bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving nutrients in cattle manure by converting it into biogas sludge and compost
Authors: Pertiwiningrum A , Wuri M A , Setiyana D , Budiarto R , Koranto C A D , Gozan M 
Published: December 2019

Abstract
In recent years livestock sector in Indonesia grows rapidly. As a consequence, organic waste will increase and cause environmental pollution and health problem if it’s not managed. The recycling of cattle manure for agriculture purpose can waste problem. Previous studies have suggested that the use of organic waste as bio-fertilizer is good for soil. The objective of this study was to investigate the difference between untreated and treated cattle manure on their chemical properties, especially nutrient elements. Untreated cattle manure, treated cattle manure by anaerobic digesting and composting were analyzed their chemical properties such as pH value, water and organic content, N-content, P2O5, and K2O concentration. The pH value of fresh cattle manure, buried cattle manure, biogas sludge, and compost were 6.8; 5.4; 6.8; and 6.9 respectively. The C organic content in treated cattle manure decreased as compared to untreated cattle manure. On the other hand, N-content, P2O5, and K2O concentration of treated manure were higher than untreated manure. The highest N-content, P2O5, and K2O concentration were performed by compost from cattle manure.
Application of choice modelling on mangrove forest valuation in West Lombok, Indonesia
Authors: Saptutyningsih Endah , Diswandi Diswandi 
Published: December 2019

Abstract
A mangrove forest in West Nusa Tenggara is one of tourist destination that attracts many local and domestic tourists thanks to their natural beauty. In addition to its natural beauty, this place is also used as mangrove conservation and education-based tourism. However, there were various critical statuses in West Nusa Tenggara which damaged. The critical status is also spread in various regions on the island of Lombok, among others in the area of West Lombok Regency. The loss of mangrove forest occurs was because mangrove forests often are converted in order to generate directly marketable products, such as aquaculture that might lead to massive economic losses for the surrounding community. To make efficient resource allocation choices, decision makers need a framework to estimate the non-use values that might be held by the community for mangrove forest conservation. Non-market valuation techniques can be used for this purpose, by applying a choice modelling (CM), appears to hold some promise because it can be used to model complex situations and to frame choices consistent with ‘real life’ choices. In this paper, a CM method applied for assessing the values that the community and tourists hold for mangrove forest conservation in West Lombok, Indonesia.
Environmental site engineering and integrated bio-cycles management for rehabilitation of degraded tin mining land in tropical ecosystem
Authors: Agus Cahyono , Wulandari Dewi , Cahyanti Pita AB , Bantara Idi , Hutahaean Benny P , Lestari Tri 
Published: December 2019

Abstract
Indonesia is known as the emerald of equator that has high values of natural resources although it also has a huge disaster risk. It is because Indonesia is located in the strategic areas, namely: (i) the equator, (ii) ring of fire, and (iii) earth plates of Eurasian, Pacific & Indo Australia. Mining activities of natural resources in tropical region exposes carbon and heavy metals and thus are the main cause of severe local, regional, and global environmental damage. The change of national economic development from extraction to empowerment of natural resource will facilitate shifting paradigm from red & green economic to blue economic concept that more smart, global, focus, and futuristic. Site engineering on critically degraded land through land preparation, soil amendment & biofertilizer could facilitate a better rehabilitation of mining land and have added value on environment, economy, sociocultural and health aspect. Synergism to genetic engineering using fast-growing species (indigenous and exotic) will improve success rate of land rehabilitation. An integrated bio-cycle management for managing land resources (i.e., soil, water, mineral, air, and microclimate) and biological resources (i.e., fauna, flora, and human) is an important strategy for sustainable productivity in protective tropical ecosystems.
Community behavior study in domestic waste management around the Ciapus River, Babakan Village, Bogor Regency, West Java
Authors: Salampessy M L , Febryano I G 
Published: December 2019

Abstract
Community behaviour is one of the dominant factors affecting the sustainability of the watershed. This study aims to identify community behaviour in the management of domestic waste around the Ciapus river in the Cisadane watershed. This research was conducted in the community in Babakan Village. The research method used is a case study. Collecting data with questionnaires, in-depth interviews and FGDs. Determination of respondents with purposive sampling method for 60 people who live around the river. The collected data were analysed and presented descriptively. The results showed that community behavior in managing waste showed that the community had not carried out good waste management as 100% did not separate wet and dry waste and 100% did not separate organic and inorganic waste, 100% did not have separate trash bins, 100% did not use waste plastic, 80% dispose of domestic waste into the river and 20% still dispose of waste in vacant land, 50% still often do garbage burning, 100% are not pleased reprimand people who dispose of garbage into the river, 80% do not know the government regulations that regulate certain distance limits from rivers that are not permitted to be used, 80% do not know that settlements around the river require special permits and 100% do not know whether there is a ban or not from the village government for settlement or economic activities around this river. This behavior has implications for the disruption of the river’s sustainability function.
Impact of land use and socio-economic changes in water catchment area on total suspended solid (TSS) in Lake Toba
Authors: Harianja A H , Suoth A E , Nazir E , Saragih G S , Fauzi R , Hidayat M Y 
Published: December 2019

Abstract
Changes of socio-economic and land use in the water catchment area are factors that affect the water quality of a lake. This study quantified the impact of socio-economic factors and the dynamics of land covers of Lake Toba water catchment area on the total suspended solid (TSS) parameter, one of the parameters in water quality indicators. Statistical analysis was run by using multiple linear regressions. Parameters observed were TSS, socioeconomic related data and land use in Samosir, Tobasa, Simalungun, Dairi, Humbang Hasundutan and North Tapanuli Regencies in 2008, 2012 and 2016. The results indicated that the water quality of Lake Toba was slightly polluted in 2016 and in 2017. Based on the regression analysis, it was found that some factors significantly affected the concentration of TSS, namely shrubland and dryland farming at 99% confidence level; the number of populations, Location Quotient (LQ) for dry land paddy field and soybean production at 95% confidence level; and settlement land area, geographic population density, LQ for rice and corn production at 90% confidence level. Managing shrubland through a land rehabilitation program and encouraging a rotational cropping system are recommended strategies to manage the increasing TSS in the Lake Toba.
Assigned value determination by expert laboratory consensus on heavy metals proficiency testing of environmental laboratory 2018
Authors: Rahmani R , Masitoh S , Nasution E L , Healthy S 
Published: December 2019

AbstractDetermination of assigned values is an important stage in proficiency testing schemes in accordance with SNI / ISO 17043: 2010. Assigned value is a reference for determining the laboratory performance status in proficiency test participants. One alternative in determining Assigned value is through expert laboratory consensus. This method has an advantage over the reference value method, namely when there is no certificate reference material (CRM) that matches the proficiency test commodity or the corresponding CRM value is not in place. This study was aimed at determining the assigned value of laboratory proficiency testing of heavy metal parameters by employing the expert laboratory consensus method. In this study, the expert laboratory tested were 20 laboratories included the one in the environmental metrology road map. The laboratories have been accredited according to ISO / IEC 17025. Statistical calculations through Algorithm A, and iteration technique were implemented in this procedure. This will make it easier to determine the assigned value because it does not need to be through the reference value calibration of the CRM value. It was found out that the assigned value in mg/L for each metal, i.e Zn, Fe, Mn and Cd were 0.08; 0.4; 0.3 and 0.06 respectively. It was also shown that the assigned value derived from this expert laboratory consensus were not significantly different from the target value, except for Zn metal that differed from the target by 0.01 mg/L. However, it is important to keep reviewing the competence of the expert laboratory on a regular basis to ensure the validity of the values produced.
Regulatory evaluation of waste management institutions in Yogyakarta, Sleman, and Bantul Metropolitan Areas
Authors: Aryantie M H , Hidayat M Y 
Published: December 2019

Abstract
Waste management of single-use plastic bags is a common problem in metropolitan areas, including Yogyakarta, Sleman, and Bantul. It urges the needs to evaluate the existing regulation that decide the most suitable institution to overcome this issue. This research used mixed method. Regulations related to Law No. 18/2008 on Waste Management were inventoried and analysed for determining institutional related keywords. The results of content analysis are related to the volume of waste at Integrated Waste Treatment Area (IWTA) and community participation’s level. Yogyakarta does not instruct specific institutions which are in charge in sorting, collecting, and transporting waste to Temporary Trash Disposal Sites. In contrast, Sleman specifies the institutions, yet it does not include the obligation of the community level. Meanwhile, Bantul clearly regulates institutions at the community level, authority, and budget. Based on the data obtained from Piyungan IWTA, Yogyakarta is the largest contributor of waste (51.02%), followed by Sleman (29.10%) and Bantul (12.79%). However, Bantul has the highest community participation in plastic waste management (93.9%), followed by Yogyakarta (89.7%) and Sleman (88.0%). It is evident that region with the absence of waste management institution tend to generate greater amount of waste, and lower level of community participation.
Comparative study of polymer-based nanocomposites microwave absorption performance in X–band
Authors: Santhosi B V S R N , Ramji K , Rao N B R Mohan , Naidu M K 
Published: December 2019

Abstract
The present work focused on electromagnetic (EM) absorption performance comparison of different polymer nanocomposite structures. Synthesis and fabrication of polymer nanocomposite composed of graphene, polyurethane (PU), epoxy was done using in situ polymerization and resin transfer moulding respectively. The effect of polymer on EM properties of composite was carried out using waveguide measurement technique in X-band. Reflection Loss (RL) and shielding effectiveness (SE) were measured for various nanocomposites using EM wave theory. From the results it is observed that 2.5 wt% of PU/epoxy graphene nanocomposite has shown RL value −35 dB at 12.1 GHz and SE value of −45 dB.
Effect of co-monomer on the adhesive performance of PP-g-MAH between cast polypropylene film and aluminum foil
Authors: Shen Chaoyuan , Xu Shiai 
Published: December 2019

Abstract
Three functionalized polypropylenes (PPs) were successfully prepared for use as the inner adhesive layer of aluminum/polymer laminated film by melt grafting of maleic anhydride (MAH) on PP with styrene (St), diallyl phthalate (DAP) and triallyl isocyanurate (TAIC) as co-monomers, respectively. The effects of these co-monomers (St, DAP and TAIC) on the grafting degree of MAH, gel content, thermal property and adhesive performance of MAH grafted PP (PP-g-MAH) were investigated. The results show that the T-peeling and heat-sealing strengths of TAIC-assisted PP-g-MAH (PP-g-MAH/TAIC) are 28.6 and 70.4 N /15 mm, which are increased by 33.6% and 20.8% compared to DAP-assisted PP-g-MAH (PP-g-MAH/DAP), and by 142.4% and 81.0% compared to St-assisted PP-g-MAH (PP-g-MAH/St), respectively. The grafting degree of MAH reaches a maximum of 2.3 wt% in PP-g-MAH/TAIC, which leads to a higher crystallization temperature than PP-g-MAH/DAP and PP-g-MAH/St. PP-g-MAH/TAIC also has better thermal stability than the other two functionalized PPs, as TAIC can effectively reduce PP chain scission and promote the formation of a cross-linked structure during the melt grafting.
Sympatric wren-warblers partition acoustic signal space and song perch height
Authors: Chitnis Shivam S , Rajan Samyuktha , Krishnan Anand 
Published: December 2019

AbstractAnimals employing acoustic signals, such as birds, must effectively communicate over both background noise and potentially attenuating objects in the environment. To surmount these obstacles, animals evolve species-specific acoustic signals that do not overlap with sources of interference (such as songs of close relatives), and issue these songs from locations that maximize transmission. In multispecies assemblages of birds, the acoustic resource may thus be interspecifically partitioned along multiple axes, including song perch height and signal space. However, very few such studies have focused on open habitats, where differences in sound transmission patterns and limited availability of song perches may drive competition across multiple axes within signal space. Here, we demonstrate acoustic signal space partitioning in four sympatric species of wren-warbler (Cisticolidae, Prinia), in an Indian dry deciduous scrub-grassland habitat. We found that the breeding songs of the four species partition acoustic signal space, resulting in interspecific community organization. Within each species’ signal space, we uncovered different intraspecific patterns in note diversity. Two species partition intraspecific signal space into multiple note types, whereas the other two vary note repetition rate to different extents. Finally, we found that the four species also partition song perch heights, thus exhibiting acoustic niche separation along multiple axes. We hypothesize that divergent song perch heights may be driven by competition for higher singing perches or other ecological factors rather than signal propagation. Acoustic signal partitioning along multiple axes may therefore arise from a combination of diverse ecological processes.
Deep learning-based clustering approaches for bioinformatics
Authors: Karim Md Rezaul , Beyan Oya , Zappa Achille , Costa Ivan G , Rebholz-Schuhmann Dietrich , Cochez Michael , Decker Stefan 
Published: December 2019

AbstractClustering is central to many data-driven bioinformatics research and serves a powerful computational method. In particular, clustering helps at analyzing unstructured and high-dimensional data in the form of sequences, expressions, texts and images. Further, clustering is used to gain insights into biological processes in the genomics level, e.g. clustering of gene expressions provides insights on the natural structure inherent in the data, understanding gene functions, cellular processes, subtypes of cells and understanding gene regulations. Subsequently, clustering approaches, including hierarchical, centroid-based, distribution-based, density-based and self-organizing maps, have long been studied and used in classical machine learning settings. In contrast, deep learning (DL)-based representation and feature learning for clustering have not been reviewed and employed extensively. Since the quality of clustering is not only dependent on the distribution of data points but also on the learned representation, deep neural networks can be effective means to transform mappings from a high-dimensional data space into a lower-dimensional feature space, leading to improved clustering results. In this paper, we review state-of-the-art DL-based approaches for cluster analysis that are based on representation learning, which we hope to be useful, particularly for bioinformatics research. Further, we explore in detail the training procedures of DL-based clustering algorithms, point out different clustering quality metrics and evaluate several DL-based approaches on three bioinformatics use cases, including bioimaging, cancer genomics and biomedical text mining. We believe this review and the evaluation results will provide valuable insights and serve a starting point for researchers wanting to apply DL-based unsupervised methods to solve emerging bioinformatics research problems.
LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data
Authors: Tosi Sébastien , Bardia Lídia , Filgueira Maria Jose , Calon Alexandre , Colombelli Julien 
Published: December 2019

Abstract

Summary
Open source software such as ImageJ and CellProfiler greatly simplified the quantitative analysis of microscopy images but their applicability is limited by the size, dimensionality and complexity of the images under study. In contrast, software optimized for the needs of specific research projects can overcome these limitations, but they may be harder to find, set up and customize to different needs. Overall, the analysis of large, complex, microscopy images is hence still a critical bottleneck for many Life Scientists. We introduce LOBSTER (Little Objects Segmentation and Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images exceeding workstation main memory. LOBSTER comes with a starting set of over 75 sample image analysis workflows and associated images stemming from state-of-the-art image-based research projects.

Availability and implementation
LOBSTER requires MATLAB (version ≥ 2015a), MATLAB Image processing toolbox, and MATLAB statistics and machine learning toolbox. Code source, online tutorials, video demonstrations, documentation and sample images are freely available from: https://sebastients.github.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation
Authors: Antonazzo Giulia , Urbano Jose M , Marygold Steven J , Millburn Gillian H , Brown Nicholas H 
Published: December 2019

Abstract
Brief summaries describing the function of each gene’s product(s) are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. However, manually writing such summaries, even for a single species, is a daunting task; for example, the Drosophila melanogaster genome contains almost 14 000 protein-coding genes. One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently. Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function. Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene. We e-mailed these researchers to ask them to draft a brief summary of the main function(s) of the gene’s product, which we edited for consistency to produce a ‘gene snapshot’. This approach yielded 1800 gene snapshot submissions within a 3-month period. We discuss the general utility of this strategy for other databases that capture data from the research literature.
Database URL: https://flybase.org/
Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes
Authors: Ocampo Daza Daniel , Haitina Tatjana 
Published: December 2019

Abstract
Glycosaminoglycans are sulfated polysaccharide molecules, essential for many biological processes. The 6-O sulfation of glycosaminoglycans is carried out by carbohydrate 6-O sulfotransferases (C6OSTs), previously named Gal/GalNAc/GlcNAc 6-O sulfotransferases. Here, for the first time, we present a detailed phylogenetic reconstruction, analysis of gene synteny conservation and propose an evolutionary scenario for the C6OST family in major vertebrate groups, including mammals, birds, nonavian reptiles, amphibians, lobe-finned fishes, ray-finned fishes, cartilaginous fishes, and jawless vertebrates.
The C6OST gene expansion likely started early in the chordate lineage, giving rise to four ancestral genes after the divergence of tunicates and before the emergence of extant vertebrates. The two rounds of whole-genome duplication in early vertebrate evolution (1R/2R) only contributed two additional C6OST subtype genes, increasing the vertebrate repertoire from four genes to six, divided into two branches. The first branch includes CHST1 and CHST3 as well as a previously unrecognized subtype, CHST16 that was lost in amniotes. The second branch includes CHST2, CHST7, and CHST5. Subsequently, local duplications of CHST5 gave rise to CHST4 in the ancestor of tetrapods, and to CHST6 in the ancestor of primates.
The teleost-specific gene duplicates were identified for CHST1, CHST2, and CHST3 and are result of whole-genome duplication (3R) in the teleost lineage. We could also detect multiple, more recent lineage-specific duplicates. Thus, the vertebrate repertoire of C6OST genes has been shaped by gene duplications and gene losses at several stages of vertebrate evolution, with implications for the evolution of skeleton, nervous system, and cell–cell interactions.
Does Sexual Orientation Relate to Health and Well-Being? Analysis of Adults 50+ Years of Age
Authors: Nelson Christi L , Andel Ross 
Published: December 2019

Abstract

Background and Objectives
Based on the Minority Stress Theory, this article examines the associations between sexual orientation and self-reported measures of physical, mental, and cognitive health, as well as health risk behaviors.

Research Design and Methods
The analytical sample included members of the 2016 wave of the Health and Retirement Study aged 50+ years. Binary and ordered logistic regressions were conducted to assess whether being a sexual minority was associated with poorer self-rated physical, mental, and cognitive health, as well as being more likely to engage in health risk behaviors.

Results
In analyses using overall and propensity-matched samples, lesbian, gay, and bisexual (LGB) participants were about twice as likely to report ever having depression as their heterosexual counterparts but were also more likely to report better self-rated health. The LGB group was more likely to report ever having smoked but were not significantly different in any of the other health risk behaviors.

Discussion and Implications
LGB individuals appear to be at greater risk of ever experiencing depression than heterosexual individuals but, at the same time, report better physical health. This may suggest a tendency for resilience. Differences in health risk behavior may also exist. Mental health and other medical professionals should receive special training to better understand the unique problems of LGB individuals.