bluuebunny/crossref_metadata_2025 huggingface dataset:
Determine alternatives environmental sustainability of bauxite downstream industry management through integration MICMAC - ANP method: a case study of Ketapang Industrial Area, Ketapang Regency, West Kalimantan Province
Authors: Hendrik  , Fauzi A , Widiatmaka  , Suryaningtyas D T , Firdiyono F
Published: December 2022

Red mud industrial cluster site is associated with increased risk of dam failure and there is an urgent need to address the environmental problem caused by the hazardous and toxic waste of red mud in alumina industry. The objective of this study was to determine the alternatives waste management of Ketapang Industrial Area by integrating the MICMAC-ANP method. The data source is from forum group discussion (FGD) and an in-depth interview with experts. The results of the study using the MICMAC showed that the relay variables were human resources, recycling technology, and raw material guarantee. Furthermore, integrated MICMAC-ANP method showed that the agreed-upon solution for environmental management is to form a partnership among companies, Ketapang industrial management, and regional-owned enterprises, with the regional-owned enterprise having the largest share of the product produced from economic waste. This can be seen from the weighting of each element that indicates the regional-owned enterprise element has the greatest weight, which is 0.4. Meanwhile, waste disposal criterion is quite important (0.44) in determining alternative environmental sustainability management of downstream bauxite industry. The primary consideration to achieve environmental sustainability management of the downstream bauxite industry are CSR, Labor, Tax, PPM, and transportation, which have a weight that is relatively similar (0.2). Regionally owned enterprises (0.4) play the most important roles in environmental management of the sustainable bauxite mining downstream industry related to economic waste management (the use of red mud).
Evaluation of the Implementation of Mangrove Thematic Environmental Education in Indramayu, West Java
Authors: Rosviani L , Kusmana C , Rachmawati E , Gunawan H
Published: December 2022

Mangroves are one of the natural habitats that we must preserve. One of the damage to mangrove forests is caused by the lack of knowledge and awareness of the community. Efforts to preserve through this knowledge and awareness can be given to the next generation from an early age. One of the conservation efforts is the existence of mangrove thematic environmental education spread from the west to the east of Indramayu. This study aim to identify the general conditions of each mangrove school and to evaluate the implementation of Mangrove Thematic Environment Education from students knowledge, attitudes, and behaviors. The analysis to be assessed is the influence of learning on knowledge, attitudes, behavior, and the influence of infrastructure on student attitudes and behavior. T-values Results Calculate learning variables with knowledge (10,707), attitudes (6,072), and behavior (3,338). While the test results for aspects of facilities and infrastructure did not have a significant influence on student attitudes and behavior. The facilities and infrastructure contained in the school have not fully supported the activities of students to study mangroves. Evaluation related to mangrove Thematic Living Environment Education, namely the need to improve learning methods and facilities externally so that students are more familiar with mangroves.
The dynamics of land cover in conservation areas using cloud computing platform: Cases in Gunung Merbabu National Park
Authors: Ardiaristo A , Prasetyo L B , Syaufina L , Kosmaryandi N
Published: December 2022

It is critical to consider all aspects of conservation areas, inside and outside, when maintaining them. Land cover dynamics in conservation areas mostly have not yet been considered in conservation area management practices, both geographically and temporally. The advancement of technology with cloud computing can speed up and simplify the acquisition of data and information on the dynamics of land cover changes. This study aimed to analyze the dynamics of land cover change in the Gunung Merbabu National Park (GMbNP) area from 1995 to the present. The method for determining land cover change dynamics was used and assessed by creating a code for land cover classification using the random forest classification algorithm on the Google Earth Engine (GEE) platform. The results showed that from 1995 to 2020, pine forests in GMbNP area decreased by 575.765 ha from the previous 1427,961 ha in 1995. The dynamics of land cover changes outside the area need to be the concern of area managers because agricultural land and built-up land are increasing of 5.42% and 113.2%, significantly beyond the area. Referring to those dynamic conditions, it should be a concern in planning and policy-making conservation management.
Comparison of municipal solid waste landfill management in Depok City and Klaten Regency
Authors: Ratnawati B , Yani M , Suprihatin S , Hardjomidjojo H , Cholik TN , Ardiyani Q T
Published: December 2022

Management at a Municipal Solid Waste Landfill (MSWLF) is necessary to save the environment from pollution. MSWLF, which previously used a sanitary landfill system, has changed to an open dumping system. An open dumping system can cause decay to the environment. This study aims to compare municipal solid waste disposal site management in two different regions. The research location is Depok City and Klaten Regency. This research was carried out from February to April 2022 with data collection techniques carried out by interview techniques, field observations, and literature studies. The analysis technique was carried out using descriptive analysis to describe the current management conditions of the two regions. In addition, it uses Strength, Weakness, Opportunity, Threats (SWOT) analysis to obtain recommendations for management improvements that can apply in the region. The Cipayung MSWF which was originally built with a sanitary landfill system has turned into open dumping, while the Troketon MSWLF is currently still able to process incoming waste using a controlled landfill system. The difference in the management of the two MSWLFs is influenced by financing, operational, and institutional aspects.
Current status of household e-waste management in Jakarta, Indonesia
Authors: Soesanto H , Maarif M S , Anwar S , Yurianto Y
Published: December 2022

Managing electronic waste or e-waste in Jakarta Province, Indonesia, is essential to support sustainable development goals (SDGs). E-waste contains toxic materials and is harmful to the environment while having the potential for a circular economy if appropriately managed. This study aims to analyze electronic waste management, formally originating from households in Jakarta Province, from the aspects of the e-waste collection mechanism, the type of e-waste, the amount of e-waste, and the flow of e-waste information using a descriptive method. The research findings are that the Jakarta Regional Government collects e-waste through three mechanisms: e-waste direct pickup (35.5%), e-waste drop box (0.6%), and e-waste temporary garbage collection (63.9%). The total amount of e-waste managed formally was 33,289 kg in 2021. In practice, there are five types of e-waste: television, lights, batteries, printer cartridges, and other e-waste. The effectiveness of the e-waste collection process needs improving. The amount of e-waste collected can be increased. One of the robust recommendations for improving e-waste management in Jakarta is integrating innovative digital platform-based technology and multi-actor collaboration. This research supports preliminary data and information on the circular economy’s potential and the formulation of specific regulations on e-waste in Indonesia.
Stakeholders analysis in agroecotourism development at Panjalu Ciamis
Authors: Saputro K E A , Hasim  , Karlinasari L , Beik I S
Published: December 2022

The Agroecotourism Village concept is an alternative for sustainable village development. This concept integrates economic growth, rural community involvement, and environmental sustainability. The synergy of stakeholders involved in development is necessary to support agroecotourism village development. This research aimed to identify the stakeholders involved in agro-ecotourism development at Panjalu Village, Ciamis Regency, West Java, Indonesia. Data research was collected through literature, observation, and key informant interviews. The data was analyzed quantitatively descriptive using the stakeholder’s analysis method. There are 37 stakeholders identified involved in agroecotourism development at Panjalu. The stakeholders studied are divided into five categories: central government, local government, community, business, and academics. Six key players are found in this result study: Ciamis Tourism Office, Ciamis Agricultural and Food Security Office, Panjalu Village Government, Panjalu Village Owned Enterprises, Citanduy River Regional Hall, and West Java Natural Resources Conservation Center. Each key player has a different form of relationship with other stakeholders depending on the role and authority of the stakeholders in the development of agroecotourism at Panjalu consists of communication, coordination, and cooperation.
Key elements structure in mangrove ecotourism management of Peropa’ea Protected Forest in North Buton Regency
Authors: Asniar  , Kusmana C , Arifin H S , Kuncahyo B
Published: December 2022

Mangrove ecosystem in Peropa’ea protected forest area has an aesthetic landscape that has a potential to be developed as ecotourism. The development of ecotourism in the protected forest area of Peropa’ea as a utilization effort of environmental services is a better strategy because it may reduce pressure on mangrove forest resources and bring socio-economic benefits to the community and area. The Peropa’ea Protected Forest Management Unit (KPHL) has prepared a service business plan environment in the form of “Banda Kawasa” mangrove ecotourism for the period 2015 to 2025. Some steps needed to be studied such as key elements in the development and management of mangrove ecotourism. Therefore, the purpose of this study was to identify elements and sub-elements in the development and management of mangrove ecotourism. The method used in this research was Interpretative Structural Modelling (ISM) with an element of related institutions, constraints, objectives, and priority programs in the development and management of mangrove ecotourism. The results indicated that the Provincial Forestry Office and Forest Management Unit (KPHL) Peropa’ea were the institutional key player in the development and management of mangrove ecotourism. Limited funding and supporting infrastructure for mangrove ecotourism was the main management constraint, and the program priority was to develop an integrated and sustainable mangrove ecotourism management plan. Therefore, it is recommended to improve the coordination among related institutions to develop and maintain the sustainability of mangrove ecotourism in this area.
Water quality status based on Pollution Index and Water Quality Index of Ciliwung River, DKI Jakarta Province
Authors: Aprilia M , Effendi H , Hariyadi S
Published: December 2022

The Ciliwung River receives loads from various sources of pollution along the border, both from agricultural waste, industrial waste, and domestic waste. The various wastes that enter the river cause a decrease in water quality. This study aims to determine the water quality status of the Ciliwung River in the Jakarta segment based on the Pollution Index (PI) and the Pesce-Wunderlin Water Quality Index (WQI). Monitoring on Ciliwung River water quality in the Jakarta segment was carried out in February-September 2021 at 18 observation stations. Most of the parameter tested for the water quality of the Ciliwung River in Jakarta does not meet the river water quality standards of class II based on Attachment VI of Government Regulation of the Republic of Indonesia Number 22 of 2021, such as total suspended solid, total dissolved solid, dissolved oxygen, ammonia, nitrite, total nitrogen, biochemical oxygen demand, chemical oxygen demand, total coliforms, and fecal coliforms. The water quality status of the Ciliwung River in the Jakarta segment is in medium to bad condition based on the Pesce-Wunderlin Water Quality Index and classified as moderately to extremely polluted based on the Pollution Index.
Monitoring thirty years of LULC change (1990 - 2021) from Landsat images of JATABEK, Indonesia
Authors: Ambarwulan W , Syetiawan A , Rahadiati A , Rahmawan G A
Published: December 2022

Monitoring land use/land cover (LULC) change is urgently needed in a sustainable environmental management process. Many management aspects require accurate information about past, present, and future projections to develop sustainable management strategies. Jakarta and its surrounding cities (Tangerang and Bekasi) called JATABEK is one area frequently flooded. This research aimed to derive the LULC map and its change by integrating remote sensing and Geographic Information Systems. Multi-year Landsat images conducted mapping using machine learning and Random Forest (RF) classifier processed through Google Earth Engine (GEE). The results showed that the two main classes that experienced drastic changes in JATABEK were built-up land and paddy fields which increased and decreased by 244% and 69%, respectively. In addition, RF and GEE are very robust in complex areas such as JATABEK. This is proved by the overall accuracy and Kappa coefficient above 80%. Planners and managers used a holistic picture of LULC in JATABEK to establish flood management strategies.
Identification method of vegetation cover changes derived from mosaic Landsat-8 Data: Case Study Sumatera, Kalimantan, and Java Island
Authors: Kartika T , Kushardono D , Setiawan Y , Ibrahim A , Kustiyo  , Sutanto A , Noviar H , Khomarudin M R , Carolita I , Tosiani A , Ubay M S N , Taufik M , Al-Khudri A
Published: December 2022

Vegetation cover changes information is essential in forest and plantation management. Low-resolution remote sensing in mosaic data format has been widely used for vegetation cover change mapping on a global scale by implementing the threshold method. However, the problem with this method in Landsat-8 - which has a higher resolution - is that it is challenging to obtain the appropriate value due to the diversity of Indonesia’s land ecosystems. This research aimed to determine the threshold value for detecting devegetation and revegetation to identify vegetation cover changes rapidly. This research used Oldeman Climate Classification with zone A and B as the references. The threshold values to classify vegetation cover changes were derived from the delta Normalized Burn Ratio (dNBR) of Analysis Ready Data (ARD) Landsat-8 - taken in Sumatera as the pilot area. Moreover, the proposed method was also applied to Kalimantan and Java Islands, with have identical climates. The results indicated that dNBR threshold for devegetation was more than 0.376, while revegetation was less than -0.269. These results were evaluated using high-resolution satellite imagery and ground-truth information. It concluded that Kalimantan Island obtained good results in mapping vegetation cover change with the threshold; however, Java Island required further adjustment for the threshold.
Modelling and mapping forest structure from aerial LiDAR data
Authors: Ruiz L A , Crespo-Peremarch P
Published: December 2022

A methodology for estimating forest structure and fuel variables from airborne LiDAR data is presented, based on the following steps: (1) data pre-treatment to obtain the digital terrain model and the canopy height model; (2) extraction of features or attributes from the LiDAR data for each sampling plot; (3) generation of prediction models for structure variables at plot level; and (4) its extension for the generation of maps of forest variables in larger areas. The methodology was applied to a study area of 4,100 ha in the municipality of Cuenca, where a LiDAR flight was carried out with a nominal density of 4 points/m2. For the generation of the prediction models, stepwise multiple regression was used, taking as reference measurements made in 110 field plots, obtaining values of R2 greater than 0.9 for total biomass, volume and fraction of canopy cover, and above 0.86 for basal area, stem biomass and root biomass. The generated models were applied to the entire work area for the creation of maps of forest structure variables, and the entire procedure was integrated into a specific software application.
Modelling spatial pattern of population distribution in 50 largest cities in the world: A geospatial approach
Authors: Subasinghe S , Wang R , Murayama Y
Published: December 2022

In past decades, gradient pattern analysis has been used effectively to characterize the spatial pattern of population distribution in cities worldwide. Most of these studies have focused only on individual case studies or a limited number of cities. However, measuring, analyzing, and understanding complex spatial patterns of city population distribution requires comparative studies that extend beyond the isolated case of cities. Therefore, the present study analyses the spatial pattern of population distribution along the gradient distance from the city centers of the world’s 50 largest cities using LandScan™ population data from 2013 through a geospatial approach. For each city, the city center was demarcated based on a landmark place, and population density was calculated using concentric buffers from the city center. The study mainly identified five basic spatial patterns of population distribution along the gradient distance to the city center. In addition, the study contrasted the spatial patterns of population distribution between cities in developing and developed countries.
Estimation of vegetation cover changes using normalized difference vegetation index (NDVI) in Mount Halimun Salak National Park, Indonesia
Authors: Hartoyo A P P , Pamoengkas P , Mudzaky R H , Khairunnisa S , Ramadhi A , Munawir A , Komarudin K , Hidayati S , Sunkar A
Published: December 2022

The forestry and Other Land Use (FOLU) sector in Indonesia is expected to contribute 60% of the greenhouse gas emission reduction. The priority location for enhancing carbon stock as the mitigation action is natural forests, such as Mount Halimun Salak National Park (MHSNP). The objectives of this research were to estimate vegetation cover changes in 2016, 2019, 2022, and to analyze the forestry programs affecting forest cover in MHSNP. This research used Landsat 8 satellite imagery. NDVI was categorized into five classes, specifically class 1 (the clouds/non-vegetation), class 2 (very low dense vegetation), class 3 (low dense vegetation), class 4 (moderately dense vegetation), and class 5 (highly dense vegetation). MHSNP vegetation cover consecutive in 2016, 2019 and 2022 is dominated by class 1 (35,94% or 31.508,45 ha), class 2 (30,86% or 27.053,73 ha), and class 5 (58,76% or 51.543,18%), respectively. In general, the large vegetation cover from 2016 to 2022 is increasing from 87.662,06 ha to 87.716,88 ha and is significantly denser. It might be caused by the success of the forestry program in MHSNP, such as increasing the rehabilitation area, tree adoptions, and restoration in collaboration with communities and companies.
Integration of LULC change/prediction and hydrological modeler for assessment of the effect of LULC Change on peak discharge in Sari Watershed, Sumbawa Island, Indonesia
Authors: Setiawan O , Nandini R
Published: December 2022

Flood is the main hazard that frequently occurs in Sari Watershed, Sumbawa Island, West Nusa Tenggara Province, Indonesia. The Land Use Land Cover (LULC) change, especially from the forest into non-forest coverage, may have contributed to the increased surface runoff and flooding frequency downstream. Because of the contradicting effects that these processes have on the risk of flooding, it is difficult to predict what the long-term impact of LULC changes will be on flooding in Sari Watershed. This study evaluated the effect of LULC change and prediction on peak discharge in the Sari watershed from 1990 to 2030. LULC maps of 1990, 1995, 2000, 2005, 2010, 2015, and 2020 were obtained by Landsat images classification, whereas 2025 and 2030 were from prediction. LULC change and prediction analysis used the ANN (Artificial Neural network)-CA (Cellular Automata) Markov model. Peak discharge for each year was calculated using the HEC-HMS model. The relationship between LULC change and peak discharge was analyzed with correlation analysis. The result showed that the trend of peak discharge dynamic was consistent with the tendencies of LULC change, particularly from forest coverage to non-forest coverage. Based on correlation analysis, the peak discharge dynamic correlated with the shift in LULC during the analysis period. The study result may provide a reference for flood risk reduction and LULC planning in Sari Watershed.
The use of texture analysis and band transformation on multispectral imagery to map open-pit mines using machine learning
Authors: Nugroho G , Sofan P , Nugroho U C , Suwarsono  , Pambudi A I , Yulianto F , Ichsan N
Published: December 2022

Indonesia has the potential for abundant natural mining resources. The Indonesian government needs to monitor mining activity to maintain environmental sustainability and the availability of mining materials in Indonesia. This study aims to map open mining areas based on remote sensing data. This mapping is one of the actions to support sustainable development goals for ensuring sustainable management and efficient use of natural resources. This study was conducted in Central Bangka Regency, Bangka Belitung Island Province, Indonesia, using the multitemporal Sentinel-2 year of 2020-2021. Gray Level Co-Occurrence Matrix and Principal Component Analysis were applied to improve the input band capability in mapping the distribution of open-pit mining locations. A pixel-based machine learning algorithm, Random Forest, was applied to classify mining and non-mining. Classification using texture analysis and spectral transformation mapped an open mining area of 30.67 km2. Classification using only image bands resulted from a mining area of 18.38 km2. The assessment showed that texture analysis and spectral transformation provided an accuracy of 1.22 % higher than the classification using a direct image input band. Overall, the accuracy obtained by both methods was 96.93 % and 95.71 %. Further research on validation with high-resolution data is still needed.
Determining of peri-urban in rice production centers area: Case study in Karawang Regency, Indonesia
Authors: Mulya Setyardi Pratika
Published: December 2022

In the last decade, the Jakarta-Bandung Mega Urban (JBMUR) corridor has experienced rapid urbanization, including the Karawang Regency. In addition, Karawang has become a national center (rice barn), with an area of rice fields in 2019 reaching 95,000 ha and covering 54% of its regency. The socio-economic spatial context of this region provides a new notion of peri-urban characteristics in the rice production center area. This study aims to identify the peri-urban areas and explain the peri-urban rice production center areas. The approach is a case study using geographic information system analysis (intersect, clip, feature to point) and data tabulation. The data are land cover time series maps from the Ministry of Environment and Forestry in 2019, village government maps (population and civil records 2019), and village potential data for 2011 and 2018. The analysis results show that the number of villages in the urban area is 49 villages, peri-urban 30 villages, and rural area 223 villages. Various variables were compared, showing urban area, peri-urban and rural area. Information on the characteristics of agricultural (rice field) centers can provide input for local governments in planning policy making.
Forest degradation and biomass changes over forest area in Indonesia’s new capital city and surrounding area
Authors: Adinugroho W C , Prasetyo L B , Kusmana C , Krisnawati H
Published: December 2022

Anthropogenic interventions in natural forests have resulted in deforestation and forest degradation. There is a reduction in the number of trees per unit area, which results in changes in forest biomass stocks. Deforestation and forest degradation are believed to contribute to increasing the atmosphere’s greenhouse gases. Satellite remote sensing has played an essential role in generating information about deforestation and forest degradation. This study aims to analyze forest degradation and biomass stock changes over forest area in Indonesia’s new capital city and surrounding area from 2010 to 2018. Spatial datasets from the Tropical Moist Forests project were used in the analysis and processed using Google Earth Engine. Changes in biomass were analyzed based on a biomass map that was produced using radar data. The results of this study clearly show that in the 2010-2018 period, there have been dynamics of forest cover changes in the new capital city of Indonesia and its surroundings, namely the occurrence of direct deforestation, deforestation after degradation, forest degradation, regrowth, and undisturbed forests. The rate of forest degradation was 34,216 ha yr-1 from 2010 to 2018. The highest rate of forest degradation occurred in 2015, along with the massive incidence of fires. The average aboveground biomass stock in the primary forest is 268 Mg ha-1, while 238 Mg ha-1 in the secondary forest. The loss of some trees resulted in a decrease forest biomass in 2018 by 6.7% of the forest biomass stock in 2010. Forest degradation events are caused mainly by logging and fires that generally occur in extreme drought conditions.
Spatial analysis of health risk due to contamination groundwater resources (a case study in Bandung District, Indonesia)
Authors: Hasanawi A , Salami I R S , Thufailah N A
Published: December 2022

Population growth affects the need for water which increases in quantity, followed by an increase in quality and continuity. The development of anthropogenic activities, agriculture, industry, and domestic resulted in a declining rate of clean water in Bandung District, especially in three areas, namely Ciparay, Dayeuhkolot and Margaasih sub-districts. Analysis samples of groundwater in South Bandung District showed an average pollution index of 11.42, which is included in the category of heavily polluted. Therefore, a public health risk assessment is carried out due to groundwater resources for hygiene and sanitation use. Risk characterization is carried out by quantitative methods of calculating the value of the Hazard Index with Monte-Carlo simulation analysis. Spatial analysis is carried out to show the range of risks that can be exposed to the community in the area. Spatial analysis can describe the effect of groundwater pollution and land use on health risk by calculating elevation on the Inverse Distance Weighted interpolation method in Geographic Information System Software. The Hazard Index value categorized child and adult values in each area, with spatial analysis resulting in high – low gradation. Range of hazard index show for Child – Ciparay and Adult – Ciparay respectively 1.15 – 0.08 and 1.16 – 0.22, for Child – Dayeuhkolot and Adult – Dayeuhkolot respectively 0.77 – 0.04 and 0.69 – 0.08, and for Child – Margaasih and Adult – Margaasih respectively 0.47 – 0.11 and 0.55– 0.14. Dermal exposure due to groundwater showed a non-carcinogenic risk in Ciparay Area in the Agriculture land use. Therefore, the stakeholder must periodically evaluate groundwater quality as hygiene and sanitation water, and the land use masterplan and management must be revised to reduce public health risks.
Biophysical landscape characterization of the upper pacal reservoir to support its sustainable management
Authors: Wahyuningrum Nining , Supangat Agung Budi , Auliyani Diah
Published: December 2022

Pacal Reservoir provides irrigation to a total area of 16,688 hectares. Because of its critical importance for the downstream, activities in the upstream must be carefully controlled to maintain their functions. Information on the basic characteristics of landscape conditions is essential at the earliest stage of planning for sustainable land management. This paper aims to determine the characteristics of the upstream Pacal Reservoir and to analyze the areas that are likely suffering from degradation and contributing sediment. Thematic maps such as Area Function, Land Systems, Administration, Roads, and Rivers were used as well as Digital Elevation Model and Google Earth Imagery. The distribution of permanent vegetation, erosion hazard, the proper use of area function with actual land cover, and landslide hazard were investigated further. The spatial analysis indicates a moderate to very severe erosion hazard distributed in all land cover types. Deviations are in protected and production forest areas (2.15%) Land with a slope of >15% should be covered by permanent vegetation but used for seasonal covers (3.65%). Landslide hazards are low and moderate. Land rehabilitation is recommended mainly by maintaining/adding permanent vegetation in the degraded and potentially degraded areas.
The role of moisture regime and hydro-topography on tropical wetland ecosystem management
Authors: Nugraha L M , Putra P B , Marpaung B A , Nugraheni M , Agus C
Published: December 2022

Moisture and hydrological conditions have a close and fundamental relationship with tropical wetland ecosystems’ existence, characteristics, and function. Peatlands and mangrove ecosystems are wetland ecosystems but both have different unique edaphic characteristics so they are interesting as reference ecosystems. Events like land clearing, drainage, flooding, drought, and fires cause the degradation of peat and mangrove ecosystems in Indonesia. Moisture dynamics and hydro-topography will affect the quality of the land and the environment, so it is very important to study them to provide ecological information for the successful management and restoration of wetland ecosystems. This paper will discuss the role of moisture regimes and hydro-topography in the management of tropical peatlands and mangroves. This study uses a review method by data and information analysis from study reports, field observation notes, and journals simultaneously and in an integrated manner. Moisture regime and hydro-topography conditions on peatlands and mangroves indicate differences in vegetation types and key species. Hydrological characteristics and edaphic conditions are expected to become critical references in the effort to preserve and restore tropical wetland ecosystems, in this case, peatlands and mangrove ecosystems.
The estimation of biomass and carbon stocks in mangrove forest ecosystem of Karawang Regency, West Java
Authors: Trissanti V N , Amalo L F , Handayani L D W , Nugroho D , Yuliani A R , Mulyana D
Published: December 2022

Mangrove forest has a role in reducing carbon levels through the absorption from the atmosphere and its storage in several compartments such as plants, litter, and soil organic matter. It is important to estimate biomass and carbon stocks in mangrove forests, because mangroves are able to store three to five times more carbon than lowland tropical forests. The estimation of biomass and carbon stocks was carried out in Karawang Regency. The Calculation of stand biomass was carried out using a non-destructive method, and the data was converted into above-ground biomass values using allometric equations according to tree species. The results showed that the mangrove ecosystem at the tree level has the largest percentage of CO2 absorption, which is 54.55%, sapling level of 44.49%, and 0.96% for the seedling level. The location that has the most significant estimated average value of carbon stock is Sedari Village; meanwhile, the lowest average carbon stock value was found in Pusakajaya Utara Village. Based on the area of the mangrove ecosystem in Pusakajaya Utara Village, with a mangrove area of 39.62 ha, the total estimated upper carbon in the mangrove ecosystem in Pusakajaya Utara Village is 1264.67 tons C.
Impact of mangrove and seagrass ecosystem on marine productivity of Pramuka Island, Seribu Islands, Indonesia
Authors: Salma U , Bengen D G , Rastina  , Kurniawan F
Published: December 2022

The connectivity between seagrass and mangrove ecosystems has synergistic benefits of conserving the land-sea ecosystems of the small islands. The physicochemical properties of the two ecosystems lead to the success of the habitat of the interconnected zone. This study aimed to analyze the physicochemical factors in the mangrove and seagrass ecosystems on Pramuka Island and understand the factors influencing the phytoplankton production of small island coastal ecosystems. Sediment and water collection were carried out on Pramuka Island, Indonesia, to measure physicochemical parameters. Mangrove and seagrass ecosystems have the highest DO, temperature, and pH values. The phytoplankton counts showed significant variation between the sampling sites with a predominance of the class Cyanophyceae. The estimated primary productivity of chlorophyll-a indicated that its concentration was higher in mangroves than in seagrass. A similar trend was observed in nutrient loads and dissolved inorganic nitrogen. Results of the present study clearly showed that an increased concentration of dissolved inorganic nutrient influence the concentration of chlorophyll-a as an indicator of primary productivity. These findings will provide a preliminary analysis of the physicochemical conditions and productivity on Pramuka Island.
Telling emissions apart in a multiphoton resonance: visualizing a conditional evolution
Authors: Mavrogordatos Th K
Published: December 2022

We find that the phase-space representation of the electromagnetic field inside a driven cavity strongly coupled to a two-level atom can be employed to distinguish photon emissions along a ladder of dressed states sustaining a two-photon resonance. The emissions are told apart by means of the different quantum beats generated by the conditional states they prepare. Sample quantum trajectories explicitly reveal the difference in the transient due to the initial condition, in a background set by the Jaynes–Cummings spectrum and revealed by the strong-coupling limit. Their ensemble-averaged evolution is tracked for a time period similar to that waited for the loss of a next photon as the maximum non-exclusive probability, indicated by the peak of the intensity correlation function.
Modeling the electronic structure of organic materials: a solid-state physicist’s perspective
Authors: Cocchi Caterina , Guerrini Michele , Krumland Jannis , Trung Nguyen Ngoc , Valencia Ana M
Published: December 2022

Modeling the electronic and optical properties of organic semiconductors remains a challenge for theory, despite the remarkable progress achieved in the last three decades. The complexity of these systems, including structural (dis)order and the still debated doping mechanisms, has been engaging theorists with different background. Regardless of the common interest across the various communities active in this field, these efforts have not led so far to a truly interdisciplinary research. In the attempt to move further in this direction, we present our perspective as solid-state theorists for the study of molecular materials in different states of matter, ranging from gas-phase compounds to crystalline samples. Considering exemplary systems belonging to the well-known families of oligo-acenes and -thiophenes, we provide a quantitative description of electronic properties and optical excitations obtained with state-of-the-art first-principles methods such as density-functional theory and many-body perturbation theory. Simulating the systems as gas-phase molecules, clusters, and periodic lattices, we are able to identify short- and long-range effects in their electronic structure. While the latter are usually dominant in organic crystals, the former play an important role, too, especially in the case of donor/accepetor complexes. To mitigate the numerical complexity of fully atomistic calculations on organic crystals, we demonstrate the viability of implicit schemes to evaluate band gaps of molecules embedded in isotropic and even anisotropic environments, in quantitative agreement with experiments. In the context of doped organic semiconductors, we show how the crystalline packing enhances the favorable characteristics of these systems for opto-electronic applications. The counter-intuitive behavior predicted for their electronic and optical properties is deciphered with the aid of a tight-binding model, which represents a connection to the most common approaches to evaluate transport properties in these materials.
Visibility graphs of animal foraging trajectories
Authors: Paiva Leticia R , Alves Sidiney G , Lacasa Lucas , DeSouza Og , Miramontes Octavio
Published: December 2022

The study of self-propelled particles is a fast growing research topic where biological inspired movement is increasingly becoming of much interest. A relevant example is the collective motion of social insects, whose variety and complexity offer fertile grounds for theoretical abstractions. It has been demonstrated that the collective motion involved in the searching behaviour of termites is consistent with self-similarity, anomalous diffusion and Lévy walks. In this work we use visibility graphs—a method that maps time series into graphs and quantifies the signal complexity via graph topological metrics—in the context of social insects foraging trajectories extracted from experiments. Our analysis indicates that the patterns observed for isolated termites change qualitatively when the termite density is increased, and such change cannot be explained by jamming effects only, pointing to collective effects emerging due to non-trivial foraging interactions between insects as the cause. Moreover, we find that such onset of complexity is maximised for intermediate termite densities.
Analytic solution of the resolvent equations for heterogeneous random graphs: spectral and localization properties
Authors: Silva Jeferson D , Metz Fernando L
Published: December 2022

The spectral and localization properties of heterogeneous random graphs are determined by the resolvent distributional equations, which have so far resisted an analytic treatment. We solve analytically the resolvent equations of random graphs with an arbitrary degree distribution in the high-connectivity limit, from which we perform a thorough analysis of the impact of degree fluctuations on the spectral density, the inverse participation ratio, and the distribution of the local density of states (LDOSs). For random graphs with a negative binomial degree distribution, we show that all eigenvectors are extended and that the spectral density exhibits a logarithmic or a power-law divergence when the variance of the degree distribution is large enough. We elucidate this singular behaviour by showing that the distribution of the LDOSs at the centre of the spectrum displays a power-law tail controlled by the variance of the degree distribution. In the regime of weak degree fluctuations the spectral density has a finite support, which promotes the stability of large complex systems on random graphs.
Introduction
Authors: Arnull Anthony
Published: December 2022

The Introduction outlines the questions that this VSI attempts to answer. Why does the EU arouse such strong passions? As an organization based on international treaties, why has it proved capable of having such far-reaching effects on its Member States and their citizens and on countries that lie beyond its borders? Part of the explanation lies in its law and legal system, which have proved remarkably effective in ensuring that Member States respect the commitments made when they signed those treaties. But what exactly is EU law about? And how has it become part of the legal DNA of its Member States so much more effectively than other treaty-based regimes?
A comprehensive assessment of cell type-specific differential expression methods in bulk data
Authors: Meng Guanqun , Tang Wen , Huang Emina , Li Ziyi , Feng Hao
Published: December 2022

Accounting for cell type compositions has been very successful at analyzing high-throughput data from heterogeneous tissues. Differential gene expression analysis at cell type level is becoming increasingly popular, yielding biomarker discovery in a finer granularity within a particular cell type. Although several computational methods have been developed to identify cell type-specific differentially expressed genes (csDEG) from RNA-seq data, a systematic evaluation is yet to be performed. Here, we thoroughly benchmark six recently published methods: CellDMC, CARseq, TOAST, LRCDE, CeDAR and TCA, together with two classical methods, csSAM and DESeq2, for a comprehensive comparison. We aim to systematically evaluate the performance of popular csDEG detection methods and provide guidance to researchers. In simulation studies, we benchmark available methods under various scenarios of baseline expression levels, sample sizes, cell type compositions, expression level alterations, technical noises and biological dispersions. Real data analyses of three large datasets on inflammatory bowel disease, lung cancer and autism provide evaluation in both the gene level and the pathway level. We find that csDEG calling is strongly affected by effect size, baseline expression level and cell type compositions. Results imply that csDEG discovery is a challenging task itself, with room to improvements on handling low signal-to-noise ratio and low expression genes.
libRoadRunner 2.0: a high performance SBML simulation and analysis library
Authors: Welsh Ciaran , Xu Jin , Smith Lucian , König Matthias , Choi Kiri , Sauro Herbert M
Published: December 2022

Motivation

This article presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using the systems biology markup language (SBML).

Results

libRoadRunner is a self-contained library, able to run either as a component inside other tools via its C++, C and Python APIs, or interactively through its Python or Julia interface. libRoadRunner uses a custom just-in-time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a large variety of processors, making it fast enough to simulate extremely large models or repeated runs in reasonable timeframes. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) as well as several SBML extensions such as hierarchical composition and probability distributions. It offers multiple deterministic and stochastic integrators, as well as tools for steady-state, sensitivity, stability and structural analyses.

Availability and implementation

libRoadRunner binary distributions for Windows, Mac OS and Linux, Julia and Python bindings, source code and documentation are all available at https://github.com/sys-bio/roadrunner, and Python bindings are also available via pip. The source code can be compiled for the supported systems as well as in principle any system supported by LLVM-13, such as ARM-based computers like the Raspberry Pi. The library is licensed under the Apache License Version 2.0.
CanMethdb: a database for genome-wide DNA methylation annotation in cancers
Authors: Zhao Jianmei , Qian Fengcui , Li Xuecang , Yu Zhengmin , Zhu Jiang , Yu Rui , Zhao Yue , Ding Ke , Li Yanyu , Yang Yongsan , Pan Qi , Chen Jiaxin , Song Chao , Wang Qiuyu , Zhang Jian , Wang Guohua , Li Chunquan
Published: December 2022

Motivation

DNA methylation within gene body and promoters in cancer cells is well documented. An increasing number of studies showed that cytosine–phosphate–guanine (CpG) sites falling within other regulatory elements could also regulate target gene activation, mainly by affecting transcription factors (TFs) binding in human cancers. This led to the urgent need for comprehensively and effectively collecting distinct cis-regulatory elements and TF-binding sites (TFBS) to annotate DNA methylation regulation.

Results

We developed a database (CanMethdb, http://meth.liclab.net/CanMethdb/) that focused on the upstream and downstream annotations for CpG–genes in cancers. This included upstream cis-regulatory elements, especially those involving distal regions to genes, and TFBS annotations for the CpGs and downstream functional annotations for the target genes, computed through integrating abundant DNA methylation and gene expression profiles in diverse cancers. Users could inquire CpG–target gene pairs for a cancer type through inputting a genomic region, a CpG, a gene name, or select hypo/hypermethylated CpG sets. The current version of CanMethdb documented a total of 38 986 060 CpG–target gene pairs (with 6 769 130 unique pairs), involving 385 217 CpGs and 18 044 target genes, abundant cis-regulatory elements and TFs for 33 TCGA cancer types. CanMethdb might help biologists perform in-depth studies of target gene regulations based on DNA methylations in cancer.

Availability and implementation

The main program is available at https://github.com/chunquanlipathway/CanMethdb.

Supplementary information

Supplementary data are available at Bioinformatics online.
Twelve-year neurocognitive decline in HIV is associated with comorbidities, not age: a CHARTER study
Authors: Heaton Robert K , Ellis Ronald J , Tang Bin , Marra Christina M , Rubin Leah H , Clifford David B , McCutchan J Allen , Gelman Benjamin B , Morgello Susan , Franklin Donald R , Letendre Scott L
Published: December 2022

Modern antiretroviral therapy (ART) has increased longevity of people with HIV and shifted the age distribution of the HIV pandemic upward toward that of the general population. This positive development has also led to concerns about premature and/or accelerated neurocognitive and physical ageing due to the combined effects of chronic HIV, accumulating comorbidities, adverse effects or possible toxicities of ART and biological ageing. Here we present results of comprehensive assessments over 12 years of 402 people with HIV in the CNS HIV ART Effects Research (CHARTER) programme, who at follow-up were composed of younger (<60 years) and older (≥60 years) subgroups.

Over the 12 years, ART use and viral suppression increased in both subgroups as did systemic and psychiatric comorbidities; participants in both subgroups also evidenced neurocognitive decline beyond what is expected in typical ageing. Contrary to expectations, all these adverse effects were comparable in the younger and older CHARTER subgroups, and unrelated to chronological age. Neurocognitive decline was unrelated to HIV disease or treatment characteristics but was significantly predicted by the presence of comorbid conditions, specifically diabetes, hypertension, chronic pulmonary disease, frailty, neuropathic pain, depression and lifetime history of cannabis use disorder. These results are not consistent with premature or accelerated neurocognitive ageing due to HIV itself but suggest important indirect effects of multiple, potentially treatable comorbidities that are more common among people with HIV than in the general population.

Good medical management of HIV disease did not prevent these adverse outcomes, and increased attention to a range of comorbid conditions in people with HIV may be warranted in their care.