bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability of Indonesian Throughflow Transport in the Indonesian Seas during Triple-Dip La Niña
Authors: Fekranie N. A. , Setiawan A. , Putri M. R. 
Published: June 2024

Abstract
The Indonesian seas serve as an important conduit for the Indonesian Throughflow (ITF), a critical system of warm water and freshwater transport connecting the Pacific and Indian Oceans. El Niño-Southern Oscillation (ENSO) significantly impacts the regional variability in the Pacific and exerts a profound influence on water mass transport from the Pacific to the Indian Oceans. This study focuses on the influence of triple-dip La Niña events during two distinct periods (1998 – 2001 and 2020 – 2023) on the variability of ITF transport in key areas of the Indonesian seas, including the Makassar, Lombok, and Ombai Straits, Flores and Banda Seas, and Timor Passage. Using forecast and reanalysis data from the Copernicus Marine Environment Monitoring Service (CMEMS), transport calculations are conducted across cross-sectional profiles representing the study areas. The results reveal that the volume transport is significantly higher at depths ranging from ∼50 – 300 m. It also shows seasonal fluctuations in volume transport across all regions, with lower transport during winter (DJF) and higher transport during summer (JJA) and transition period (SON) in the Makassar and Lombok Straits. In the Flores and Banda Seas, Ombai Strait, and Timor Passage, the surface volume transport follows seasonal patterns, while at deeper depths (∼50 – 300 m and 300 – 800 m) exhibits distinct fluctuations compared to the surface. Triple-dip La Niña events lead to an overall increase in volume transport during both periods, with the 2019 – 2023 period showing larger values (∼19 Sv) compared to the 1997 – 2001 period (∼14 Sv). The strengthened ocean current during triple-dip La Niña events results in more significant variations in total transport, leading to larger differences between minimum and maximum transport during these periods. The volume transport in Makassar Strait is further analyzed using the Empirical Orthogonal Function (EOF) that identifies three dominant modes (86.4%), revealing the influence of semi-annual, interannual, and decadal factors on the observed variability.
Actinobacteria diversity associated with sponge Amorphinopsis exacavans from Rancabuaya Beach, Garut, Indonesia
Authors: Srikandace Y , Hapsari Y , Andriani D 
Published: June 2024

Abstract
Sponges are complex marine organisms known for their symbiotic relationships with various bacterial communities, which play structural and functional roles within the sponge holobiont. Actinobacteria have received much attention because of their potential pharmaceutical applications. This study examines Amorphinopsis excavans profile, distinguishing between endosymbionts and ectosymbionts. The microbial grouping was characterized using Next Generation Sequencing (NGS) anchored to the 16S rRNA marker. The results showed that Proteobacteria and Firmicutes dominated both the endosymbiont and ectosymbiont communities at the phylum level. The actinobacterial diversity index at the genus level in both communities was 2.77 and 3.11, indicating moderate to high diversity without a dominant genus. For the genus level, the evenness scores of 0.81 and 0.89 indicated a high population type within the bacterial community. Relative abundance revealed the three most prevalent genera in the endosymbiont community were Rothia, Thermoplyspora, and Thermomonospora. In contrast, Kocuria, Mycobacterium, and Bifidobacterium were the three most common genera of ectosymbionts. Leuconostoc citreum was the first species known to be associated with a sponge. This study is a developing metagenomic assessment of actinobacterial diversity in A. excavans, providing novel insights into the sponge’s complex microbial ecosystem.
Ichthyoplankton Biodiversity in the Indonesian Fisheries Management Area-573 in 2015
Authors: Taufik M , Restiangsih Y H , Ma’mun A , Hidayat T , Wagiyo K , Panggabean A S , Nurulludin  , Prihatiningsih  
Published: June 2024

Abstract
Studying ichthyoplankton is crucial for understanding the impact of fish larvae mortality on the recruitment of adult fish and fishing resources. Fish larvae samples were collected in the southern waters of Java using the Baruna Jaya IV research vessel in September - October 2015. Fish larvae were collected using bongo-net and oceanographic data were collected using Conductivity Temperature Depth (CTD) are Temperature and salinity and chlorophyll-a using Aqua MODIS satellite L3 at 36 stations. The results showed the range of fish larvae abundance was 0 - 2,074 ind/1000 m3 with an average of 174 ind/1000 m3. The fish eggs were found with an abundance of 0 - 1,601 eggs/1000 m3. and an average of 213 eggs/1000 m3. The composition of fish larvae recorded 22 families, there were 5 dominant families namely Scombridae (28.60%), Bregmacerotidae (22.96%), Carangidae (7.93%), Blennidae (7.52%), and Gobiidae (7.52%). The diversity of fish larvae was most prevalent at station 28 (SST 26.7 0C; SSS 34.4 PSU; and CHL-a 0.43 mg/m3) and station 36 (SST 27.4 0C; SSS 34.4 PSU) each found 9 families. The abundance of fish larvae was mostly found at stasion 11 had SST 23.50 0C; SSS 34.56 PSU; and CHL-a 0.33 mg/m3 with the dominance of the family Bregmacerotidae. Scombridae was mostly found at stasion 22 with sea surface temperature (SST) 26.52 0C; sea surface salinity (SSS) 34.28 PSU; and sea surface chlorophyll-a (CHL-a) 0.41 mg/m3 which is in the southern waters of Lombok.
Analysis of natural occurring radionuclide activity concentration of fish in west coast waters of Sabah, Malaysia
Authors: Nur Rashidi Rosli Muhammad , Abd Azis Nurashikin , Jafar Sidik Madihah 
Published: June 2024

Abstract
Fish is an important source of protein in human diets, but concerns arise due to natural radionuclide contamination in food and water sources. The study aimed to assess the concentration radionuclides activities (232Th, 238U, and 40K) in three commercial fish species from west coast waters of Sabah, Malaysia. Additionally, the annual effective dose and cancer risk for adults consuming these fish were evaluated. The concentration analysis was conducted using the inductively coupled plasma-mass spectrometer (ICP-MS) technique. The average concentration levels of radionuclide activity detected, and the annual effective dose was estimated to be much lower than UNSCEAR recommendations. The collective effective dose was estimated at 1.88 μSv y−1 for 232Th, 1.11 μSv y−1 for 238U, and 15.12 μSv y−1 for 40K. The cancer risk for adults from the annual effective dose was also found to be much lower than UNSCEAR and ICRP recommendations. Based on the study’s findings, consuming fish from west coast waters of Sabah is deemed safe. However, it is recommended to establish a long-term monitoring system for radionuclide bioaccumulation in fish to gather valuable information for assessing the potential health risks associated with radionuclides in Malaysia, particularly in the Sabah.
Characterization of Underwater Landslides in Krui Waters, Lampung-Indonesia using Shallow Seismic and Sonar Data
Authors: Ardhyastuti S , Irfan M , Haryadi Y , Santoso E.W , Isnaniawardhani V , Putra P S , Iskandarsyah T Y W M , Tohari A 
Published: June 2024

Abstract
Krui Waters, Lampung, Indonesia, is an area that has the potential for a tsunami disaster. Local tsunamis can be caused by underwater landslides owing to ground movement and gravitational forces. Imaging underwater conditions using sonar and shallow seismic systems is an interesting research topic for geological disaster researchers. Underwater landslides are very important for disaster mitigation, especially for tsunami prediction. This research aims to identify the characteristics of underwater landslides around Krui Waters, Lampung, Indonesia, using imaging analysis methods from sonar data and a sub-bottom profiler (SBP). The underwater landslide phenomenon in this area is still not known in detail, and therefore requires further research. All data were obtained from the results of hydrographic, geological, and geophysical surveys of RV Baruna Jaya IV in 2020. The sonar data shows surface characteristics such as the presence of Furrows (Gravel Waves), Cobble (Boulder), as well as Canyons and landslides or mass movements rocks. SBP data show the characteristics of the seabed in the form of a canyon with a slope greater than 160. Finally, the morphological characteristics and features obtained could possibly be a potential source of local tsunamis owing to the high slope.
Potential Sunda Strait tsunami hazard due to the current deformation of Anak Krakatau
Authors: Karima S , Sujatmiko K A , Latief H , Abdurrachman M , Ihsan U , Husrin S 
Published: June 2024

Abstract
The tsunami Sunda Strait event at 2018 is a prove that volcanic activity may trigger a devastating and unpredictable tsunami. Several findings indicate that this catasrophe generated by flank collapse caused by the instability of Gunung Anak Krakatau (AK). Other processes of volcanic activity that cause tsunamis include pyroclastic flows, subaerial and submarine landslides, underwater explosions, blasts, and caldera collapse. In the 1883, Krakatau Mount produced the largest tsunami event, and it is apparent that AK is one of threats in Sunda Strait that may potentially produce tsunami in the future since it is still active until now. Some latest research shows there are two submarine landslide threats near Gunung Anak Krakatau; in the northeast part of AK and an elliptical landslide source in the west part of AK with the estimated landslide volume about 0.014 km3 and 0.6 km3, respectively. Those threats will be simulated by shallow water equation model to obtain the tsunami wave height near the source and at crucial areas along Sunda Strait as well as its tsunami time arrival. The first scenario is sourced from a new deposit from the 2018 eruption, and the latter is a change of slopes bathymetry due to volcanic or seismic activity. It is observed that the highest elevation of tsunami from the first scenario reached only 2.5 cm at Tanjung Lesung, Banten and 80 cm at the nearest island, Panjang Island. The second scenario has the height of 50 cm at Labuan, Banten and 70 cm at Panjang Island. The tsunami time travel at the surrounding islands is ranging between 0.6 - 5.8 minutes (scenario 1) and 0.7-4.9 minutes (scenario 2). Both scenario reached the inexpensive device of sea level monitoring at the east side of Rakata after 5 minutes and the height is 30 cm and 1.6 cm respectively for scenario 1 and 2.
Profile of seawater quality in Cirebon, northern coast of West Java, Indonesia
Authors: Oktaviani D F , Widyananto P A , Nur A A , Jeon C K 
Published: June 2024

Abstract
Cirebon is a coastal area where the economic activities of some people rely on water conditions. Besides that, the city is known to have an industrial area. Therefore, along with the rapid development of industrializations and urbanizations, it will also have an impact on the environmental quality particularly in coastal area. Assessing the profile of water quality could be the approach to knowing the environmental conditions. This research was aimed to understanding the current coastal condition based on the physical-chemical properties in Cirebon seawater. The data was collected using Conductivity-Temperature-Depth (CTD) and nutrient auto analyzer (NAA). Several parameters were collected including temperature, salinity, pH, levels of dissolved oxygen (DO), concentration of chlorophyll, nitrate (NO3-N), nitrite (NO2-N), ammonia (NH3-N), orthophosphate (PO4-P) and silicate (SiO2) from 11 points of survey area. The results showed that several parameters were similar in all stations, while some had different values between stations. Nutrient’s enrichment and chlorophyll were found to be higher in particular areas. The highest NO2-N content found in station 10 (0.005 mg/L), NO3-N in station 7 (0.343 mg/L), NH3-N in station 10 (0.044 mg/L), PO4-P in station 1 (0.087 mg/L), SiO2 in station 6 (1.281 mg/L) and chlorophyll in station 11 (2.12 ug/L). The average concentration was relatively found to be high in the station near the coastal area compared to the open sea. This can happen due to supply of organic substances into the coastal waters from the rivers that were being carried away by the current.
Coastal Hazards in the Sunda Strait: Mitigation Strategy and Coastal Management
Authors: Heriati A , Mustikasari E , Solihuddin T , Salim H L , Daulat A , Purbani D 
Published: June 2024

Abstract
Sunda strait is one of the strategic waters in Indonesia situated at the Indonesian archipelagic sea lane passage. The water is also known as one of the national strategic regions as governed in the Presidential Decree of 32/2019 about marine spatial planning. The coasts of the region have been developed as industrial areas, marine tourism and associated facilities, fisheries, agriculture, mining, etc. Despite the huge economic potency, Sunda Strait has high coastal hazards due to volcanic and tectonic activities. The Krakatau volcanic eruption in 1883 generated a tsunami run-up to ∼35 m high causing catastrophic damage along the coasts of Banten and Lampung and more than 36.000 people were reported killed. More recently, the eruption and flank collapse of the Anak Krakatau volcano generated a tsunami in the Sunda Strait causing severe damage, extensive inundation, and more than 430 deaths. Likewise, the Sunda Strait has a high potency of tsunami impacts generated by the earthquake sourced from the subduction zone known as megathrust. These conditions must become a valued lesson learned to all of us to raise awareness and preparedness through mitigation-based disaster management. Thus, we can reduce the impacts of the disaster and the high investment for post-disaster rehabilitation and reconstruction.
Spatial and temporal pattern of thermal front in Republic of Indonesia fisheries management area 571 (FMA 571)
Authors: Lukman A A , Tarya A , Pranowo W S 
Published: June 2024

Abstract
The spatial pattern of thermal front were obtained by processing sea surface temperature (SST) data using the SIED (Single Image Edge Detection) method. The objective of this research is to establish the characteristics of the surface thermal front in the Republic of Indonesia Fisheries Management Area (FMA) 571 based on its spatial and temporal map in the year of 2010-2020. SST & chlorophyll-a of AquaMODIS satellite imagery and FMA 571 bathymetry of the Indonesian Geospatial Information Agency data are used in this research. This research results that the maximum & the minimum average thermal front are found in the southwest monsoon and the first inter-monsoon with values of 135 and 39 events, respectively. The maximum (minimum) SST average is 32.182°C (30.483°C) and the maximum (minimum) average chlorophyll-a concentration value is 0.858 mg/l (0.577 mg/l). The optimum SST is estimated ranges of 30.483°C – 31.831°C for thermal front formation. The Pearson correlation analysis reveals a significant positive correlation coefficient of 0.674 during the northeast monsoon, highlighting the association between thermal fronts and chlorophyll-a concentration. Spatially persistent thermal front always appears in the northern part of FMA 571.
The added value of Himawari-8 satellite radiance data assimilation for very heavy rainfall prediction in the Indonesian Maritime Continent (Case study: East Kalimantan)
Authors: Mukhsinin H.M. , Trilaksono N.J. , Giriharta I.W.G. , Simanjuntak J.T. 
Published: June 2024

Abstract
This study evaluates the impact of assimilating Advanced Himawari Imager (AHI) radiance data on the 8-10 water vapor channel using the three-dimensional variational (3DVAR) technique for the very heavy rainfall events in East Kalimantan on June 2-4, 2019. We utilized the Weather Research and Forecasting (WRF) and WRF Data Assimilation (WRFDA) system to run assimilation and prediction model simulations. To compare the assimilated model with AHI data and without assimilation, we devised two experimental schemes: 3DVAR and NODA. We assessed the enhancement in model prediction by comparing simulation results based on convection evolution, vertically integrated moisture flux convergence (VIMFC) increment, and rain prediction skill metrics, including Threat Score (TS), Equitable Threat Score (ETS), and Fractions Skill Score (FSS). Our findings suggest that the incorporation of AHI data results in a substantial improvement of the WRF model’s prediction of the very heavy rainfall events in East Kalimantan.
Human iPSC-derived liver co-culture spheroids to model liver fibrosis
Authors: Cools Laura , Dastjerd Mina Kazemzadeh , Smout Ayla , Merens Vincent , Yang Yuwei , Reynaert Hendrik , Messaoudi Nouredin , Smet Vincent De , Kumar Manoj , Verhulst Stefaan , Verfaillie Catherine , van Grunsven Leo A 
Published: June 2024

Abstract
The lack of adequate human in vitro models that recapitulate the cellular composition and response of the human liver to injury hampers the development of anti-fibrotic drugs. The goal of this study was to develop a human spheroid culture model to study liver fibrosis by using induced pluripotent stem cell (iPSC)-derived liver cells. iPSCs were independently differentiated towards hepatoblasts (iHepatoblasts), hepatic stellate cells (iHSCs), endothelial cells (iECs) and macrophages (iMΦ), before assembly into free floating spheroids by culturing cells in 96-well U-bottom plates and orbital shaking for up to 21 days to allow further maturation. Through transcriptome analysis, we show further maturation of iECs and iMΦ, the differentiation of the iHepatoblasts towards hepatocyte-like cells (iHeps) and the inactivation of the iHSCs by the end of the 3D culture. Moreover, these cultures display a similar expression of cell-specific marker genes (CYP3A4, PDGFRβ, CD31 and CD68) and sensitivity to hepatotoxicity as spheroids made using freshly isolated primary human liver cells. Furthermore, we show the functionality of the iHeps and the iHSCs by mimicking liver fibrosis through iHep-induced iHSC activation, using acetaminophen. In conclusion, we have established a reproducible human iPSC-derived liver culture model that can be used to mimic fibrosis in vitro as a replacement of primary human liver derived 3D models. The model can be used to investigate pathways involved in fibrosis development and to identify new targets for chronic liver disease therapy.
High Quality of Care Delivery Improves Patient Satisfaction and Quality of Life Outcomes After Breast Augmentation
Authors: Luong Kim Phi , ter Stege Marloes H P , Hummelink Stefan , Zaal Laura , Slijper Harm P , Ulrich Dietmar J O 
Published: June 2024

Abstract

Background
Breast augmentation is one of the most common aesthetic procedures worldwide. Most studies have focused on evaluating the outcome with validated patient-reported outcome measures (PROMs) and factors that may influence them. However, the influence of care delivery, which can be measured with patient-reported experience measures (PREMs), is rarely considered in studies of breast augmentation patients.

Objectives
In this study we aimed to evaluate the associations between PREMs and PROMs in patients who underwent breast augmentation.

Methods
A multicenter cohort study was conducted in breast augmentation patients. Patients completed PREMs, including items such as communication between physician and patient, expectation management, welcome, and hygiene, and the BREAST-Q PROM (satisfaction with breasts and psychosocial, physical, and sexual well-being) preoperatively and 6 months postoperatively. Regression analyses were performed to investigate the associations between PREMs and PROMs.

Results
Overall, 329 patients were included between 2018 and 2022. Univariate regression analysis showed a positive association between PREM and PROM scales. The feeling of being heard (B = −38.39 and B = −18.90), the opportunity to ask questions (B = −9.21), and trust in their physician (B = −39.08) had the highest association with change in the 4 BREAST-Q scales. The multivariable regression analysis showed that the variance in PROMs related to changes in PREMs (19%) was little influenced by patient characteristics (1%).

Conclusions
Patient outcomes are more positive after breast augmentation when patients feel they are being heard, have the opportunity to ask questions, and have trust in their physician. Future studies should be targeted at optimizing patient-reported experience to investigate whether this improves patient-reported outcomes.

Level of Evidence: 3
Approaches to embryonic neurodevelopment: from neural cell to neural tube formation through mathematical models
Authors: Rafati Ali H , Joca Sâmia , Vontell Regina T , Wegener Gregers , Ardalan Maryam 
Published: June 2024

Abstract
The development of the human central nervous system initiates in the early embryonic period until long after delivery. It has been shown that several neurological and neuropsychiatric diseases originate from prenatal incidents. Mathematical models offer a direct way to understand neurodevelopmental processes better. Mathematical modelling of neurodevelopment during the embryonic period is challenging in terms of how to ‘Approach’, how to initiate modelling and how to propose the appropriate equations that fit the underlying dynamics of neurodevelopment during the embryonic period while including the variety of elements that are built-in naturally during the process of neurodevelopment. It is imperative to answer where and how to start modelling; in other words, what is the appropriate ‘Approach’? Therefore, one objective of this study was to tackle the mathematical issue broadly from different aspects and approaches. The approaches were divided into three embryonic categories: cell division, neural tube growth and neural plate growth. We concluded that the neural plate growth approach provides a suitable platform for simulation of brain formation/neurodevelopment compared to cell division and neural tube growth. We devised a novel equation and designed algorithms that include geometrical and topological algorithms that could fit most of the necessary elements of the neurodevelopmental process during the embryonic period. Hence, the proposed equations and defined mathematical structure would be a platform to generate an artificial neural network that autonomously grows and develops.
Deletion variants calling in third-generation sequencing data based on a dual-attention mechanism
Authors: Wang Han , Li Chang , Yu Xinyu , Gao Jingyang 
Published: June 2024

Abstract
Deletion is a crucial type of genomic structural variation and is associated with numerous genetic diseases. The advent of third-generation sequencing technology has facilitated the analysis of complex genomic structures and the elucidation of the mechanisms underlying phenotypic changes and disease onset due to genomic variants. Importantly, it has introduced innovative perspectives for deletion variants calling. Here we propose a method named Dual Attention Structural Variation (DASV) to analyze deletion structural variations in sequencing data. DASV converts gene alignment information into images and integrates them with genomic sequencing data through a dual attention mechanism. Subsequently, it employs a multi-scale network to precisely identify deletion regions. Compared with four widely used genome structural variation calling tools: cuteSV, SVIM, Sniffles and PBSV, the results demonstrate that DASV consistently achieves a balance between precision and recall, enhancing the F1 score across various datasets. The source code is available at https://github.com/deconvolution-w/DASV.