost and efficiency in experiments and tests in determining the properties of the welded structure is a challenge in friction stir spot welding (FSSW) optimization. Employing the machine learning technique of artificial neural network (ANNs) to develop a prediction model with fewer experiments and tests is a gentle solution to forecast the properties of the spot weld structures. In this study, the extended full factorial design with respect to thetool speed, plunge depth, anddwell time are applied to the FSSW specimens of aluminium A5052-H122 of 2mm thick through 27 experiments and evaluated via tensile shearing load testing. The multilayer neural network of feed-forward and back-propagation (FFBP) algorithm was engaged to learn and train the neural network iteratively with a set of weights and bias of 27 variations of inputs to fit the predicted tensile shear loads of the spot weld structures. Based on the resulted of regression plot, it is shown that the correlation coefficient (R) is perfect for training with the value of 0.999 and for testing the correlation coefficient (R) is reached to 0.958. However, the correlation coefficient is relatively good for validation with R equal to 0.921. For all data sets, the correlation coefficient is good with R of 0.833. It can be seen that the ANNs prediction model is relatively good since the correlation coefficient relatively close to 1.
Navigation assistant for vision impaired people using ultra sonic (sonar vision) and global positioning system (GPS)
Authors: Prabowo Raditya Eko , Julian Nicholas , Mae Johannes , Susanto Rudy , Hedwig Rinda
Published: March 2020

People with low vision usually use stick to find their way or to face an obstacle in front of them. However, this detection only can be felt as long as the length of the stick from its handle is as far as the reach of the hand. Seeing this limitation, a set of sonar vision was made using sonar sensor, which equipped as a wristwatch and a buckle of a belt. The sonar vision was designed to detect an obstacle for up to 3 meters away. A hundred low vision people already got the benefit of this system, which 84% of them felt that the sonar vision helped them in the navigation. The new design based on the feedback is presented in this paper, which is equipped with GPS for positioning information.
Design and Implementation of Artificial Grow Light for Germination and Vegetative Growth
Authors: Pratama Bagus Wira , Glenn Fabian , Atmadja Wiedjaja , Liawatimena Suryadiputra , Susanto Rudy
Published: March 2020

The purpose of this research is to build artificial grow light using LED for growing leafy vegetables from germination to harvesting (vegetative growth). Plants need to capture photons as energy for photosynthesis in 400nm – 780nm spectrum. Different plant species will respond differently to specific light spectrum. Many studies have been done to find optimal light spectrum for plant growth, but there are still many researches to be done because there are still many combinations of light and plants species to be discovered. Specific light spectra combination is called light recipe. This research will help botanist to discover new light recipe for plant species by mixing 6 light spectra with individual intensity and time control. The developed grow light system has graphical user interface that run in Android tablet, and uses MQTT protocol for communication between android application and grow light system. Light recipe and setting are stored in database and the system also has light sensor to monitor light environmental conditions. Grow light consists of 6 types of 3W high power LED with specific color spectrum: Royal Blue, Deep Red, Ultraviolet, Full Spectrum, Far Red, and Natural White. Testing result shows that the system can produce uniform light distribution across the 50 x 50 cm grow area on average 22.6 µmol m-2s-1 using 60° lens. Germination result of lettuce using grow light shows good results compared to sunlight.
IoT Solution for Intelligent Pond Monitoring
Authors: Darmalim Usin , Darmalim Ferdinan , Darmalim Sutristo , Hidayat Alam Ahmad , Budiarto Arif , Mahesworo Bharuno , Pardamean Bens
Published: March 2020

Channa striata or the striped snakehead fish is one of snakehead fish species which inhabits all types of freshwater bodies distributed across Asian countries. Because this fish is known to have higher albumin fraction (64.61%) of protein and other economic values, domestication, and cultivation of this fish has been done in many Asian countries such as Indonesia, China, Malaysia, Thailand, Bangladesh, and India. Environmental factors such as temperature, water pH, dissolved oxygen, total dissolved solids, and turbidity are important parameters must be considered inbreeding and growing this type of fish. The aim of this paper is to propose an IoT solution to automatically monitor these environmental factors. It is designed with affordable and open-source electrical components to provide a cost-efficient solution for farmers. Five sensors are used to measure each parameter. A web application prototype is also presented as a companion application for the users to get useful information from the IoT device. It is developed using a Pythonframework. By accessing this web application, the users can immediately detect any abnormal conditions of the pond.
Analysis of Implementation and Proposal Development of ERP System in CV Indah Jaya
Authors: Supangi P , Rahayu P C , Christiani A
Published: March 2020

CV Indah Jaya is a company engaged in printing since 1960. Many requests and various products in the company that became a trigger for CV Indah Jaya to use an ERP system. The company want its process to be more efficient and effective. Starting 2013 CV Indah Jaya implements an ERP system with a MySQL database. An ERP system that is already running can be used to receive orders, calculate order calculations, calculate inventory and also payment and shipping. However, the company has not yet felt the benefits of implementing this system optimally. The purpose of this study is to implement an ERP system and provide development support so that business processes are more efficient and effective. The first step is to analyze the current system workflow and decomposition of the ERP system that is being used by the company. Then make a questionnaire and interview with stakeholders regarding the use of ERP systems referring to the PIECES Framework to find out the actual user needs for the ERP system. The results of the analysis are application users who do not have clear procedures for using an ERP system, the same data input must be done repeatedly, the flow menu is not clear, the user interface is not user friendly, and there are still many reports that the system cannot yet produce. To overcome this problem, several standard operating procedures (SOP) were made in accordance with the ERP system workflow and gave the ERP system blueprint for further development. The results of the questionnaire after the application of the SOP have increased for Information and Data of 0.45, Economy of 0.38, Control and Security of 0.38 and Services of 0.14.
QR Label for Handicapped Exhibition Visitors Queue Built-Up Avoidance
Authors: Tanutama Lukas , Seikka Ricardo , Hardy Albert
Published: March 2020

Most exhibitions such as in museums items are provided with printed labels that contain information of interest. A queue of visitors will be formed both to view the items and read the labels for information of interest. Visitors have limited time to read and view as a queue will built-up in due time. Handicapped visitors on wheel chair are very disadvantaged in enjoying exhibits due to the possibility of queue built-up that could cause inconvenience to other visitors. Current visitors most likely possess smartphones as communication device. Smartphones can be exploited to satisfy the need of information. QR labelling together with private cloud or network for information retrieval is presented as a viable solution. The system could cater the need of handicapped visitors. Visitors can conveniently collect information and study it at their convenience using their smartphones. Excessive queue forming can be avoided. This research is to find the position where a handicapped or any person can reliably scan the QR code label and the advisable size of label. The result is beneficial both for the exhibition organizer and the visitor. The parameters of interest are the distance and angle where a QR code label of certain can be reliably scanned.
Drones Computer Vision using Deep Learning to Support Fishing Management in Indonesia
Authors: Liawatimena Suryadiputra , Atmadja Wiedjaja , Abbas Bahtiar Saleh , Trisetyarso Agung , Wibowo Antoni , Barlian Erland , Hardanto Lilik Tri , Triany Natassya Afdalena , Faisal  , Sulistiawan Jaka , Yojana Albert Cahya
Published: March 2020

It is necessary to study technical factors such as bait used, oceanographic conditions of fishing areas and skipjack tuna trade patterns (Katsuwonus pelamis) as well as other factors in Sulawesi Fisheries. Supporting data to study these technical factors need to be obtained so that it can be improved throughout the year as a skipjack fishing standard with weights taken by the skipjack weights. Therefore, drones and underwater drones with cameras with high-resolution video and images to be fed and processed by computer vision. These drones are operated via Huhate ships which are then used to test efficient technical factors as expected, can be used in determining the size, shape, and colour as well as the analysis of skipjack fish that are in the Fish Aggregating Devices (FADs or Rumpon) in order to manage the management of fisheries managed in Indonesia.
Economic analysis for solvent recovery system (solvent as cleaning liquid for the processing equipment)
Authors: Nasution Januar , Mahardini Karunia Agung
Published: March 2020

The purpose of this paper is to aggravate more reuse and recover material in chemical or in any industry that use mixing process or cleaning equipment that use solvent. This study also gave new approach on sustainable solution that assess by economic advantage. In many industry solvents is used for cleaning the processing equipment’s to avoid cross contamination from one batch to the other, due to the solvent scrap is being generated in the cleaning process. In often times, this scrap has been thrown away since it is already contaminated with the products, so it is being considered as scrap. In order to minimize the scrap, recovery of solvent is one method to recover the solvent. For the research, the distillation process was proposed, so the contaminated solvent can be purified so it can be use again for cleaning, or in some case it can be also use again as raw material for products. The solvent recovery is not only minimizing carbon foot print but also provides more sustainability. The solvent recovery gives also cost advantage for the industry.
Improve Understanding and Dissemination of Disaster Management and Climate Change by Using Knowledge Management Systems
Authors: Sardjono Wahyu , Harisno  , Perdana Widhilaga Gia
Published: March 2020

In Law Number 24 Year 2007 concerning Disaster Management, it is stated that the central government and regional governments are responsible for implementing disaster management, with an emphasis on preparedness and mitigation in dealing with natural disasters, as well as based on the provisions of article 1 of Presidential Regulation No. 46 of 2008 concerning the National Council on Climate Change that climate change is a change in average conditions of climate and / or climate diversity from one period of time to another as a result of human activity. However, the socialization of these two matters is not regulated in existing laws and regulations, so that the information dissemination plan and dissemination of the information must be carried out to the community itself. In line with developments in technology and information systems that have entered the era of media convergence, the acceleration of the process of spreading government programs can also be done by using this technology. The SECI method model (Socialization, Externalization, Combination, Internalization) was developed through implementation based on the ‘Knowledge Management System Cycle’ theory, so that a knowledge management system was formed. The results of research on community preparedness in the application of Knowledge Management Systems (KMS) for natural disaster preparedness and mitigation can be used to support the dissemination and dissemination of disaster management mitigation, global warming, and community-based climate change, including performance measurement of success.
Development of Fish Separator Conveyor based on Fish Identification System
Authors: Dzulfiqar Agung Muhammad Rangga , Elian Adrian Adhe , Astuti Winda , Puji Muhammad Nurul
Published: March 2020

Indonesia as the largest archipelago and maritime country in the world has a very large marine resources. Fish is one of the marine wealthties (marine biota), which have large numbers in Indonesia. Fishermen is an important role in the process of fishing, however fish caught by fishermen are often mixed with other types of fish. Currently, the process of fist separation is done manually, which takes longer time and many error occur due to fatigue. In this work the conveyer separator based on the fish identification system is developed. The fish conveyer separator is designed and developed. The fish identification system is based on Fast Fourier Transform (FTT) technique and Artificial Neural Network (ANN). The system is working properly, since it resulting the training and testing accuracy of 80% and 66%, respectively.
Genie Enterprise Resource Planning for Small Medium Enterprises Implementing Single Page Web Application
Authors: Gunawan J , Kosala R R
Published: March 2020

The exponential growth of Small Medium Enterprises (SMEs) in Indonesia has led to the greater competition among them. However, their business processes are often inefficiently managed, which increase the cost of operation. The current Enterprise Resource Planning system could address the problem, but the price is relatively expensive for current condition of SME in Indonesia. The problem continues when the business operation run in different places, where data inconsistencies reduce operation efficiency. Cloud-based ERP is a possible solution, but it is relatively slow to fully maximize the benefit. Therefore, new affordable solution with remote access, which use less internet bandwidth is needed to answer problems in implementing ERP. This study aims to analyze the problem and use the findings to provide a prototype that could address the existing problem. Through implementation of various technologies such as Single Page Application, Gzip Compression, and Webpack Module Bundler, the author successfully developed the prototype of ERP system. Several tests, including compatibility test and user acceptance test were performed to evaluate the prototype. Although this prototype has not been able cover the whole modules, the test results showed a satisfactory result in terms of accessibility and basic functionality.
Analysis and Design of E-Commerce on the Game Information Portal
Authors: Hon C W , Hartono I K
Published: March 2020

The gaming industries stated to have income up to USD 40.6 million or around IDR 541 billion in 2016 with around 43.7 million gamers but unfortunately this growth only on gaming platforms and developers but not information providers. The purpose of the study is to provide facilities and information to everyone who is engaged in gaming and technologies industries. The research is designated using analysis design method with the unified modelling language (UML) diagram by Satzinger, Jackson, and Burd. The analysis are conducted merely on the social-business environment process in order to provide an all-in-one package that can help answers all the potential users’ requirements. The aim of this studyisto show the business possibilities and opportunities for those who might want to expand their business or knowledge in gaming information platform industries.
Extraction of Phenolic Compounds using Subcritical Hot Water Extraction: A Review
Authors: Romulo Andreas
Published: March 2020

Subcritical hot water extraction (SHWE) is a green technique for extraction of the bioactive compound using water in the subcritical state. This condition occurs when the temperature and pressure are changing between the boiling point and critical point, increasing its solubility on the low and middle polar compounds. It is considered as an environmentally friendly solvent, and many publications have revealed the advantages of using this technique for the extraction of phenolic compounds. The main aim of this review is to provide a brief description of the SHWE application on the extraction of phenolic compounds for the last two years (2018-2019). By optimizing the main parameter of extraction such as extraction time and temperature, the desirable final product could be obtained.
Mechanistic Hypotheses on Colorectal Cancer and Red Meat Intake: A Review
Authors: Surya Reggie
Published: March 2020

Red meat is classified as probably carcinogenic to humans by International Agency for Research on Cancer (IARC) based on evidence on how it may affect the development of colorectal cancer, the third most common cancer worldwide. A plethora of scientific experiments prevailing to establish a positive association between red meat and colorectal cancer suggested different mechanistic hypotheses in order to explain such a phenomenon. This paper aims to discuss major hypotheses related to how red meat consumption may lead to colorectal cancer. Such hypotheses involve the role of natural compounds present in red meat (such as lipid, protein, N-glycolylneuraminic acid and heme iron) and neoformed substances during meat processing (such as heterocyclic amines, polyaromatic hydrocarbons and N-nitroso compounds).
Enrichment of Soft Ice Cream with Different Fibrous Fruit Puree: Physicochemical, Textural Characteristics and Sensory Properties
Authors: Rawendra Reynetha D.S. , Dwi Gabrielle Natasha
Published: March 2020

The objective of this study was to improve nutritional, physical, chemical, and sensory properties of soft ice cream with the addition of fibrous fruit puree. The research design was carried out with 2 factors, namely the different types of fruit puree (durian, melon, guava, and jackfruit) and the concentration of the addition of different puree (15% and 25%). Data obtained were analyzed using ANOVA with Duncan Multiple Range Test at a 95% confidence level. Results of the study shows that the addition of durian, melon, guava and jackfruit puree can increase overrun, melt rate, viscosity, dietary fiber, protein, total solids, fat content, but reduce water content in soft ice cream products. Sensory acceptance test shows that ice cream with 25% melon puree has the highest preference score of aroma, taste, texture, and overall. Soft ice cream with the addition of 25% guava puree has the highest preference score of aftertaste while ice cream with 25% of jackfruit puree has the highest preference score of texture.
The Effects of Subculture on The Mutant Plant Regeneration of Rodent Tuber (Typhonium flagelliforme) In Vitro Mutagenesis Using Gamma-Ray Irradiation
Authors: Sianipar Nesti Fronika , Assidqi Khoirunnisa , Abbas Bahtiar Saleh
Published: March 2020

The combination of gamma-ray irradiation treatment and somaclonal variation may cause morphological changes in vitro culture of rodent tuber. In vitro shoots were irradiated with several gamma-ray doses. Rodent tuber plantlets were irradiated with the doses of 20 Gy. The plantlets were subcultured up to 5 times then produced MV1 to MV5. Plantlets MV4 and MV5 were acclimatized and transplanted at the greenhouse. The purpose of this study was to analyze the morphological characteristics in the fourth mutant vegetative propagation (MV4) and the fifth mutant vegetative propagation (MV5) of rodent tuber from the combination of gamma-ray irradiation and somaclonal variation. Subcultures were performed to regenerate from MV1 to MV5 with optimal MS (Murashige & Skoog) medium. Subcultures were done at eight weeks. The morphological measurement in MV4 with the average number of shoots, number of leaves and plant height, i.e. 5.21, 14.41 and 5.52 cm, respectively. The highest average number of shoots, number of leaves and plant height was generated in MV5, i.e. 5.23, 16.54 and 5.18 cm, respectively. Pre-acclimatization were successfully produced in the greenhouse of about 30% (MV4) and 39.5% (MV5). Post acclimatization was obtained 100% in control, MV4, and MV5 at the greenhouse. MV5 had better morphological characteristics. The morphological changes were occurring in MV4 and MV5 compared with controls due to the combination of gamma-ray irradiation and somaclonal variation.
John Campbell Brown OBE (1947–2019)
Authors: Fletcher Lyndsay , Labrosse Nicolas , Mackinnon Alexander
Published: March 2020

Astronomer Royal for Scotland and inspirational solar physicist, by Lyndsay Fletcher, Nicolas Labrosse and Alec MacKinnon.
Johannes Geiss (1927–2020)
Authors: Bonnet Roger
Published: March 2020

Roger Bonnet remembers a researcher who pioneered the use of space science in planetary, cometary and cosmic research, playing a vital role in European space research.
Bicentenary: Celebrating the Society
Authors: Bunce Emma
Published: March 2020

On 23 January 2020, the Royal Astronomical Society gathered in London to celebrate its bicentenary, welcomed by RAS president-elect Emma Bunce
Bicentenary: Turning 200
Authors: Rees Martin
Published: March 2020

The Astronomer Royal, Martin Rees, spoke about the past and the future at the celebration of the bicentenary of the Royal Astronomical Society on 23 January 2020.
The things binaries do …
Authors: Eldridge J J
Published: March 2020

Binary interactions change stellar evolutionary pathways and models of stellar populations – but they are largely ignored. Here J J Eldridge outlines some recent history around the development of stellar evolution and population models, and highlights the significant differences that arise when binary interactions are included.
Song overlapping, noise, and territorial aggression in great tits
Authors: Akçay Çağlar , Porsuk Y Kağan , Avşar Alican , Çabuk Dilan , Bilgin C Can
Published: March 2020

Communication often happens in noisy environments where interference from the ambient noise and other signalers may reduce the effectiveness of signals which may lead to more conflict between interacting individuals. Signalers may also evolve behaviors to interfere with signals of opponents, for example, by temporally overlapping them with their own, such as the song overlapping behavior that is seen in some songbirds during aggressive interactions. Song overlapping has been proposed to be a signal of aggressive intent, but few studies directly examined the association between song overlapping and aggressive behaviors of the sender. In the present paper, we examined whether song overlapping and ambient noise are associated positively with aggressive behaviors. We carried out simulated territorial intrusions in a population of great tits (Parus major) living in an urban–rural gradient to assess signaling and aggressive behaviors. Song overlapping was associated negatively with aggressive behaviors males displayed against a simulated intruder. This result is inconsistent with the hypothesis that song overlapping is an aggressive signal in this species. Ambient noise levels were associated positively with aggressive behaviors but did not correlate with song rate, song duration, or song overlapping. Great tits in noisy urban habitats may display higher levels of aggressive behaviors due to either interference of noise in aggressive communication or another indirect effect of noise.
How to get your goat: automated identification of species from MALDI-ToF spectra
Authors: Hickinbotham Simon , Fiddyment Sarah , Stinson Timothy L , Collins Matthew J
Published: March 2020

Motivation

Classification of archaeological animal samples is commonly achieved via manual examination of matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) spectra. This is a time-consuming process which requires significant training and which does not produce a measure of confidence in the classification. We present a new, automated method for arriving at a classification of a MALDI-ToF sample, provided the collagen sequences for each candidate species are available. The approach derives a set of peptide masses from the sequence data for comparison with the sample data, which is carried out by cross-correlation. A novel way of combining evidence from multiple marker peptides is used to interpret the raw alignments and arrive at a classification with an associated confidence measure.

Results

To illustrate the efficacy of the approach, we tested the new method with a previously published classification of parchment folia from a copy of the Gospel of Luke, produced around 1120 C.E. by scribes at St Augustine’s Abbey in Canterbury, UK. In total, 80 of the 81 samples were given identical classifications by both methods. In addition, the new method gives a quantifiable level of confidence in each classification.

Availability and implementation

The software can be found at https://github.com/bioarch-sjh/bacollite, and can be installed in R using devtools.

Supplementary information

Supplementary data are available at Bioinformatics online.
κ-helix and the helical lock and key model: a pivotal way of looking at polyproline II
Authors: Meirson Tomer , Bomze David , Markel Gal , Samson Abraham O
Published: March 2020

Motivation

Polyproline II (PPII) is a common conformation, comparable to α-helix and β-sheet. PPII, recently termed with a more generic name—κ-helix, adopts a left-handed structure with 3-fold rotational symmetry. Lately, a new type of binding mechanism—the helical lock and key model was introduced in SH3-domain complexes, where the interaction is characterized by a sliding helical pattern. However, whether this binding mechanism is unique only to SH3 domains is unreported.

Results

Here, we show that the helical binding pattern is a universal feature of the κ-helix conformation, present within all the major target families—SH3, WW, profilin, MHC-II, EVH1 and GYF domains. Based on a geometric analysis of 255 experimentally solved structures, we found that they are characterized by a distinctive rotational angle along the helical axis. Furthermore, we found that the range of helical pitch varies between different protein domains or peptide orientations and that the interaction is also represented by a rotational displacement mimicking helical motion. The discovery of rotational interactions as a mechanism, reveals a new dimension in the realm of protein–protein interactions, which introduces a new layer of information encoded by the helical conformation. Due to the extensive involvement of the conformation in functional interactions, we anticipate our model to expand the current molecular understanding of the relationship between protein structure and function.

Availability and implementation

We have implemented the proposed methods in an R package freely available at https://github.com/Grantlab/bio3d.

Supplementary information

Supplementary data are available at Bioinformatics online.
M2IA: a web server for microbiome and metabolome integrative analysis
Authors: Ni Yan , Yu Gang , Chen Huan , Deng Yongqiong , Wells Philippa M , Steves Claire J , Ju Feng , Fu Junfen
Published: March 2020

Motivation

Microbiome–metabolome association studies have experienced exponential growth for an in-depth understanding of the impact of microbiota on human health over the last decade. However, analyzing the resulting multi-omics data and their correlations remains a significant challenge due to the lack of a comprehensive computational tool that can facilitate data integration and interpretation. In this study, an automated microbiome and metabolome integrative analysis pipeline (M2IA) has been developed to meet the urgent needs for tools that can effectively integrate microbiome and metabolome data to derive biological insights.

Results

M2IA streamlines the integrative data analysis between metabolome and microbiome, from data preprocessing, univariate and multivariate statistical analyses, advanced functional analysis for biological interpretation, to a summary report. The functionality of M2IA was demonstrated using TwinsUK cohort datasets consisting of 1116 fecal metabolites and 16s rRNA microbiome from 786 individuals. Moreover, two important metabolic pathways, i.e. benzoate degradation and phosphotransferase system, were identified to be closely associated with obesity.

Availability and implementation

M2IA is public available at http://m2ia.met-bioinformatics.cn.

Contact

yanni617@zju.edu.cn or fjf68@zju.edu.cn

Supplementary information

Supplementary data are available at Bioinformatics online.
Janus-faced spatacsin (SPG11): involvement in neurodevelopment and multisystem neurodegeneration
Authors: Pozner Tatyana , Regensburger Martin , Engelhorn Tobias , Winkler Jürgen , Winner Beate
Published: March 2020

Hereditary spastic paraplegia (HSP) is a heterogeneous group of rare motor neuron disorders characterized by progressive weakness and spasticity of the lower limbs. HSP type 11 (SPG11-HSP) is linked to pathogenic variants in the SPG11 gene and it represents the most frequent form of complex autosomal recessive HSP. The majority of SPG11-HSP patients exhibit additional neurological symptoms such as cognitive decline, thin corpus callosum, and peripheral neuropathy. Yet, the mechanisms of SPG11-linked spectrum diseases are largely unknown. Recent findings indicate that spatacsin, the 280 kDa protein encoded by SPG11, may impact the autophagy-lysosomal machinery. In this update, we summarize the current knowledge of SPG11-HSP. In addition to clinical symptoms and differential diagnosis, our work aims to link the different clinical manifestations with the respective structural abnormalities and cellular in vitro phenotypes. Moreover, we describe the impact of localization and function of spatacsin in different neuronal systems. Ultimately, we propose a model in which spatacsin bridges between neurodevelopmental and neurodegenerative phenotypes of SPG11-linked disorders.
Pyramid-Shape Crossings and Intercrossing Fibers Are Key Elements for Construction of the Neural Network in the Superficial White Matter of the Human Cerebrum
Authors: Shinohara Harumichi , Liu Xiaoliang , Nakajima Riho , Kinoshita Masashi , Ozaki Noriyuki , Hori Osamu , Nakada Mitsutoshi
Published: March 2020

Structural analysis of the superficial white matter is prerequisite for the understanding of highly integrated functions of the human cerebral cortex. However, the principal components, U-fibers, have been regarded as simple wires to connect adjacent gyri (inter-gyral U-fibers) but have never been thought as indispensable elements of anatomical structures to construct the cortical network. Here, we reported such novel structures made of U-fibers. Seven human cerebral hemispheres were treated with Klingler’s method and subjected to fiber dissection (FD). Additionally, tractography using diffusion spectrum imaging (DSI) was performed. Our FD and DSI tractography succeeded disclosing a new type of U-fibers that was hidden in and ran along the white matter ridge of a gyral convolution (intra-gyral U-fibers). They were distinct from inter-gyral U-fibers which paved sulcal floors. Both intra- and inter-gyral U-fibers converged from various directions into junctional areas of white matter ridges, organizing novel anatomical structures, “pyramid-shape crossings”. U-fibers to form pyramid-shape crossings also render routes for communication between crossings. There were 97 (mean, range 73–148) pyramid-shape crossings per lateral cortical surface. They are key structures to construct the neural network for intricate communications throughout the entire cerebrum. They can be new anatomical landmarks, too, for the segmentation of the cerebral cortex.
Reverse hysteresis? Persistent effects of autonomous demand expansions
Authors: Girardi Daniele , Paternesi Meloni Walter , Stirati Antonella
Published: March 2020

Empirical works documenting highly persistent effects of negative demand shocks (‘hysteresis’) have questioned the prevailing wisdom that potential output is exogenous to aggregate demand fluctuations. We assess whether the effects of positive demand shocks also tend to persist beyond the short run. We estimate the impact of 126 aggregate demand expansions in OECD countries between 1960 and 2015 through local projections, using a dynamic two-way fixed-effects model and a propensity score-based specification. We find that demand expansions exert positive persistent effects on GDP, participation rate and capital stock. Effects on the unemployment rate and productivity are also strong and quite persistent, but evidence regarding their permanence is mixed. The effect on the inflation rate is positive but small and imprecisely estimated, and there is no sign of accelerating inflation. Our results bear relevant implications for existing models of hysteresis and for theories of demand-led growth.
Phenotypic plasticity of two M. oleifera ecotypes from different climatic zones under water stress and re-watering
Authors: Brunetti Cecilia , Gori Antonella , Moura Barbara Baesso , Loreto Francesco , Sebastiani Federico , Giordani Edgardo , Ferrini Francesco
Published: March 2020

Moringa oleifera is a fast-growing hygrophilic tree native to a humid sub-tropical region of India, now widely planted in many regions of the Southern Hemisphere characterized by low soil water availability. The widespread cultivation of this plant worldwide may have led to populations with different physiological and biochemical traits. In this work, the impact of water stress on the physiology and biochemistry of two M. oleifera populations, one from Chaco Paraguayo (PY) and one from Indian Andhra Pradesh (IA) region, was studied in a screenhouse experiment where the water stress treatment was followed by re-watering. Through transcriptome sequencing, 2201 potential genic simple sequence repeats were identified and used to confirm the genetic differentiation of the two populations. Both populations of M. oleifera reduced photosynthesis, water potential, relative water content and growth under drought, compared to control well-watered plants. A complete recovery of photosynthesis after re-watering was observed in both populations, but growth parameters recovered better in PY than in IA plants. During water stress, PY plants accumulated more secondary metabolites, especially β-carotene and phenylpropanoids, than IA plants, but IA plants invested more into xanthophylls and showed a higher de-epoxidation state of xanthophylls cycle that contributed to protect the photosynthetic apparatus. M. oleifera demonstrated a high genetic variability and phenotypic plasticity, which are key factors for adaptation to dry environments. A higher plasticity (e.g. in PY plants adapted to wet environments) will be a useful trait to endure recurrent but brief water stress episodes, whereas long-term investment of resources into secondary metabolism (e.g. in IA plants adapted to drier environments) will be a successful strategy to cope with prolonged periods of drought. This makes M. oleifera an important resource for agro-forestry in a climate change scenario.
Relationship between quality of life and burden of recurrent atrial fibrillation following ablation: CAPCOST multicentre cohort study
Authors: Essebag Vidal , Azizi Zahra , Alipour Pouria , Khaykin Yaariv , Leong-Sit Peter , Sarrazin Jean-Francois , Sturmer Marcio , Morillo Carlos , Terricabras Maria , Amit Guy , Roux Jean Francois , Patterson Sherri , Verma Atul
Published: March 2020

Aims

Atrial fibrillation (AF) significantly impairs patients’ quality of life (QOL). We performed this study to investigate the effect of AF-ablation success and atrial fibrillation burden (AFB) on QOL measures.

Methods and results

Overall, 230 patients with paroxysmal AF refractory to antiarrhythmic drugs were enrolled and underwent ablation in a multicentre, prospective cohort. Electrocardiogram, 48-h Holter, Canadian Cardiovascular Society Severity of Atrial Fibrillation (CCS-SAF), short form-12 (SF-12), and Atrial Fibrillation Effect on Quality of life (AFEQT) scales were used to assess patients. Atrial fibrillation burden was defined as total duration of AF during the month prior to each visit (h/month). The change in AFB was calculated as the difference between the month prior to the 12-month post-ablation and the baseline pre-ablation. The Minimal Clinically Important Difference (MCID) was considered as a 19-point change for AFEQT and 3–5-point change for SF-12 scores. There was significant rise in the AFEQT and SF12 and decrease in CCS-SAF score post-AF ablation; however, the magnitude of these changes was greater in patients without AF recurrence (P < 0.05). The QOL score that best differentiated patients with and without recurrence was AFEQT, while, CCS-SAF was the most specific score. Patients with AFB decrease >19 h/month had significantly greater change in QOL scores. Atrial fibrillation burden < 24 h/month at 12-months post-ablation was associated with significant changes in QOL and CCS-SAF when adjusting for baseline scores and other covariates. These changes were consistent with the MCID of these measures.

Conclusion

Patients experience significant improvements in QOL post-ablation, which correlate with a decrease in AFB despite ongoing brief recurrences of AF.

Clinical Trial Registration

NCT01562912. https://www.clinicaltrials.gov/ct2/show/NCT01562912? term=capcost&rank=1
Choice of statistical model in observational studies of ART
Authors: Dodge Laura E , Farland Leslie V , Correia Katharine F B , Missmer Stacey A , Seidler Emily A , Wilkinson Jack , Modest Anna M , Hacker Michele R
Published: March 2020

Analyzing data on ART presents unique and sometimes complicated challenges related to choosing the unit(s) of analysis and the statistical model. In this commentary, we provide examples of how these challenges arise and guidance for overcoming them. We discuss the implications of different ways to count treatment cycles, considering the perspectives of research questions, data management and analysis and patient counseling. We present the advantages and disadvantages of different statistical models, and finally, we discuss the definition and calculation of the cumulative incidence of live birth, which is a key outcome of research on ART.
Convergence in Hölder norms with applications to Monte Carlo methods in infinite dimensions
Authors: Cox Sonja , Hutzenthaler Martin , Jentzen Arnulf , van Neerven Jan , Welti Timo
Published: March 2020

We show that if a sequence of piecewise affine linear processes converges in the strong sense with a positive rate to a stochastic process that is strongly Hölder continuous in time, then this sequence converges in the strong sense even with respect to much stronger Hölder norms and the convergence rate is essentially reduced by the Hölder exponent. Our first application hereof establishes pathwise convergence rates for spectral Galerkin approximations of stochastic partial differential equations. Our second application derives strong convergence rates of multilevel Monte Carlo approximations of expectations of Banach-space-valued stochastic processes.
Clinical Outcomes in 55 Patients With Severe Acute Respiratory Syndrome Coronavirus 2 Who Were Asymptomatic at Hospital Admission in Shenzhen, China
Authors: Wang Yanrong , Liu Yingxia , Liu Lei , Wang Xianfeng , Luo Nijuan , Li Ling
Published: March 2020

An epidemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has spread unexpectedly in Wuhan, Hubei Province, China, since December 2019. There are few reports about asymptomatic contacts of infected patients identified as positive for SARS-CoV-2 through screening. We studied the epidemiological and clinical outcomes in 55 asymptomatic carriers who were laboratory confirmed to be positive for SARS-CoV-2 through nucleic acid testing of pharyngeal swab samples. The asymptomatic carriers seldom occurred among young people (aged 18–29 years) who had close contact with infected family members. In the majority of patients, the outcome was mild or ordinary 2019 novel coronavirus disease during hospitalization.
Effect of porcine reproductive and respiratory syndrome virus infection and soy isoflavone supplementation on carcass cutability and meat quality of pigs
Authors: Bryan Erin E , Smith Brooke N , Honegger Lauren T , Boler Dustin D , Dilger Ryan N , Dilger Anna C
Published: March 2020

The objective was to evaluate the effects of porcine reproductive and respiratory syndrome virus (PRRSV) infection and dietary soy isoflavone (ISF) supplementation on carcass cutability and meat quality of commercial pigs. Barrows (21 d of age) were randomly allotted to experimental treatments that were maintained throughout the study: noninfected pigs received an ISF-devoid control diet (CON, n = 22) and infected pigs received either the control diet (PRRSV–CON, n = 20) or that supplemented with total ISF in excess of 1,500 mg/kg (PRRSV–ISF, n = 25). Pigs were penned by treatment, with six pigs within a pen. Following a 7-d adaptation, weanling pigs were inoculated once intranasally with either a sham-control (phosphate buffered saline [PBS]) or live PRRSV (1 × 105 tissue culture infective dose [TCID]50/mL, strain NADC20). Pigs were maintained on experimental diets for 166 d after inoculation and then slaughtered (192 or 194 d of age; approximately 120 kg body weight [BW]). At 1-d postmortem, left sides were separated between the 10th and 11th rib for the determination of loin eye area (LEA), backfat (BF) thickness, and loin quality (ultimate pH, instrumental color, drip loss, visual color, marbling, and firmness). Loin chops were aged 14 d postmortem prior to Warner–Bratzler shear force (WBSF) determination. Belly width, length, thickness, and flop distance were determined. Data were analyzed as a one-way ANOVA with pig as the experimental unit. Carcass yield, LEA, BF, and estimated lean percentage did not differ (P > 0.26) among treatments. Loins from CON pigs had increased ultimate pH (P = 0.01), reduced L* scores (P = 0.005) coupled with darker visual color scores (P = 0.004), were firmer (P < 0.0001), and exhibited reduced drip loss (P = 0.01) compared with PRRSV–CON and PRRSV–ISF pigs. However, WBSF did not differ (P = 0.51) among treatments after 14 d of aging. Bellies from CON pigs were more firm compared with bellies from PRRSV–CON and ISF pigs (P < 0.01). These data suggest PRRSV infection did not alter carcass characteristics but may have marginally reduced loin and belly quality. Supplementation with dietary soy isoflavones did nothing to mitigate the detrimental effects of PRRSV infection.
The Practice of First Aid for Burn Injuries Among the Population of East Coast of Peninsular Malaysia for 2012–2016
Authors: Seow Sul Na , Halim Ahmad Sukari , Wan Sulaiman Wan Azman , Mat Saad Arman Zaharil , Mat Johar Siti Fatimah Noor
Published: March 2020

Burns are a devastating public health problem that result in 10 million disability-adjusted life-years lost in low- and middle-income countries. Adequate first aid for burn injuries reduces morbidity and mortality. The rate of proper first aid practices in other countries is 12% to 22%.1,2 A 5-year retrospective audit was performed on the database of the Burn Unit in Hospital Universiti Sains Malaysia for 2012–2016; this involved 485 patients from the east coast of Malaysia. The mean age of the patients is 17.3 years old. The audit on first aid practices for burn injury showed poor practice. Out of 485 burned patients, 261 patients (53.8%) claimed that they practiced first aid. However, only 24 out of 485 patients (5%) practiced the correct first aid technique where they run their burn wound under cool water for more than 20 minutes. Two hundred and twenty-two patients had not received any first aid. Two patients did not respond to the question on the first aid usage after burn injury. The mean age of patients who practiced first aid was 15.6 years old. Out of the 261 patients who practiced first aid, 167 (64%) run their wound under tap water for different durations. Others practiced traditional remedies such as the application of “Minyak Gamat” (6.5%), soy sauce (5.5%), other ointments (3.6%), milk (1.8%), and eggs (0.7%), as well as honey, butter, and cooking oil (0.4% each). First aid practices for burn injuries in the population of east coast Malaysia are still inadequate. The knowledge and awareness of school children and the general Malaysian population must be enhanced.