bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential activity of recombinant laccase for biodegradation of ampicillin
Authors: Nuryana I , Dewi K S , Andriani A , Laksmi F A
Published: June 2023

The broad applications of antibiotics in the field of medicine and animal husbandry to treat bacterial infections in humans and animals have affected the rise of risks related to antibiotic contamination. Since the presence of antibiotics in the environment is harmful to the ecological system, this concern needs to be addressed. Among various methods, biodegradation by harnessing specific enzymes such as laccase to eliminate antibiotics has attracted huge attention due to its excellent ability and performance. In this study, the laccase-encoding gene fromTrametes hirsutawas introduced and integrated into an expression host,Pichia pastoris. Furthermore, the recombinant laccase was then investigated for its potential activity to degrade ampicillin. The enzyme activity was determined using syringaldazine as a substrate, while biodegradation of ampicillin was tested againstEscherichia coliandStaphylococcus aureususing disk diffusion assay. The laccase could be successfully expressed inP. pastoriswith the highest activity at 716 U L−1and showed its potential to functionally deactivate ampicillin as an antibacterial. This study indicates that the use of recombinant laccase for the biodegradation of ampicillin is considered a promising approach since it is safe, sustainable, and eco-friendly.
The removal of mercury using Penicillium sp. strain A4 and its toxic effects on fish
Authors: Dewi R S , Yoga G P , Andriyani R , Ridwan Y S , Pujiwati A , Sari A A
Published: June 2023

Mercury (Hg) is a heavy metal that is commonly found in waters and sediments. Mercury and its derivatives are highly toxic). Their presence in the aquatic environment can be very detrimental. Aspergillus fungi are known to reduce Hg levels in pollutants. Our research aim was to evaluate the toxic effect of Hg after being reduced by local isolates of Penicillium sp. strain A4. A toxicity test was conducted on juvenile Caroline platyfish (Xiphophorus maculatus). The research was conducted by growing fungal isolates on potato dextrose broth (PDB) medium with the addition of Hg at 7 days of incubation. The Hg concentration was measured before and after the incubation. The acute toxicity test was conducted with two serial concentrations: 50% and 100% of PDB-Hg media from fungal removal, as well as one control. The acute toxicity test was carried out for 48 hours and the number of deaths of Xiphophorus maculatus was counted. The results showed a decrease of mercury concentration from 3.14 ppm to 0.797 ppm in PDB-Hg media on the activity of isolates of Penicillium sp. strain A4 resulting in 74.6% mercury removal. Acute toxicity test results showed that concentrations of 50% and 100% of PDB-Hg media caused 100% death of the fish. The results of this study can be used as initial data to determine the quality criteria for waste containing mercury that can be discharged into river bodies and strategies for using fungi applications using local isolates of Penicillium sp. strain A4, which has the potential for wastewater treatment before being discharged into the waters to reduce its toxic effects.
The efficacy of Vetiveria zizanioides in horizontal subsurface flow constructed wetland for treating textile wastewater
Authors: Rohaningsih D , Henny C , Susanti E , Sudiyono B T , Febrianti D , Waluyo A , Sugiarti  , Lestari F S
Published: June 2023

Textile wastewater discharged into rivers often triggers a decrease in water quality and causes harm to its aquatic ecosystem. Textile wastewater, which may contain nutrients, organic compounds, and heavy metals, can be managed using a constructed wetland system. Vetiver grass is known for its ability in treating polluted waters, though the information related to its potential in controlling textile wastewater pollution in riparian areas is still limited. This study aimed to determine the efficacy of a pilot scale constructed wetland system using vetiver grass (Vetiveria zizanioides) for the removal of several pollutants in a riparian area polluted by textile wastewater. The wastewater flowed horizontally through the sub-surface layer of the system with a hydraulic retention time of two days. The wastewater was diluted to 20%. Three systems were made by varying the porous size of planting media using coarse gravel, fine gravel, and sand. The systems were then run for three months. Of the three constructed wetland systems, the highest removal efficiency (RE) was achieved for the NH4+parameter with an average removal efficiency higher than 60%. The highest nutrient RE was achieved by the system with sand in the growing media, with NH4+RE of more than 80%. RE values were fluctuating until the end of the experiment, which might occur because the system was not yet stable. It may take longer operation time to get a better system performance in removing the pollutants contained in the textile industry waste.
Converting sawdust to biochar and its mineral content: A preliminary analysis
Authors: Rahmat A , Pramudya Y , Triwisesa E
Published: June 2023

In Indonesia, soil degradation is occurring. A strategy to improve soil conditions is by applying biochar as a soil amendment. On the other hand, Indonesia is an agricultural country with many types of biomass that can be converted into biochar. Sawdust of mahogany, teak, and sappan wood from the furniture industry is easy to find and has great potential as raw materials for biochar. This study used X-ray fluorescence spectrometry to determine the mineral content of sawdust biochar from mahogany, teak, and sappan wood sawdust, especially the ash fraction. Biochar was created by burning sawdust woods in a furnace at temperatures ranging from 250°C to 350°C. In general, the main mineral (ash fraction) content of wood sawdust biochar was calcium (CaO) at concentrations ranging from 51 to 72%, with sappan sawdust biochar having the highest concentration at 70–72%. The potassium (K2O) concentration ranged from 9–23%, with mahogany sawdust biochar having the highest concentration (23%). The phosphorus (P2O5) content ranged from 2 to 10%, with teak sawdust biochar having the highest concentration at 7–10%. Moreover, teak sawdust contained 15-20% silica, and sappan sawdust biochar contained 6-8% Fe. The mineral content in biochar ash included alkaline cations; if the biochar is applied to the soil, then a mineralization process may occur and the cations could improve pH conditions through a liming mechanism. This result is only general information; further research is required to produce more comprehensive data.
Chromium (VI) bioremediation potential of dark septate endophytic (DSE) fungi
Authors: Melati I , Rahayu G , Surono  , Effendi H , Henny C , Susanti E
Published: June 2023

Manufacturing activities release an extensive quantity of wastes containing hazardous materials like hexavalent chromium [Chromium VI, Cr(VI)] into the surroundings, threatening human health and the ecosystem. Fungi can be utilized as an efficient Cr(VI) remediation implement. The six isolates of dark septate endophytic (DSE) fungi (KSP, CPP, PP, DD, K.III.3.4, TKC) were evaluated for their tolerance and removal ability of various Cr(VI) concentrations (10, 30, and 50 mg/L). The quantification of Cr(VI) removal was analyzed using the 1,5-diphenylcarbazide method by UV-Visible spectrophotometer (Hitachi-U 2900). The results showed that all the DSE isolates were highly tolerant to Cr(VI) concentrations up to 50 mg/L with a tolerance index (TI) of 0.89-1.22. These fungal strains showed no significant growth (p > 0.05) from the controls. Furthermore, all test fungi exhibited an efficient removal capacity of up to 99% of 50 mg/L Cr(VI). The results indicated that DSE fungi are potential agents for bioremediation of Cr(VI) polluted surroundings like manufacturing wastewater. It is the first report on the ability of DSE fungi to remove Cr(VI).
Phyto-assisted synthesis of zinc oxide nanoparticles using mango (Mangifera indica) fruit peel extract and their antibacterial activity
Authors: Endah E S , Saraswaty V , Ratnaningrum D , Kosasih W , Ardiansyah A , Risdian C , Nugroho P , Aji E S , Setiyanto H
Published: June 2023

A facile and eco-friendly procedure was developed to fabricate zinc oxide nanoparticles (ZnO NPs) using an aqueous extract of mango fruit peel (MFP), a by-product of agroindustry. The ZnO NPs were fabricated using zinc acetate as a precursor and MFP extract as a reducing and capping agent in a neutral environment (pH 7). The UV-visible spectrum supported the formation of ZnO NPs, showing a distinctive absorption peak at 368 nm. The presence of a ZnO crystalline phase was identified by X-ray diffraction (XRD) analysis. The Fourier transform infrared (FTIR) evaluation demonstrated that the biomolecules present in the MFP extract actively contributed to zinc ion reduction. According to the scanning electron microscopy (SEM) image, the surface morphology of ZnO NPs showed a mixture of spherical and flake-like shapes with particle sizes ranging from ~20 to ~90 nm. Based on antibacterial analysis using the agar diffusion method, the biosynthesized ZnO NPs at 3% w/v were active against Escherichia coli, Bacillus subtilis, and Staphylococcus aureus with diameter inhibitions of 8, 19, and 10 mm, respectively. In summary, this present work highlights that ZnO NPs can be synthesized using a by-product of agroindustry. More importantly, the biosynthesized ZnO NPs can be applied as an antibacterial agent.
Carbon Dots for Improving Water and Oil Absorption of Sponges
Authors: Isnaeni  , Sugiarto I T , Yudasari N , Mohar R S
Published: June 2023

An oil spill is one of the hazardous problems in the ocean. Cleaning the oil spill requires expensive and specific technologies. Nowadays, advanced techniques such as skimmers, oil dispersion agents, in-situ burning and solar-heated oil-absorbent are frequently used to solve the problem. For oil-absorbent materials, further, development is still required to enhance oil dan water absorption. Carbon dots is one of the promising nanoparticles that can be used to improve oil absorption. In this work, we conjugated carbon dots made of pencil leads into several types of sponges. The purpose of this work was to improve oil and water absorption. Our experiment results showed that 2 to 5 nanometres size of ethanol soluble carbon dots were successfully synthesized using a simple electrochemical process. UV-Vis absorption and FTIR spectra showed clear energy transition and functional groups in carbon dots. We used six different sponges with various mass densities from 9 to 174 mg/cm3. Conjugation of carbon dots into the sponge was simply done by immersing the sponge in carbon dot solution and drying it. The conjugation made the mass of the sponge increase. We examined the water and oil absorption capacity of each sponge. Oil absorption capacities were different for each sponge. In general, the addition of carbon dots in sponges increased the mass density of sponge water twice. Furthermore, one type of sponge decreased oil absorption capacity after carbon dots conjugation. Other types of sponges showed an improvement of oil absorption capacity by 60% after carbon dot conjugation. We believe that this work can be further improved to get higher water and oil absorption.
Uncaria gambir Roxb. mediated synthesis of stable silver nanoparticles in the presence of triethanolamine as the capping agent
Authors: Labanni Arniati , Arief Syukri , Zulhadjri  , Handayani Dian
Published: June 2023

The study of silver nanoparticles (AgNPs) fabrication has gained great interest especially for pharmaceutical applications due to its excellent antibacterial properties. AgNps are well known for their inhibitory and bactericidal effects both on positive and negative gram bacteria. However, the utilisation of some chemical reducing agents in the synthesis process can be harmful to the environment and the human body. Green synthesis of silver nanoparticles has been successfully conducted using an aqueous extract of Uncaria gambir Roxb. (UGR) leaves as a bioreducing agent and triethanolamine as a capping agent, reacted with aqueous AgNO3 as the precursor. The formation of silver nanoparticles was visually revealed by colour change from yellow to brown. It was also confirmed by UV-visible (UV-Vis) spectrophotometer analysis by absorption peaks at 402–414 nm. The result of X-ray diffraction (XRD) analysis showed 5 peaks referring to face-centred cubic silver nanoparticles. Transmission electron microscope (TEM) analysis showed that spherical silver nanoparticles with a size range of 2–18 nm with a mean diameter of 8 nm have been formed. The result showed that the addition of 1/50 mL triethanolamine (TEA) could enhance the stability of colloidal nanoparticles and reduce the particle size up to 65%. This study confirmed that UGR aqueous leaf extract can be used to mediate rapid, environmentally friendly, and less expensive silver nanoparticles fabrication.
Distribution of Phenolic Compounds from Ulva Lactuca and Sargassum sp. via Slow-Pyrolysis
Authors: Amrullah A , Farobie O
Published: June 2023

Ulva Lactuca and Sargassum sp. are rapidly expanding algae that can be used as a source of bioenergy. Due to its high moisture and inorganic content, the direct use of Ulva Lactuca and Sargassum sp. for energy purposes is deep. Therefore, thermochemical processing, such as pyrolysis, is required to produce useful products, such as bio-oil. This study seeks to undertake a detailed investigation of bio-oil production from Ulva Lactuca and Sargassum sp. to provide useful information for its continued commercialization. The pyrolysis of Ulva Lactuca and Sargassum sp. was investigated for bio-oil production within the temperature range of 400-600 °C and reaction time of 10-50 min. The highest proportion of bio-oil was retrieved at 500 °C with yields between 18.5 and 30.2 wt%. As the pyrolysis temperature rose to 600 °C, the bio-oil yields slightly increased, but the prolonged reaction time did not significantly increase in bio-oil yields. Gas chromatography-mass spectrometry (GC-MS) was employed to elucidate the chemical composition found in the bio-oil product. The results showed that phenolic compounds increased from 9.64 to 16.73 area% with an increase in temperature. The highest phenolic compounds for Ulva Lactuca and Sargassum sp. were obtained at about 13.25% and 16.73%, respectively. The variations in the distribution of total phenols may be due to variations in species, sediment, and surrounding water quality. The high phenolic achieved at the highest possible yield indicates its potential to be used for the production of renewable phenolic resins.
Optimization of edible film production: natural dyes addition
Authors: Andriani D , Karina M , Priatni Sri , Indriyati  , Apriyana A Y , Srikandace Y
Published: June 2023

Several studies have been conducted to enhance the properties of nata de coco (NDC) based edible films. Previous works include the use of different concentrations of plasticizers, NDC slurry preparation to improve solubility, and the incorporation of essential oils as antibacterial agents. This paper focuses on enhancing the appearance of edible film by adding natural dyes. Commercial natural dyes at varying concentrations were added to the NDC-based edible film formulation and subjected to characterization. The physical properties analysis revealed that the use of natural brown dye from caramelized carrots was the most suitable option. The edible film with 1% v/v brown dye demonstrated 18.701% GL, 20.163 MPa, and 213.900 MPa for elongation, tensile strength, and Young’s modulus, respectively. The water vapor transmission rate (WVTR) of NDC edible film with brown dye also complies with the Japanese Industrial Standard (JIS), measuring 1.395 g/m2. Given the increasing demand for environmentally friendly packaging that also offers food preservation, it is anticipated that further improvements in edible films will continue to be explored in the food industry.
Analysis of rice husk biochar characteristics under different pyrolysis temperature
Authors: Hidayat  , Rahmat A , Nissa R C , Sukamto  , Nuraini L , Nurtanto M , Ramadhani W S
Published: June 2023

Rice is the main food for Indonesian. In production, it produces rice husk in huge amounts as waste. Rice husks have tough fibers, so their natural decomposing takes a long time. One strategy to take advantage of and add value to rice husk waste is to convert it into biochar. Biochar is a material that produced by a pyrolysis process of organic material, which is beneficial for the soil. The quality of biochar is influenced by pyrolysis temperature. This research aimed to analyze the biochar characteristics under various pyrolysis temperatures. The results showed that increasing the pyrolysis temperature will increase the element concentration of SiO2(ash fraction). On the other hand, increasing the pyrolysis temperature decreases the biochar yield, calorific value, carbon and hydrogen content, and K2O, CaO, P2O5, MnO, and TiO2concentration. The dominant elemental content of biochar (ash fraction) is SiO2with a concentration of 85.35–89.47%. Biochar yield was 37.4–68.18%. The carbon, hydrogen, and nitrogen content ranged from 31.77–38.11; 1.67–3.61; and 0.63–0.73%, respectively. The calorific value of the biochar ranged from 14.48 to 11.61 MJ/Kg. The highest biochar yield, with the highest carbon, hydrogen, and calorific value content, was obtained using the lowest pyrolysis temperature of 250 °C. Fourier transform infrared (FTIR) analysis showed that the functional groups in the biochars were O-H, C=O, and C-OH. Following the X-Ray diffraction (XRD) analysis result, the amorphous biochar of rice husk decreases with increasing pyrolysis temperature and vice versa. The rice husk biochar has excellent potential to produce silicate crystals.
Deep eutectic solvent as an eco-friendly catalyst for the synthesis of hydroxyphenylglycine methyl ester
Authors: Listiana S , Bahua H , Utami I D , Rahayu M D , Firdayani  , Alifah I , Kusumaningrum S
Published: June 2023

The development of deep eutectic solvent (DES) as a green medium and catalyst for sustainable organic synthesis is expanding due to environmental consciousness. DES components are inexpensive, easy to synthesize, non-toxic, biodegradable, and have tunable physicochemical properties. In this study, DESs were formed by a mixture of choline chloride (ChCl) as a hydrogen bond acceptor (HBA), while oxalic acid, glycerol, and urea acted as hydrogen bond donors (HBD). The formed DESs were then characterized by FTIR and their physicochemical properties. DES was applied as a catalyst in the esterification reaction of hydroxyphenylglycine (HPG) to produce hydroxyphenylglycine methyl ester (HPGME), an intermediate material for beta-lactam antibiotics. The result demonstrated that using DES consisting of ChCl-oxalic acid (1:1) could produce HPGME with a yield of 40%. However, further research is essential to investigate the optimum reaction condition, such as the composition of added DES, reaction time, and temperature to obtain a higher yield of HPGME.
Production of antibacterial and antioxidant agents by Actinobacteria using soybean meal as a nitrogen source
Authors: Risdian C , Endah E S , Saraswaty V , Wulansari H A , Diwan A M , Ratnaningrum D , Hidayati N A , Mozef T
Published: June 2023

Actinobacteria are mainly found in soil and some of them have properties that are common to bacteria and fungi, despite having quite distinct characteristics. Unlike bacterial colonies in general, which are clearly slimy and grow rapidly, some groups of actinobacteria colonies grow slowly by showing a powdery consistency and are tightly attached to the agar surface. Observations on a colony under the microscope showed that many of them form asexual spores for their reproduction. Many metabolite compounds generated by actinobacteria have promising activities like antioxidant and antagonistic activity against bacteria and fungi. The production of these compounds depends not only on the strain of the organism but also on the medium in which it is grown and the growth conditions. Moreover, agricultural by-products such as soybean meal are known to have high protein content, thus it can be potentially used as an alternative media for actinobacteria. In this research, ten actinobacterial strains were isolated from the soil. After seven days of cultivation with the medium containing soybean meal, the cultures were subjected to ethyl acetate extraction. Five extracts exhibited antibacterial properties against Bacillus subtilis with a zone of inhibition ranging from 10–14 mm. One extract could strongly inhibit Staphylococcus aureus with an inhibition zone of 21 mm. However, none of them were active against Escherichia coli. Five extracts demonstrated antioxidant DPPH radical scavenging activity with more than 40%.
Application of the concept of smart city and smart water management for the new capital city
Authors: Hernaningsih T , Said N I , Yudo S , Wahyono H D , Widayat W , Rifai A
Published: June 2023

The Indonesian government has decided to move the State Capital (IKN) from DKI Jakarta to East Kalimantan Province. One of IKN’s visions is to build a smart, modern city that meets international standards. This paper examines the concept of smart city and smart water management (SWM) that will be applied to the new IKNs to build an integrated, sophisticated and sustainable clean water supply system. The method used was analyzing concepts related to smart cities and SWM applications in the world and Indonesia. Based on the results of the analysis of the abovementioned concepts, several conclusions were obtained, namely that an SWM support system is indispensable in water system management, leak detection, and water quality monitoring. Then, a smart water grid is used to develop control over water resources, infrastructure, and water discharge with high efficiency and sustainability. The flood early warning system must be utilized to minimize losses or victims caused by flood disasters. In addition, an online water quality monitoring system is needed to monitor water quality online and in real time. The integrated implementation of the smart city and SWM concepts described in the paper is expected to produce safe, healthy, and sustainable drinking water services.
Evaluation of human urine purification using rice husk charcoal as the adsorbent
Authors: Sintawardani N , Adhilaksma C A , Hamidah U , Pradanawati S A , Suharno S M
Published: June 2023

The abundant amount and availability of human urine potentially can be re-used for water and nutrient resources. Nutrient content in urine, primarily nitrogen and phosphorus, can cause eutrophication in waters and worsen the environment. Urine is not easy to be managed separately because it is usually integrated with black water or domestic wastewater that flows to the sewer from households or other public facilities. The decline in water quality and the increase in water consumption by the global community have given many driving forces to technological breakthroughs that can recover important nutrients from waste for reuse. In addition, the high-water content of urine also provides an incentive to reuse or recycle most of the water contained in urine for public purposes. Rice husk charcoal is a waste product from burning husks used as fuel in the tofu-making process. It is usually used for poultry bedding or soil enhancer in gardening. This research aimed to characterize the utilization of rice husk charcoal as an adsorbent to treat urine to obtain clean water. The urine was processed using 30-mesh rice husk charcoal as an adsorbent. The soaking time and hose type were varied to identify the effect on the adsorption performance. The urine absorption using rice husk charcoal with 60 minutes soaking time showed the highest removal based on the absorbance value of 27.18% at 487 nm wavelength and 28.25% at 668 nm wavelength. On the other hand, the adsorption using a curved hose showed better performance than the straight hose. The adsorption using the curved hose could decrease the urine concentration by 25.30-29.24% at 487 nm wavelength and 28.50-30.19% at 668 nm wavelength. In addition, the urine total dissolved solids (TDS) decreased by 73-76%. Therefore, rice husk charcoal could be used as the adsorbent in the adsorption of human urine.
The Effect of Communication on Supply Chain Management Performance on Construction Projects in Jakarta
Authors: Ramadhan Wahyu , Prasetyo R F , Raflis
Published: June 2023

The information flow has a positive influence on the performance of a supply chain where if there is a miss communication, it can risk causing construction delays and causing problems such as delayed delivery from suppliers, poor decision making between the two parties, and many more, where good communication and coordination are needed for all those involved in the supply chain so that the maximum results are obtained in the process. This study aims to determine the effect of communication on supply chain performance in the construction industry. The sample in this study amounted to 53 respondents who were directly involved in 4 projects classified B1 and B2 in Jakarta. Data collection was done by using a questionnaire. The data processing technique in this study is multiple regression analysis. Based on the results of research conducted using the SPSS application, where all independent variables have a significant effect either partially or simultaneously on supply chain performance. From the results of R square, the independent variable in this study has an influence of 51.7% on supply chain performance.
Development of Infiltration Map Using Geographical Information System Based on Ground Test in Cisadane Watershed Indonesia
Authors: Hidayat D P A , Darsono S L W , Farid M
Published: June 2023

Infiltration is one of the watershed parameters that are essential for integrated water resources management. Infiltration can be measured directly by a ground test such as using a double infiltrometer. But for the very large watersheds, the ground test methods take a lot of time, require a lot of skilled manpower, and cost. Geographical information systems (GIS) and remote sensing applications have been developed and used in various fields such as water resources, and produce good and fairly accurate results. The present study aims to develop an infiltration map based on a limited point of survey using GIS. This study uses the Cisadane watershed in Indonesia as the case study with an area of 154547 ha. Furthermore, it will be compared with the potential recharge zone map that has been generated from previous research. The resulting map of infiltration generated by GIS with a limited point of the survey is quite close to the potential recharge zone map using the weighted method with watershed physical and hydrological factors.
The Effect of Petung Bamboo Reinforcement Threads on Reinforced Concrete (RC) Beams
Authors: Rakhmawati Anis , Nisak Chudzaifatur Rohmatun , Arnandha Yudhi
Published: June 2023

The bamboo reinforced concrete (RC) beam is used as an alternative to steel reinforcement (a non-renewable material), due to the high tensile stress value, readily available, and relatively cheap. Therefore, this study aims to evaluate the effect of petung bamboo reinforcement threads on reinforced concrete beams. This provided several treatments for various analyses, namely (1) Petung reinforcement without apus bamboo skin thread (P). (2) Petung reinforcement thread using apus bamboo skin at distances of 5 and 10 mm (U5 and U10). Based on the compressive strength of concrete cylinders, a quality of 21.212 MPa was produced. The average flexural strength also provided the P, U5, and U10 variants of 12.606, 17.916, and 14.383 MPa, respectively. This indicated that the addition of apus bamboo skin threads in petung reinforcement increased the flexural strength of the reinforced concrete beams. These conditions were subsequently capable of increasing the cross-sectional area of the petung bamboo’s main reinforcement.
Comparison of GPR (Ground Penetrating Radar) Penetration Results Using the GCB-400 Antenna on Flexible and Rigid Pavement
Authors: Nugroho Untoro , Susanto Norick Cahya Jonathan
Published: June 2023

GPR (Ground Penetrating Radar) has been known as a tool used in non-destructive testing or in other words GPR can find out the conditions below the surface without damaging the layer above it. The GPR method is generally applied to roads namely flexible pavements and rigid pavements. This method has non-destructive properties because it utilizes electromagnetic waves in its operation, such as detecting the presence of objects or constituent layers at a certain depth. The penetration depth that can be achieved by GPR is influenced by three physical parameters, namely conductivity, relative dielectric permittivity (RDP), and magnetic permeability. In this study, GPR used the GCB-400 antenna model produced by the Swedish company Geoscanners. The research was conducted on roads with 2 different types of materials, namely asphalt (flexible pavement) and concrete (rigid pavement). Asphalt and concrete have different relative dielectric permittivity (RDP), where asphalt has an RDP of 5 and concrete has an RDP of 5.5. The results showed that there were significant differences between roads with asphalt and roads with concrete materials. On roads with asphalt material, GPR can reach a depth of more than 3 meters. On roads with concrete materials, GPR can only reach a depth of less than 2 meters.
Estimating of Post-liquefaction Settlement Based on SPT Data in Klaten Regency, Central Java
Authors: Hasiholan F , Ismanti S , Rifa’i A
Published: June 2023

A strong earthquake with Mw 6.3 occurred in Yogyakarta on May 27, 2006, causes of damage to DI Yogyakarta Province and Central Java Province, including Klaten Regency. The geological stratigraphy consists of volcanic breccias, lava and tuff in this area and generally shallow groundwater levels, which can trigger liquefaction. The potential liquefaction analysis in this study uses Standard Penetration Test (SPT) data carried out in 3 districts, namely Delanggu, Polanharjo, and Karanganom District uses Idriss-Boulanger method. The peak ground acceleration was calculated by Next Generation Attenuation (NGA) method using data obtained from the Pacific Earthquake Engineering Research (PEER) Center database. The peak ground acceleration that causes liquefaction in this study is at least 0.29 g in bedrock. All areas indicated potential liquefaction with varying depths. Polanharjo District is the most susceptible to potential liquefaction. The method proposed by Zhang estimates post-liquefaction settlement in this study from 3.3 – 42.4 cm (light to extensive damage) in Klaten Regency. Based on the results, further mitigation studies are needed in Klaten Regency to minimize settlement that will occur due to liquefaction. This study is required in planning the construction of toll road in Klaten Regency.
Evaluation of Krueng Tripa River Capacity in Ujung Krueng Village, Nagan Raya Regency, Indonesia
Authors: Safriani Meylis , Amir Astiah , Ikhwali M. Faisi
Published: June 2023

Flood events are very common in the lowlands as often happens in Ujong Krueng Village, Tripa Makmur District. This study aims to determine the magnitude of the design flood discharge using the Nakayasu method and evaluating the cross-sectional capacity of the Krueng Tripa River in Ujong Krueng Village. The data used are both primary and secondary. Primary data consists of measurements of river slope, river flow velocity, river depth and river width, while secondary data consists of rainfall data, Krueng Tripa watershed maps and Krueng Tripa River situation maps. The results of the design flood discharge calculation using the Nakayasu method show that the 2-year return period (RP) is 3237.46 m3/s, the 5-year RP is 4389.53 m3/s, the 10-year RP is 5177.08 m3/s, the 10-year RP is 5177.08 m3/s, the 25-year RP is 6199.32 m3/s, the 50-year RP is 6979.04 m/s, and the 100-years RP is 7778.23 m3/s. From the results of hydraulic analysis on the section of the Krueng Tripa river in Ujong Krueng Village using the HEC-RAS 6.1.0software, it shows that in the 2-year return period, on pias 1, 7 and 8 experienced overflows on both sides while on pias 2, 3, 4, 5 and 6 only overflow on the right side. In the return periods of 5th, 10th, 25th, 50th- year and 100th, all the streams had overflowed, the highest overflow reached 4.84 m, while the lowest overflow reached 0.30 m.
The Potential Bioethanol Production from The Starch of Breadfruit Peel– A Review Case in Indonesia
Authors: Bahlawan Z A S , Megawati  , Triwibowo B , Damayanti A , Maulana A Y , Tassabila D E C , Ichwan R
Published: June 2023

The need for fossil energy is increasing over time and is not proportional to its availability which continues to decline. The consumption of fossil fuels in Indonesia is one of the highest in the world, reaching 75 billion liters in 2019. One of the alternative fuels that can substitute for fossil fuels is bioethanol. The potential utilization of agricultural waste in the form of breadfruit peel (Artocarpus altilis) into bioethanol is studied in Indonesia in this paper. Breadfruit peels contain a concentration of monosaccharides in the form of starch up to 39.5%. In addition, breadfruit production in Indonesia is also relatively high, up to 190,551 tons in 2020. Processing starch into bioethanol requires several stages of processing first. Pre-treatment with enzyme catalysts resulted in higher concentrations of reducing sugars than chemical catalysts. This was followed by fermentation with yeastSaccharomyces cerevisiaeto convert reducing sugars into bioethanol. In the final stage, the purification process is carried out by a multilevel distillation process and adsorption to obtain a 99.9% bioethanol purity. It is hoped that this review can help the strategy of processing breadfruit peel waste into bioethanol with an efficient process.
Smart Micro Grid Architecture for Realtime Monitoring of Solar Photovoltaic Based on Internet of Things
Authors: Iksan Nur , Purwanto  , Sutanto Heri
Published: June 2023

The use of PV solar energy as an alternative renewable energy source has increased worldwide. The smart grid monitoring system is applied on a micro scale for the fulfilment of household electricity needs or Smart Home Micro Grid (SHMG) using Artificial Intelligent (AI) and Internet of Things (IoT) approaches. Problems in solar PV systems include uncertainty and non-linearity which have an impact on the increasingly complex structure of the energy data generated and accelerate control and decision making. The forecasting process carried out using the AI approach is indispensable for the utilization of PV systems, especially for distributed residential PV that is operated and maintained independently. Furthermore, the use of IoT technology is also important to accelerate information processing and improve performance in the monitoring system. The purpose of this research is to develop a solar PV monitoring system framework at SHMG to optimize the performance of the electricity supply sourced from solar PV basen on IoT.
Effect of Solvent Type and Extraction Time on Binahong Leaf Extraction Process
Authors: Kusumaningrum M , Fardhyanti D S , Jai J , Yulianto D N , Suminar I S , Nurjaya
Published: June 2023

Extraction of binahong leaf essential oil was carried out using the soxhletation method. This research was conducted to study how the influence of solvent type and the length of extraction time and to determine the optimal soxhletation conditions of binahong leaf essential oil (Anredera Cordifolia (Ten.) Steenis). Soxhletation was carried out with variations in solvents of 96% ethanol, n-hexane, and chloroform and time variations of 4, 5, and 6 hours. The yield of essential oil obtained is affected by extraction time and the solvent type. The volatile oil components obtained from soxhletation are the terpenoid and fatty acid groups. The best yield obtained is 5.23% at 5 hours using 96% ethanol as solvent.
Degradation of Methylene Blue Dye in Wastewater Using Ozonation Method with H2O2 Catalyst
Authors: Wulansarie R , Jannah RF , Bismo S , Safitri R , Rengga WDP
Published: June 2023

Water pollution is still a serious problem in Indonesia. One of the pollutants that contribute to water pollution is dye. One type of dye that is often used in the textile industry is methylene blue. There are several methods for treating dye waste, one of which is the ozonation method. Ozonation is a chemical oxidation process to remove the color of organic dyes. The catalytic ozonation process can increase the ability of ozone in sewage treatment. The catalyst used is H2O2 which can decompose into OH radicals. OH radicals have a higher reduction potential than other oxidizing agents. Ozonation research with H2O2 catalyst aims to determine changes in the concentration of dyes, COD and BOD5. In testing the ozonation time (0.15,30,45,60) minutes, the pH conditions (5,7,9) and the total mass concentration of H2O2 (0.2,5,5,7,5,10) % showed that the longer the time ozonation, the higher the pH value. and the more H2O2 used, the less concentration of dye, COD and BOD5.
Photodegradation of methylene blue dye by hematite-biochar composite prepared from Dendrocalamus asper using microwave-assisted pyrolysis (MAP)
Authors: Astuti W , Meysanti D , Salsabila M T , Sulistyaningsih T , Rusiyanto
Published: June 2023

Petung bamboo (Dendrocalamus asper) stem-based hematite-biochar composite (HBC) has been synthesized using microwave-assisted pyrolysis (MAP) to replace conventional pyrolysis. The bamboo sawdust contains 19.8-26.6% lignin and cellulose as much as 4.24-5.36% so that it can be used as precursors in biochar preparation. In general, bamboo-based biochar has a low adsorption capacity. In this study, biochar was modified by hematite (Fe2OH3) to increase its ability in dye removal through the photocatalytic-adsorption process. Biochar was prepared by the MAP process and impregnated with FeCl3and Fe2SO4compounds to produce HBC. The performance of HBC was then tested using methylene blue with variations in solution acidity level, adsorption duration, and starting concentration. The results show that HBC prepared using a MAP process has a higher adsorption ability (90.56%) than HBC prepared through a conventional pyrolysis process (84.85%). At an adsorption duration of 240 minutes and a solution acidity level (pH) of 9, methylene blue was best absorbed.
The impossible challenge of estimating non-existent moments of the Chemical Master Equation
Authors: Wagner Vincent , Radde Nicole
Published: June 2023

Motivation

The Chemical Master Equation (CME) is a set of linear differential equations that describes the evolution of the probability distribution on all possible configurations of a (bio-)chemical reaction system. Since the number of configurations and therefore the dimension of the CME rapidly increases with the number of molecules, its applicability is restricted to small systems. A widely applied remedy for this challenge is moment-based approaches which consider the evolution of the first few moments of the distribution as summary statistics for the complete distribution. Here, we investigate the performance of two moment-estimation methods for reaction systems whose equilibrium distributions encounter fat-tailedness and do not possess statistical moments.

Results

We show that estimation via stochastic simulation algorithm (SSA) trajectories lose consistency over time and estimated moment values span a wide range of values even for large sample sizes. In comparison, the method of moments returns smooth moment estimates but is not able to indicate the non-existence of the allegedly predicted moments. We furthermore analyze the negative effect of a CME solution’s fat-tailedness on SSA run times and explain inherent difficulties. While moment-estimation techniques are a commonly applied tool in the simulation of (bio-)chemical reaction networks, we conclude that they should be used with care, as neither the system definition nor the moment-estimation techniques themselves reliably indicate the potential fat-tailedness of the CME’s solution.
Characterizing alternative splicing effects on protein interaction networks with LINDA
Authors: Gjerga Enio , Naarmann-de Vries Isabel S , Dieterich Christoph
Published: June 2023

Motivation

Alternative RNA splicing plays a crucial role in defining protein function. However, despite its relevance, there is a lack of tools that characterize effects of splicing on protein interaction networks in a mechanistic manner (i.e. presence or absence of protein–protein interactions due to RNA splicing). To fill this gap, we present Linear Integer programming for Network reconstruction using transcriptomics and Differential splicing data Analysis (LINDA) as a method that integrates resources of protein–protein and domain–domain interactions, transcription factor targets, and differential splicing/transcript analysis to infer splicing-dependent effects on cellular pathways and regulatory networks.

Results

We have applied LINDA to a panel of 54 shRNA depletion experiments in HepG2 and K562 cells from the ENCORE initiative. Through computational benchmarking, we could show that the integration of splicing effects with LINDA can identify pathway mechanisms contributing to known bioprocesses better than other state of the art methods, which do not account for splicing. Additionally, we have experimentally validated some of the predicted splicing effects that the depletion of HNRNPK in K562 cells has on signalling.
Reprohackathons: promoting reproducibility in bioinformatics through training
Authors: Cokelaer Thomas , Cohen-Boulakia Sarah , Lemoine Frédéric
Published: June 2023

Motivation

The reproducibility crisis has highlighted the importance of improving the way bioinformatics data analyses are implemented, executed, and shared. To address this, various tools such as content versioning systems, workflow management systems, and software environment management systems have been developed. While these tools are becoming more widely used, there is still much work to be done to increase their adoption. The most effective way to ensure reproducibility becomes a standard part of most bioinformatics data analysis projects is to integrate it into the curriculum of bioinformatics Master’s programs.

Results

In this article, we present the Reprohackathon, a Master’s course that we have been running for the last 3 years at Université Paris-Saclay (France), and that has been attended by a total of 123 students. The course is divided into two parts. The first part includes lessons on the challenges related to reproducibility, content versioning systems, container management, and workflow systems. In the second part, students work on a data analysis project for 3–4 months, reanalyzing data from a previously published study. The Reprohackaton has taught us many valuable lessons, such as the fact that implementing reproducible analyses is a complex and challenging task that requires significant effort. However, providing in-depth teaching of the concepts and the tools during a Master’s degree program greatly improves students’ understanding and abilities in this area.
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities
Authors: Wang Qi , Nute Michael , Treangen Todd J
Published: June 2023

Motivation

Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully decipher and control microbial communities.

Results

We present a novel approach for identifying species driving interactions within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species (MDS) using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile (rCDI) infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn's disease patients, uncovering driver species consistent with previous work. Bakdrive represents a novel approach for capturing microbial interactions.

Availability and implementation

Bakdrive is open-source and available at: https://gitlab.com/treangenlab/bakdrive.
SynBa: improved estimation of drug combination synergies with uncertainty quantification
Authors: Zhang Haoting , Ek Carl Henrik , Rattray Magnus , Milo Marta
Published: June 2023

Motivation

There exists a range of different quantification frameworks to estimate the synergistic effect of drug combinations. The diversity and disagreement in estimates make it challenging to determine which combinations from a large drug screening should be proceeded with. Furthermore, the lack of accurate uncertainty quantification for those estimates precludes the choice of optimal drug combinations based on the most favourable synergistic effect.

Results

In this work, we propose SynBa, a flexible Bayesian approach to estimate the uncertainty of the synergistic efficacy and potency of drug combinations, so that actionable decisions can be derived from the model outputs. The actionability is enabled by incorporating the Hill equation into SynBa, so that the parameters representing the potency and the efficacy can be preserved. Existing knowledge may be conveniently inserted due to the flexibility of the prior, as shown by the empirical Beta prior defined for the normalized maximal inhibition. Through experiments on large combination screenings and comparison against benchmark methods, we show that SynBa provides improved accuracy of dose–response predictions and better-calibrated uncertainty estimation for the parameters and the predictions.

Availability and implementation

The code for SynBa is available at https://github.com/HaotingZhang1/SynBa. The datasets are publicly available (DOI of DREAM: 10.7303/syn4231880; DOI of the NCI-ALMANAC subset: 10.5281/zenodo.4135059).
SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data
Authors: Lee Eric , Chern Kevin , Nissen Michael , Wang Xuehai ,   IMAXT Consortium, Huang Chris , Gandhi Anita K , Bouchard-Côté Alexandre , Weng Andrew P , Roth Andrew
Published: June 2023

Motivation

Recent advances in spatial proteomics technologies have enabled the profiling of dozens of proteins in thousands of single cells in situ. This has created the opportunity to move beyond quantifying the composition of cell types in tissue, and instead probe the spatial relationships between cells. However, most current methods for clustering data from these assays only consider the expression values of cells and ignore the spatial context. Furthermore, existing approaches do not account for prior information about the expected cell populations in a sample.

Results

To address these shortcomings, we developed SpatialSort, a spatially aware Bayesian clustering approach that allows for the incorporation of prior biological knowledge. Our method is able to account for the affinities of cells of different types to neighbour in space, and by incorporating prior information about expected cell populations, it is able to simultaneously improve clustering accuracy and perform automated annotation of clusters. Using synthetic and real data, we show that by using spatial and prior information SpatialSort improves clustering accuracy. We also demonstrate how SpatialSort can perform label transfer between spatial and nonspatial modalities through the analysis of a real world diffuse large B-cell lymphoma dataset.

Availability and implementation

Source code is available on Github at: https://github.com/Roth-Lab/SpatialSort.