bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative consideration in selection of breakwater concrete armor unit based on unit’s internal tensile stress response
Authors: Wurjanto Andojo , Hardaya Adi Putra
Published: August 2022

Concrete armor units are essential for the protection of rubble mound breakwaters, yet their selection is generally not based on structural integrity considerations. In this study, the authors used static finite element simulations, as implemented by Ansys software, to compare the structural integrity of five armor units: Accropode, A-Jack, BPPT-Lock, tetrapod, and dolos. All armor units have a mass of around 11,500 kg and have the same quality of concrete at f’c
of 30 MPa. The study involves two different loading cases: Armor units were (1) arranged on a breakwater slope subjected to their own weight and (2) placed on a horizontal ground subjected to idealized wave attacks. In Case #1, the armor units were modelled fixed to the ground and bonded to each other. In Case #2, the wave attack was modelled as a unidirectional and uniform pressure. From the simulation results, the authors compare the highest tensile stresses which could be found on the corner regions of the armor units—their most vulnerable region. In both cases, armor units with stocky shapes experience lower tensile stresses compared to those with slender shapes. These results confirm that Accropode, BPPT-Lock, and tetrapod are structurally safer than dolos and A-Jack.
Numerical modelling of land subsidence effect on coastal sediment transport in Pekalongan
Authors: Wijaya F S , Kurniawan A , Yuanita N , Nugroho E O , Martin R J , Muhammad I F , Yola  , Fauzi N
Published: August 2022

This study examines the condition of sediment transport on the Pekalongan coast by a numerical model computation using the Delft3D Flow module. The research was started by collecting and analysing field data both primary and secondary. Thus, the hydrodynamic and sediment transport model are then calculated in two scenarios which are representing the conditions before (2016) and after (2021) land subsidence by assuming a land subsidence of 10 cm/year. The numerical model is then calibrated and verified on the data of tidal water level elevation and current velocity, the best results are obtained at a chezy number of 60 m0.5/s, and sensitivity tests are carried out on changes in sediment grain size, wave height and wave direction in order to determine the characteristics of the numerical model. The sensitivity analysis of sediment grain size is the most sensitive effect to sediment transport characteristic. The results of the numerical model are then compared based on the scenarios before (2016) and after the occurrence of land subsidence (2021). The results indicate that after land subsidence, the sedimentation rate is increasing by 56.34%, whereas the erosion rate is decreasing by 3.98% after one neap-spring tidal cycle (around 15 days) in the study area.
The eco enzyme application to reduce nitrite in wastewater as the sustainability alternative solution in garbage and wastewater problems
Authors: Wikaningrum T , Anggraina P L
Published: August 2022

The increasing population growth has an impact on increasing problems in wastewater quality and garbage volume. It is a need to develop a sustainability solution for both problems. In this research, the papaya fruit and spinach vegetable garbage were used as raw organic materials and fermented for six months. This study objective was to determine whether eco enzymes can be used to reduce nitrite concentration in wastewater. The research method was conducted on a laboratory scale with the artificial samples in a batch system. The result showed that eco enzyme made from a mixture of papaya and spinach can reduce the nitrite concentration in the water sample. The t-test showed that the effect of eco enzyme application in reducing nitrite in water samples was significant. The application of eco enzyme 0%, 2%, 4%, and 6% respectively during 10 hours exposure showed the nitrite removal were 0.3 %, 20%, 29%, and 35 %. It can be seen that the reduction of nitrite concentration in samples added by eco enzyme was caused by eco enzyme activity. The application at a higher concentration of 10%, 15%, and 20% showed that nitrite removal efficiencies were 35.7%, 36.7%, 46.7%, 49.4% respectively during 7 hours exposure. It can be concluded that a longer time exposure, and also the more eco enzyme concentration, showed the more result in the effect of nitrite reduction concentration in water. 4. By this study it is proven that application of eco enzyme made from organic garbage can be an alternative solution for garbage and wastewater quality problem.
Economic Valuation and Potential Pollution Load Analysis of Domestic Wastewater in Greater Bandung
Authors: Rakhmadi Adhitya , Suharyanto  , Nastiti Anindrya
Published: August 2022

Sanitation is still a significant problem in most developing countries. The lack of awareness and low education level are the main factors causing 30% of people to still practice open defecation. The problems are getting worse because of the population growth. They are not followed by the availability of sanitation infrastructure and services, leading to people mainly still discharging their domestic wastewater into the river. According to the Ministry of Environment and Forestry (2017), domestic wastewater contributes significantly to Citarum River’s pollution by 68. From the calculation of domestic waste pollution estimation potential and analysis using SFD tools, the people in Greater Bandung produced 292 tons of BOD/day (106.580,25 ton/year), 401,5 tons of COD/day (131.101 ton/year), and 277,4 tons of TSS/day (101.251 ton/year). Ironically only 10,54% of the waste generated are safely managed, and 89,46% of the rest are unsafely managed. Pollution can cause several problems, including health and some more economic loss. The financial loss of the people of MBR is IDR 4.234.059.114.465/year or IDR 461.543/person/year. The economic loss from the health sector is responsible for about 29% of the total cost, it costs IDR 1.217.720.640.356/year or Rp 148.016/person/year. This is followed by clean water access cost for IDR 3.054.566.638.642/year or IDR 371.289/person/year (71%). This cost is equivalence to 1,3% of the Gross Domestic Product (GDP) of the people in the Metropolitan Bandung Area.
Modular incinerator with pre-treatment plant for municipal solid waste treatment in the super-priority tourism destination of Labuan Bajo Indonesia
Authors: Purwanta Wahyu , Prawisudha Pandji , Juangsa Firman Bagja , Fani Ayudia Mutiara , Philander Evan
Published: August 2022

One of the competitiveness parameters of tourist destinations is the cleanliness index. Labuan Bajo as a super-priority tourist destination has a very serious municipal solid waste (MSW) problem. Waste generation in Labuan Bajo and Komodo National Park in 2020 reached 14.06 tons/day and is projected to be 15.51 tons/day in 2023. The main sources of MSW come from settlements, hotels, traditional markets, and seaports. The current MSW management system is that waste is collected from the source and then transported to a temporary storage tank to be transported by truck to the Warloka landfill. This system poses a threat in the form of shortening the service life of the landfill. Management through recycling is still a very low percentage because the recycling ecosystem has not yet developed. One alternative for MSW management that is currently being carried out by the central government in Labuan Bajo is to implement a modular incinerator. This paper describes the process of designing and operating a test incinerator with a combustion capacity of 20 tons/day consisting of 2 lines each with a capacity of 10 tons/day. The incinerator is equipped with a pre-treatment plant consisting of a sorting conveyor, thermal dryer, and storage conveyor. The incinerator furnace consists of two chambers and each is equipped with a burner. This furnace is designed to be able to burn waste with a calorific value of 1300 kcal/kg with a maximum moisture content (MC) of 60%. The test results show that the temperature in the primary chamber can reach a minimum of 800°C and a maximum of 1000°C in the secondary chamber. The burning rate has obtained a maximum of 527 kg/h which means it has passed the initial design of 417 kg/h. To meet emission-quality standards, exhaust gas is processed through flue gas treatment consisting of a cyclone, quencher scrubber, and chimney. Emissions measured by CEMS include parameters of particulates, CO, SO2, and NOx, all of which are below the national emission-quality standards. The heat generated from partial combustion will be channeled to the thermal dryer to reduce MC so that it can reach 40%. The results of burning waste with this incinerator produce fly ash and bottom ash about 4% of the weight of the input waste.
Spatial Analysis of Potential Greenhouse Gas (GHG) Emissions from Household-Scale LPG Consumption in Urban and Sub-Urban Areas of Medan City during the COVID-19 Pandemic
Authors: Suryati I , Hasibuan N , Hanisah M , Nadapdap L , Ruadelia M , Sigalingging J
Published: August 2022

Household activities such as the use of electricity, LPG, and fuel for vehicles are sources of greenhouse gas emissions. Energy consumption at the household scale continues to increase, especially during the COVID-19 pandemic due to the policy of working from home. The global COVID-19 pandemic also affects household-scale energy consumption for urban and suburban areas. The increase in energy consumption is in line with the increase in greenhouse gases so to reduce greenhouse gas emissions, spatial mapping is necessary. This mapping aims to determine the potential distribution of greenhouse gas emissions from household-scale LPG consumption so that programs, plans, or policies can be determined in strategies for reducing greenhouse gas emissions. The stages of this research begin with calculating GHG emissions using the IPPC method and making a GHG potential map. The research results from the calculation of greenhouse gas emissions in the household-scale LPG sector in the study area ranged from 110 – 2792 tons CO2eq/year. GHG emissions in sub-urban areas are greater than in urban areas because they are influenced by population, LPG usage patterns, and income per capita.
Estimation of Extreme Rainfall over Kalimantan Island based on GPM IMERG Daily Data
Authors: Kuntoro A A , Hapsari R K , Adityawan M B , Farid M , Widyaningtias  , Radhika
Published: August 2022

Rainfall is one of the critical data for water resources infrastructure planning. In many cases in developing countries such as Indonesia, rainfall stations are not evenly distributed. In many cases, regional development occurs much faster than the improvement of hydrological measurement instruments. The plan to move the capital city of Indonesia to Kalimantan is one example. Satellites rainfall products can be utilized, especially for areas with a limited number of rainfall stations. This study examines the potential use of Global Precipitation Measurement (GPM) satellite products to estimate the spatial distribution of rainfall in the Kalimantan region. Twenty years data of daily maximum rainfall from GPM satellite rainfall products in 2001-2020 were compared to twenty years data of daily maximum rainfall from 16 rainfall stations under the Meteorology, Climatology, and Geophysical Agency (BMKG), with data time spanning from the 1970s to 2020. The analysis results show a significant difference between extreme rainfall analysis computed by using station data and the satellite. The use of the correction function can increase the accuracy of the GPM rainfall product. It can be used as an alternative data source for a region with limited rainfall stations.
Study of Clean Water and Sanitation Access and Its Relationship to Waterborne and Stunting Prevalence in Bandung Regency
Authors: Kamila Putri S , Salami Indah R S
Published: August 2022

Water and proper sanitation access in Bandung Regency has not covered all population. Lack of availability of water and sanitation is certainly related to public health. This research was conducted to identify clean water access in terms of quality, quantity, and continuity as well as sanitation access in Bandung Regency, and then to determine its relationship to waterborne diseases and stunting prevalence. The study was conducted in three locations representing domestic, agricultural, and industrial areas. The study collected 33 water samples for physical and microbial analysis, and questionnaires to 75 household respondents about the waterborne disease and stunting prevalence, household income levels, hygiene behaviour, mother’s education, and birth weight. The results showed clean water quality differences in those areas for parameters Total Coliform (p=0,051), temperature (p=0,044), and pH (p=0,002) as well as differences of wastewater system types (p=0,002). Factors namely clean water quantity and continuity, personal hygiene, and household income level have an association with waterborne diseases prevalence (PR>1). Whereas stunting is associated with sanitation access, personal hygiene, household income level, mother’s education, and children’s birth weight (PR>1). However, only household income level has significant relationship with stunting (p=0,005; PR=4.0; 95% CI=1.33-12). These factors should be improved to prevent waterborne disease and stunting children in the community.
Numerical Study on Connections of Replaceable Shear Link with Inserted Pins
Authors: Moestopo M , Kusumastuti D , Wibowo S
Published: August 2022

The link end plate of replaceable shear link in eccentrically braced frames has been modified with the ‘inserted-pins’ to ensure the high seismic performance and to reduce the number of bolts in its slip-critical connections. The maximum shear force in the connection is resisted by the pins, while the bolts resist the bending moment at the link-ends. Numerical work has been conducted using a non-linear ABAQUS program to study the deformation as well as the stress distribution of the shear-link and its connection elements: end plates, bolts, pins, and beam-outside the link. The results showed an adequate performance of the proposed modified shear link connections, where the end plate of the beam outside the link remained elastic as the shear-link reached 0.08 rad plastic rotation due cyclic loading.
Comparative Study in Bill of Quantity Estimates on Reinforcement Works of Pile Cap, Single Pier and Double Pier of Flyover Between Conventional Methods and BIM (Building Information Modelling)
Authors: Putra Atanasius Agri Permadi , Oei Natanael Indrawan Wiharno , Hermawan  , Hasiholan Budi
Published: August 2022

One of the construction materials with a high level of demand is steel rebar. Globally, the demand for steel rebar has quadrupled from 1960 to 2005—and this increase is predicted to double by 2050. In one project, steel rebar accounts for 16% to 60% of the total project budget. Therefore, if the volume of steel rebar is not estimated correctly it will have an impact on project budget wastage and swelling. The project budget wastage is indicated by the large volume of material remaining, while the budget swelling is indicated by the procurement of additional steel rebar because the material requirement is greater than the initial estimate. To minimize this, a comprehensive understanding of volume estimation is required. Currently, the method of estimating the reinforcement volume that is widely used is the conventional estimation method and the BIM (Building Information Modeling)-based estimation method. The conventional method is done manually based on the BBS (Bar Bending Schedule) as a reference. Meanwhile, the BIM-based method used in this study is the Allplan Engineering 2021 software and is a more modern estimation alternative because it is considered more practical, fast and efficient. Although these two methods are widely used, there are limitations and advantages that are taken into consideration when choosing the most appropriate method. Therefore, a study is needed to prove and compare the accuracy of the estimation of reinforcement volume between the conventional method and the BIM-based method. This study also highlights the advantages and limitations of the two methods for comparison. The conventional method is more transparent in terms of the estimation formula used because it is done manually. This can help the estimator track the estimation process to ensure the accuracy of the results. Whereas, the BIM-based estimation method is superior in terms of work automation and accuracy compared to the conventional method. Furthermore, the limitations of the conventional method are that it does not have a 3D visual model and requires a relatively long time to complete if there is a revision of the plan drawing. On the other hand, the BIM-based estimation method offers convenience in the form of data input using 3D drawings. The practical data input process is proven to provide accurate results. However, the main limitation of the BIM-based method, especially for the software used in this study, is that the estimation formula cannot be traced because it relies more on three-dimensional modeling. This causes the estimator to be unable to ensure the accuracy of the estimation results. However, this limitation may differ from other BIM software products outside of this study.
Evaluating the use of Google Maps as navigation application by identifying hazards and assessing risks using HIRA matrix
Authors: Kusumasari Wildi , Ilmi Friska M , Ellizar Estiara , Rabung Yos Y
Published: August 2022

Google Maps as a navigation application provides route information with the shortest route or fastest travel time, but this technology has a weakness as it does not consider the suitability of road condition with the type of vehicles, therefore the choice of the routes does not accommodate traffic safety aspects. This research aims to evaluate the use of Google Maps as a navigation application by identifying hazards and assessing risks. The method used is based on an analysis using the HIRA (Hazard Identification and Risk Assessment) matrix to determine the level of risk thus the step of mitigation can be executed. The data source obtained was from the results of questionnaires distributed to 1,114 respondents. As the results of analysis, it was found that 11 hazards from the usage of Google Maps came from the driver’s aspect, Google Maps feature’s aspect, and road conditions aspect. Evaluation of risks came from the three sources of hazard classified into 2 risks in the intolerable risk category and 9 risks in the tolerable risk category. After the mitigation efforts were arranged to control the risk, all risks are expected to meet the acceptable risk level. To anticipate the road traffic accident due to the usage of Google Maps, the recommendation for this navigation application is to add more features to warn the users about the road characteristics in the form of voice notification or pop up if not disturb the driver while driving and providing a specific route for truck/heavy vehicle as now the Google Maps is only available for light vehicle.
Impact analysis from visual improvement program of slums to sanitation management: case study Kampung Cibunut, Bandung City, Indonesia
Authors: Kusumayanti I , Defi L P , Fatimah W M , Sarli P W , Soewondo P
Published: August 2022

Visual improvement of slum settlements in urban areas is a new breakthrough to increase public awareness of sanitation management; a capital to foster community participation and ensure the sustainability of implemented sanitation program. This study identified the impact from visual improvement program of slums to the sanitation management intention and behavior of the Kampung Cibunut community using the Theory of Planned Behavior. The sampling technique used in this research is cluster random sampling. A sample size of 86 households was obtained using the Yamane formula with a confidence interval of 10%, a population of 369 households, and a cluster technique proportional to size. The research used correlational design with Likert scale questionnaire. Based on the correlation test of the Spearman method, it was found that the visual improvement has a significant correlation with the intention to treat domestic wastewater. However, the visual improvement has no significant correlation with the behavior of treating domestic wastewater, intention and behavior of paying the cost of domestic wastewater management.
Analysis of Biodegradation Characteristics Based on Visual Observation and Mass Loss Percentage in Soil Burial Test of Sustainable Geo-bag Materials as Temporary Structures in Natural Coastal Protection System
Authors: Gunawan W , Rildova  , Yuanita N , Kurniawan A , Kahdar K , Herbenita V
Published: August 2022

Coastal erosion is a significant hazard that causes heavy loss of land and damage to structures in coastal areas globally. To mitigate this problem, coastal engineers worldwide are focusing on sustainable coastal development practices. To this end, many countries are using natural protective methods, including vegetation such as mangroves. However, this practice is not without challenges; to ensure that mangroves could grow strongly required at least two years. A natural coastal protection system is the proposed solution, which combines mangrove vegetation as the main structure and geo-bag-dykes as temporary structures to solve this problem. The role of geo-bag-dykes is needed until mangrove plants mature. So, the length of time for geo-bags to degrade naturally is vital to get considered because otherwise, it will become hazardous coastal debris. Today, commonly used geo-bags are made from synthetic fibers that take a long time to degrade. Thus, this study tested alternative materials made from natural fibers, such as lyocell, kenaf, cotton, and rayon. The objective is to determine whether these alternative materials can be used as sustainable geo-bag materials or not in terms of biodegradation. Based on the soil burial test results contained in ISO 11721-1, these alternative materials degrade much faster when compared to commonly used geo-bag materials.
Assessment of water quality and challenges for vegetable irrigation in Greater Bandung Area, Indonesia
Authors: Firdayati M , Anindita R , Krisnamurti P A , Handajani M
Published: August 2022

The high demand of water mainly used for industry and domestic purposes puts pressure on water for agriculture. In addition, the change of massive land use and poor sanitation condition affect the availability of water sources and quality for irrigation. These are very important due to the increase of consumer needs for good, healthy, and safe food, especially for raw vegetables. This study identified water sources and then examined and assessed water quality for raw vegetables irrigation in Greater Bandung Area (GBA) as one of the main vegetable producers in West Java Province. This produced around 2.26-million tons of vegetables in 2019 whose harvest was distributed for local and regional consumption. The research was conducted by field surveys in four vegetable plantations having about 350 farmers, spreading over 3 regencies, Bandung City (city boundary), West Bandung Regency, and Bandung Regency. Water quality was analysed based on National Water Quality Standard Class II and other parameters such as SAR (Sodium Adsorption Ratio), RSC (Residual Sodium Carbonate) and %Na. Field survey showed that farmers used different water sources for agriculture, namely groundwater, springs, lake, and greywater. Assessment of water quality using Pollution Index method showed that the dominant water source was slightly polluted with pollutant parameters of conductivity, BOD, %Na, ammonia, chloride, and sulphate exceeding the standards. It showed possibility of domestic wastewater contamination to irrigation water source. Based on the measured parameters, water used for irrigation, even groundwater, was polluted and might cause potential health risk for consumer.
Groundwater salinity and its effect on elevated concentrations of other contaminants in a coastal plain: a perspective for infrastructure protection
Authors: Rusydi A F , Onodera S-I , Ioka S , Maria R , Firmansyah F , Saito M , Purwoko W , Sukmayadi D
Published: August 2022

Salinization is a serious threat to coastal groundwater because it degrades water quality and results in trace metal dissolution. Meanwhile, groundwater quality is critical for human and development, as contaminated groundwater cause a negative effect on human`s health and infrastructure. Our investigation of a specific area, Indramayu, on West Java’s north coast revealed that most groundwater samples are brackish to saline in existence. TDS concentrations in groundwater samples were predominantly in the >1,000 to nearly 30,000 mg/L range. Concentration contours were disproportionately high in the north tip area. Numerous factors contribute to the high salinity of this area, including the interaction of saline water and sediment with low-salinity groundwater and evaporation. Additionally, high TDS levels were significantly correlated with Fe2+ and Mn2+ concentrations (p < 0.001). The area’s high salinity was thought to facilitate the dissolution of trace metals from minerals such as siderite and rhodochrosite (SI of the minerals > 1). Concentrations of Fe2+ and Mn2+ were very likely to damage the water piping system. In terms of water quality, less than 30% of samples were fit for human consumption. Finally, the government should take into account the groundwater environment when developing the area in order to protect human health and infrastructure.
Comparative of material properties between natural fibers and geo-bag synthetic fibers as sustainable material of temporary structure in natural coastal protection systems
Authors: Herbenita V , Rildova  , Yuanita N , Kurniawan A , Kahdar K , Gunawan W
Published: August 2022

The natural coastal protection system is a proposed solution to the coastal erosion problem, including in Indonesia’s coastal areas, which combines primary natural protection (vegetation such as mangroves) and temporary artificial structures as sustainable coastal development practices. The geo-bag-dike was chosen as a possible temporary structure to protect the growth of mangrove seedlings from sea waves for about two to five years before they are strong enough to prevent erosion. In today’s practice, the geo-bag-dike is made of polymeric synthetic fibers (nonwoven geo-bag), which take a relatively long time to degrade naturally. Thus, this study focused on finding sustainable alternative materials from natural fibers, such as lyocell (Tencel), kenaf, cotton, and rayon, that can be applied as the primary material of geo-bag-dikes by comparing their material properties to nonwoven geo-bag. The results of the laboratory testing method show that kenaf textile has the highest values of tensile and tearing strength, but not higher than nonwoven geo-bags (768 N, 1080 N, and 2140 N for the tensile strength of kenaf, local nonwoven geo-bag, and imported nonwoven geo-bag, respectively). Therefore, kenaf textiles have the potential as a sustainable alternative material. By extrapolating, it is necessary to increase the layer number of kenaf textiles to at least three layers of fabric to resemble the tensile strength of nonwoven geo-bags.
Palu Housing Reconstruction Process: Reviewing and Learning after the 2018 Earthquake
Authors: Pradoto R G K , Oktavianus A , Pribadi K S , Rasmawan I M A B , Wulandari L D
Published: August 2022

The strong earthquake that hit the Province of Central Sulawesi on 28 September 2018 (M7.4), followed by tsunami and liquefaction has caused many casualties, injuries as well as damages in the housing sector. In the rehabilitation and reconstruction (R&R) program, the Government policy was to provide the affected community with aid to rebuild their houses (for houses outside the red zone), the Government also will build new settlements for relocation (for houses inside the red zone), which both are expected to be more earthquake-resistant. In order to understand what happens in the field related to various issues, an investigation to study the whole processes and to document the lessons learnt from the reconstruction process is conducted in Central Sulawesi Province. One of the highlights of this study is the impact of the three types of disasters that occurred in Palu Municipality (earthquake, tsunami, and liquefaction) on the housing reconstruction process after the disaster occurred. The primary field survey and Focus Group Discussion were conducted through interviews with various parties in the earthquake-affected areas to reveal the findings of problems and obstacles in the field during its two years of implementation, from 2018 to 2020. This study focuses on reviewing and learning from the post-disaster housing sector reconstruction process. The result of this study is expected to provide future lessons for the post-disaster housing reconstruction process in Indonesia and other countries.
Comparative Analysis of Municipal Solid Waste to RDF Pretreatment Methods in Indonesia
Authors: Widyarsana I M W , Saraswati D
Published: August 2022

Municipal solid waste in Indonesia has a high potential to be used as an alternative energy source. One of the methods is by producing refuse-derived fuel (RDF) as coal substitution. Pre-treatment is needed to reduce high water content in domestic waste, especially in Indonesia, to produce high-quality RDF. This study compares and analyzes the optimal pre-treatment method to produce RDF from domestic waste based on each RDF product characteristic. The research reviewed and analyzed the data of RDF characteristics of various pre-treatment methods applied in Indonesia from pilot-scale experiments as primary data and previous research as secondary data. The methods compared are fermentation method, sun-drying, and bio drying. RDF from each method was tested to collect the proximate and ultimate characteristics data. Statistical analysis of RDF characteristics is carried out to determine whether there is a significant difference from different pre-treatment methods. This analysis shows no significant effect on the difference in the characteristics of the RDF. RDF from bio drying provides the highest average number of calorific values and lowest moisture content. The study concluded that the bio drying method is recommended in more waste treatment facilities in Indonesia to increase waste as an alternative energy resource.
Coastal protection system design at the Indonesian Mangrove Center in Pekalongan, Central Java – Indonesia
Authors: Yola  , Yuanita N , Kurniawan A , Nugroho E O , Martin R J , Muhammad I F , Wijaya F S , Fauzi N
Published: August 2022

The Pekalongan area suffered from coastal flooding and heavy coastal erosion due to land subsidence and increasing wave condition in the last decade. Pekalongan government built a land dike in 2018 to protect Pekalongan city from coastal flooding. This study aims to determine a suitable coastal protection system, consisting of hard-structures and mangroves, to solve the erosion problem at the Pekalongan coast, specifically at the future Pekalongan Mangrove Information Centre (PIM). Environmental data, i.e., wind, wave, current, tidal, sediment, and soil data, were obtained by field survey and secondary data collection from open-source data. The selection of the most suitable coastal protection design concepts was performed by comparing several alternatives of structure materials. Coastal protection layout was obtained based on a numerical sediment transport model result using Delft3D software. From environmental data processing and analysis with various design aspects, the top elevation of the coastal protection structure is +4.5 m MSL (Mean Sea Level). The configuration of the mangrove planting media consists of ‘guludan’ structure technique with dimension 10 m x 5 m x 4 m.
Health risk-based prioritization approaches of pharmaceuticals in the Upper Citarum River Basin
Authors: Utami R R , Salami I R S , Geerling G W , Notodarmojo S , Ragas A M J
Published: August 2022

Two methods were developed to prioritize human health risks of pharmaceuticals based on defined daily doses (DDDs) obtained from the WHO and acute toxicity data on pharmaceuticals (TDLo) obtained from the PubChem database. A major advantage of these methods is that it requires no acceptable daily intake (ADI), reference dose (RfD), or tolerable daily intake (TDI) values, which are often unavailable or difficult to obtain for pharmaceuticals group. Both methods were applied to prioritize 16 pharmaceuticals detected by passive samplers in the water source of Ciwalengke Village, a peri-urban area in the Upper Citarum River Basin. Ten out of 16 pharmaceuticals could be prioritized by using both methods. The risk indicator values (RIhum) showed good agreement between the two approaches, especially for Caffeine and Trimethoprim. The priority ranking of Caffeine and Lidocaine were always in the top 3 highest human health risks. The ranking comparison showed considerable consistency, indicating that both prioritization methods are reasonably in line with each other. The pharmaceutical intake through the exposure of contaminated river water was expected to pose negligible human health risks (i.e. RIhum < 1) but can be refined more by conducting supplementary effects studies for other individual pharmaceuticals or pharmaceuticals mixtures.
Preliminary studies of Bandung City Health System Resilience (case study : Covid-19 pandemic)
Authors: Roosmini D , Kanisha T F , Nastiti A , Kusumah S W , Salami I R S
Published: August 2022

The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus causes the COVID-19 pandemic globally. The city of Bandung is the city that became the cluster of Covid-19 spread after DKI Jakarta at the beginning of the pandemic. In 2019, the Global Health Security Index (GHSI) was developed to assess countries’ readiness to face a pandemic. The index obtained shows that globally the value of this readiness is still minimal. In improving community health system services, health system resilience has been developed and studied in recent years. This study conducted a preliminary evaluation of the Bandung City health system in dealing with the Covid-19 pandemic using the concept of resilience. This research uses the West Java and Bandung City Health Office website. Methods used for evaluating the health system resiliency are comparing the cases of Covid-19 at the sub-district to the health facilities, the incidence of infectious diseases in 2019, and the socio-economic conditions of each sub-district. Research shows that the health system in Bandung City has not met the targets in the 2018-2023 Regional Medium-Term Development Plan. Overall, the initial research on the Bandung City health system still does not meet the criteria for resilience.
Emerging machine learning strategies for diminishing measurement uncertainty in SPM nanometrology
Authors: Nguyen Linh Thi Phuong , Liu Bernard Haochih
Published: August 2022

Scanning probe microscopy (SPM) is an outstanding nanometrology tool for characterizing the structural, electrical, thermal, and mechanical properties of materials at the nanoscale. However, many challenges remain in the use of SPM. Broadly speaking, these challenges are associated with the acquisition of the SPM data and the subsequent analysis of this data, respectively. Both problems are related to the inherent uncertainty of the data obtained in SPM-based measurements due to the nanoscale geometry of the SPM probe tip, the state of the sample imaging region, the data analysis methods themselves, and the experience of the users. Machine learning (ML) approaches have been increasingly applied to address these problems in recent years. In general, ML approaches involve constructing a well-organized and representative SPM dataset from experimental and theoretical trials, and then using the data features of this dataset for ML models to learn and produce appropriate predictions. Herein, this review examines the development of recent ML strategies for reducing measurement uncertainty in SPM-based measurements. The review commences by introducing the ML models and algorithms commonly used in SPM-related applications. Recent approaches for collecting and preprocessing the SPM data to extract significant data features for further ML processing are then introduced. A review of recent proposals for the applications of ML to the improvement of SPM instrumentation and the enhancement of data processing and overall understanding of the material phenomena is then presented. The review concludes by presenting brief perspectives on future opportunities and open challenges in the related research field.
Almost automorphic solutions of second-order equations involving time scales with boundary conditions
Authors: Choquehuanca Mario , Mesquita Jaqueline , Pereira Aldo
Published: August 2022

In this article, we investigate the existence and uniqueness of solutions of linear and semilinear second–order equations involving time scales. To obtain such results, we make use of exponential dichotomy and fixed point results. Also, we present some examples and applications to illustrate our main results.
Revisiting the multisite phosphorylation that produces the M-phase supershift of key mitotic regulators
Authors: Tan Tan , Wu Chuanfen , Liu Boye , Pan Bih-Fang , Hawke David H. , Su Zehao , Liu Shuaishuai , Zhang Wei , Wang Ruoning , Lin Sue-Hwa , Kuang Jian
Published: August 2022

The work in this paper demonstrates that the substantial increase in the apparent molecular weight of Cdc25C, Myt1, Wee1, Greawall, and APC3 during M-phase induction are each due to simultaneous phosphorylation of a considerable portion of S/T/Y residues in a long intrinsically disordered region that is enriched in both S/T residues and S/TP motifs.
Performance evaluation of computational methods for splice-disrupting variants and improving the performance using the machine learning-based framework
Authors: Liu Hao , Dai Jiaqi , Li Ke , Sun Yang , Wei Haoran , Wang Hong , Zhao Chunxia , Wang Dao Wen
Published: August 2022

A critical challenge in genetic diagnostics is the assessment of genetic variants associated with diseases, specifically variants that fall out with canonical splice sites, by altering alternative splicing. Several computational methods have been developed to prioritize variants effect on splicing; however, performance evaluation of these methods is hampered by the lack of large-scale benchmark datasets. In this study, we employed a splicing-region-specific strategy to evaluate the performance of prediction methods based on eight independent datasets. Under most conditions, we found that dbscSNV-ADA performed better in the exonic region, S-CAP performed better in the core donor and acceptor regions, S-CAP and SpliceAI performed better in the extended acceptor region and MMSplice performed better in identifying variants that caused exon skipping. However, it should be noted that the performances of prediction methods varied widely under different datasets and splicing regions, and none of these methods showed the best overall performance with all datasets. To address this, we developed a new method, machine learning-based classification of splice sites variants (MLCsplice), to predict variants effect on splicing based on individual methods. We demonstrated that MLCsplice achieved stable and superior prediction performance compared with any individual method. To facilitate the identification of the splicing effect of variants, we provided precomputed MLCsplice scores for all possible splice sites variants across human protein-coding genes (http://39.105.51.3:8090/MLCsplice/). We believe that the performance of different individual methods under eight benchmark datasets will provide tentative guidance for appropriate method selection to prioritize candidate splice-disrupting variants, thereby increasing the genetic diagnostic yield.
ProteinPrompt: a webserver for predicting protein–protein interactions
Authors: Canzler Sebastian , Fischer Markus , Ulbricht David , Ristic Nikola , Hildebrand Peter W , Staritzbichler René
Published: August 2022

Motivation

Protein–protein interactions (PPIs) play an essential role in a great variety of cellular processes and are therefore of significant interest for the design of new therapeutic compounds as well as the identification of side effects due to unexpected binding. Here, we present ProteinPrompt, a webserver that uses machine learning algorithms to calculate specific, currently unknown PPIs. Our tool is designed to quickly and reliably predict contact propensities based on an input sequence in order to scan large sequence libraries for potential binding partners, with the goal to accelerate and assure the quality of the laborious process of drug target identification.

Results

We collected and thoroughly filtered a comprehensive database of known binders from several sources, which is available as download. ProteinPrompt provides two complementary search methods of similar accuracy for comparison and consensus building. The default method is a random forest (RF) algorithm that uses the auto-correlations of seven amino acid scales. Alternatively, a graph neural network (GNN) implementation can be selected. Additionally, a consensus prediction is available. For each query sequence, potential binding partners are identified from a protein sequence database. The proteom of several organisms are available and can be searched for binders. To evaluate the predictive power of the algorithms, we prepared a test dataset that was rigorously filtered for redundancy. No sequence pairs similar to the ones used for training were included in this dataset. With this challenging dataset, the RF method achieved an accuracy rate of 0.88 and an area under the curve of 0.95. The GNN achieved an accuracy rate of 0.86 using the same dataset. Since the underlying learning approaches are unrelated, comparing the results of RF and GNNs reduces the likelihood of errors. The consensus reached an accuracy of 0.89.

Availability and implementation

ProteinPrompt is available online at: http://proteinformatics.org/ProteinPrompt, where training and test data used to optimize the methods are also available. The server makes it possible to scan the human proteome for potential binding partners of an input sequence within minutes. For local offline usage, we furthermore created a ProteinPrompt Docker image which allows for batch submission: https://gitlab.hzdr.de/proteinprompt/ProteinPrompt. In conclusion, we offer a fast, accurate, easy-to-use online service for predicting binding partners from an input sequence.
STAT3 in porcine endometrium during early pregnancy induces changes in extracellular matrix components and promotes angiogenesis
Authors: Jalali Beenu Moza , Likszo Pawel , Lukasik Karolina
Published: August 2022

A molecular interaction between maternal endometrium and implanting conceptus can lead to activation of a variety of transcription factors that regulate expression of several genes necessary for the process of embryo implantation. While, signal transducer and activator of transcription 3 (STAT3) is responsible for decidualization and epithelial remodeling in humans and mice, its role in porcine endometrium has not been explored before. In the present study, we observed a pregnancy dependent increase in gene and protein expression of STAT3. Phosphorylated STAT3 was predominantly present in the endometrium of pregnant animals in luminal and glandular epithelium and in the endothelium of blood vessels with a weak staining in stromal cells. Interleukins, IL-1β and IL-6, and epidermal growth factor (EGF)-induced STAT3 expression and phosphorylation in endometrial explants collected on Day 13 of the estrous cycle. Biological significance of STAT3 was evaluated by blocking its phosphorylation with STAT3-specific inhibitor, Stattic. Using porcine extracellular matrix (ECM) and adhesion molecule array, EGF was shown to induce changes in gene expression of ECM components: MMP1, MMP3, MMP12, LAMA1, SELL, and ICAM1, which was abrogated in the presence of Stattic. Transcriptional activity of STAT3 was observed in promoter regions of MMP3 and MMP12. Additionally, IL-6-induced STAT3 phosphorylation upregulated VEGF and VCAM1 abundances in endometrial-endothelial cells (EEC). Moreover, IL-6 resulted in an increase in EEC proliferation and capillary formation which was reversed in the presence of Stattic. Results of present study reveal a role for STAT3 phosphorylation in regulating extracellular matrix remodeling and angiogenesis in porcine endometrium to facilitate embryo implantation.
On boosting the power of Chatterjee’s rank correlation
Authors: Lin Z , Han F
Published: August 2022

The ingenious approach of Chatterjee (2021) to estimate a measure of dependence first proposed by Dette et al. (2013) based on simple rank statistics has quickly caught attention. This measure of dependence has the appealing property of being between 0 and 1, and being 0 or 1 if and only if the corresponding pair of random variables is independent or one is a measurable function of the other almost surely. However, more recent studies (Cao & Bickel 2020; Shi et al. 2022b) showed that independence tests based on Chatterjee’s rank correlation are unfortunately rate inefficient against various local alternatives and they call for variants. We answer this call by proposing an improvement to Chatterjee’s rank correlation that still consistently estimates the same dependence measure, but provably achieves near-parametric efficiency in testing against Gaussian rotation alternatives. This is possible by incorporating many right nearest neighbours in constructing the correlation coefficients. We thus overcome the ‘ only one disadvantage’ of Chatterjee’s rank correlation (Chatterjee, 2021, § 7).
Kernel two-sample tests in high dimensions: interplay between moment discrepancy and dimension-and-sample orders
Authors: Yan Jian , Zhang Xianyang
Published: August 2022

Motivated by the increasing use of kernel-based metrics for high-dimensional and large-scale data, we study the asymptotic behaviour of kernel two-sample tests when the dimension and sample sizes both diverge to infinity. We focus on the maximum mean discrepancy using an isotropic kernel, which includes maximum mean discrepancy with the Gaussian kernel and the Laplace kernel, and the energy distance as special cases. We derive asymptotic expansions of the kernel two-sample statistics, based on which we establish a central limit theorem under both the null hypothesis and the local and fixed alternatives. The new nonnull central limit theorem results allow us to perform asymptotic exact power analysis, which reveals a delicate interplay between the moment discrepancy that can be detected by the kernel two-sample tests and the dimension-and-sample orders. The asymptotic theory is further corroborated through numerical studies.
Thoracoabdominal aneurysm causing functional mitral valve stenosis after total arch replacement
Authors: Hugas Maria , Schoenhoff Florian , Schmidli Jürg , Weiss Salome
Published: August 2022

Large thoracic and thoraco-abdominal aneurysms may compress adjacent mediastinal structures. We present a case of a large thoraco-abdominal aneurysm compressing the left atrium and leading to functional mitral valve stenosis after total aortic arch repair, requiring urgent open thoraco-abdominal aneurysm repair.