bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractRed 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

Abstract
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

Abstract
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.
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

AbstractCommunication 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

Abstract

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

Abstract

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

Abstract

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

Abstract
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

Abstract
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

AbstractEmpirical 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.