bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fish length estimation of free-swimming grouper in the cage culture using Underwater Televisual System (UTS), De-haze water correction, and deep learning methods
Authors: Ahmadi Y , Jaya I , Rahmat A , Iqbal M 
Published: October 2023

AbstractThis study aimed to obtain growth parameters for free-swimming grouper in cage culture by using a stereo camera Underwater Televisual System (UTS) for video recording. The UTS technology, utilizing two cameras, enables 3D perception and triangulation of rays for accurate depth estimation. The collected data underwent de-hazing water correction, preprocessing, and labeling. The length of the grouper was detected using the SSD Mobilenet v3 algorithm, with localization loss of 0.06%, accuracy of 92.00%, precision of 92.00%, recall of 100%, and F1-score of 95.83%. The measured length results indicated averages of 12.65 ± 3.81 cm and 26.00 ± 19.79 cm for two different sizes of free-swimming grouper. The study demonstrated that combining de-hazing water correction with the SSD Mobilenet v3 algorithm allows direct and accurate measurement of free-swimming grouper length. The integration of UTS technology and advanced algorithms significantly enhances the accuracy and efficiency of fish growth measurement in cage culture. These findings have practical implications for the development of sustainable fish farming practices, enabling optimized feed and water management, reduced mortality rates, and maximized production yields. Accurate growth monitoring contributes to the growth of the aquaculture industry, meeting the increasing demand for seafood sustainably.
North Pacific Water Mass Contribution in the Northern Sea of Lembata Island, East Nusa Tenggara
Authors: Slamet A , Naulita Y , Hermawan U 
Published: October 2023

Abstract
As the Indonesian Throughflow (ITF) passes through the Flores Sea, we expect it will affect the water mass character in the northern sea of Lembata Island. Therefore, we examined the contribution of North Pacific (NP) water mass, i.e., the North Pacific Subtropical Water (NPSW) and the North Pacific Intermediate Water (NPIW) in the study area. We used 30 CTD casts from OTEC Geological Survey Center Expedition 2017 and ARGO float data, analyzed through the TS diagram and Optimum Multiparameter (OMP). The remnant of the NPSW (NPIW) core layer was found at 140-190 (220-330) m depth, deeper than it occurs in the NP source regime, and of previous pathway seas i.e. Makassar Strait. The OMP results show NPSW (NPIW) contribution is about 20-75 (50-70)%. Contrary to the ITF direction from the western pathway, the value of NP water mass contribution is larger in the eastern than in the western part of the northern sea of Lembata Island. We speculated the ITF flows away from the northern sea of Lembata Island, blocked by the headland in the eastern part of Flores Island. Then a small part of ITF is deflected back to the west, but unfortunately, no detailed current is available in the study area.
Bathymetry mapping for pioneer ship voyages using side scan sonar in Sembulang Waters, Riau Islands
Authors: Marpaung S H , Pujiyati S , Agus S B , Solikin S , Lubis M Z 
Published: October 2023

Abstract
The SSS C-MAX CM2 Tow fish instrument is an acoustic instrument that operates at a frequency of 325 kHz with a maximum sounding distance of 200 m towing cable length of 50 m, producing images and textures within a large area. This study aimed to process data from the SSS C-max CM2 measurement survey to obtain MSL and LLWL tidal corrected bathymetry data, which is used to create a sailing map for pioneer ships in Sembulang Waters, Riau Islands. The SSS data acquisition was carried out on March 15 - 18, 2021, in Sembulang Waters using a 5GT vessel with a Batam State Polytechnic team. Tidal data was taken using a tidal board placed at Sembulang Pier. SSS data processing used Sonar Wiz 7 licensed software obtained from Pushidrosal with the application of several geometric and radiometric corrections. Geometric corrections included layback, bottom tracking, and slant range correction. Radiometric correction consists of Beam angle Correction (BAC), Automatic Gain Control (AGC), Time-Varying Gain (TVG), and Empirical Gain Normalization (EGN). Tidal data was processed using the Admiralty method. SSS data was exported into .csv format for making topographic maps of the seabed based on the depth and width of the ideal shipping lane based on the specifications of traditional fishing vessels used at the research site. The actual depth value of the Sembulang Waters ranges from 0.5 meters to 27.7 meters. The depth of the waters towards the east is getting deeper. The depth value of the Sembulang Waters in LLWL conditions ranges from 0 meters to 26.5086 meters, shows that several locations need to be avoided for ships sailing area and need to be dredging for the safety of ships ≥ 5GT.
Diversity of non-targeted species on blue swimming crab Portunus pelagicus collapsible trap fishery in Pemalang, Central Java
Authors: Arofah N , Ervinia A 
Published: October 2023

Abstract
A collapsible trap is one of the fishing gears commonly used by fishermen to catch blue swimming crabs. However, non-target species or by-catch are often caught by fishing gear. This study aimed to determine the diversity of non-target species caught by collapsible traps used in the blue swimming crab fishery. This study was conducted in Pemalang waters from January to June 2020. The Shannon-Wiener diversity, the evenness, and the Simpson dominance indices were analyzed. The results showed that the non-target species comprised seven crustaceans, six fish species, and four mollusks. The highest number of by-catches was observed in June from the mollusk group (5,762 ind of tiger snails), while the lowest catches were observed in Jan-March from the groups of fish, crustaceans, and mollusks. The predominated by-catch from collapsible traps in Pemalang was Babylonia sp. (87.64%), Podophthalmus vigil (9.74%), Charybdis feriatus (1.5%), and Portunus sanguinolentus (0.36%). The highest diversity index value was estimated in Jan at 1.73%, while the lowest was in June at 0.05%. The evenness index was highest in May and lowest in June. The by-catch biodiversity of blue swimming crab fishery in Pemalang was classified as low diversity category, low evenness, and moderate dominance.
Characteristics and density of the horseshoe crab (Tachypleus gigas) from gillnet fishery in Pamekasan, Madura Island
Authors: Maulana P. , Asih E N N , Arisandi A , Azis A , Darmawan D 
Published: October 2023

Abstract
The horseshoe crab is included in the category of protected species (ETP) because of its rare existence. Therefore, it is essential to identify the characteristics and density of horseshoe crabs. This study aimed to examine horseshoe crabs’ morphometric characteristics and density (Tachypleus gigas) on the coast of Polagan Village, Pamekasan Regency, Madura. This study was conducted from November to December 2020. Results showed that 45 horseshoe crabs were found in Pamekasan waters during the study period, consisting of 30 males and 15 females. The total average length was 164.57±40.92 mm and 163.67±31.30 mm for males and females, respectively. Males than females dominated horseshoe crabs. The density was based on the size class, consisting of 9 ind of small size (73-132 mm), 31 ind of medium size (133-222 mm), and 5 ind of large size (223-282mm). The water quality was classified as good for the growth of the horseshoe crab population, with sediments dominated by sand and silt. Further study is needed regarding the seasonal variation of horseshoe crab in Pamekasan Water.
The impact of mangrove environmental conditions on the growth rate of juvenile blue swimming crab (Portunus pelagicus) in Polagan Beach, Pamekasan, Madura Island
Authors: Aprilianto R Y , Hairuddin Q B A , Anwar S , Masnagari L M S , Sukma M A , Taqiyuddin M W 
Published: October 2023

Abstract
Mangrove forests have essential ecological functions, especially for coastal areas, one of which is as a shelter for small crab species at the juvenile stage. The research was conducted in Polagan Beach, Pamekasan Regency in November 2020-January 2021. The methods were divided into three sequential parts: pre-survey (processing of mangrove density data through Sentinel 2 satellite imagery), survey (calculating water quality and mangrove density parameters) and post-survey (determining each point/station that was used to support the continuity of the research). Data used in analysis are primary data (field) and secondary data (satellite image). The satellite image used in this research was acquired from Sentinel 2 satellite. The result concluded that temperature and salinity affect the growth rate of juvenile blue swimming crabs, but it does not occur significantly. The pH and heavy metal levels affect the survival rate of juvenile blue swimming crabs. Optimal temperature and salinity levels that can produce maximum juvenile growth are temperatures around 28-32°C and salinity around 32-34ppt. The level of mangrove density affected the water quality parameters (temperature and salinity).
Improving size and selectivity of blue swimming crab (Portunus pelagicus) by using collapsible trap with escape vents in Pamekasan, Madura Island
Authors: Ramadhan F , Taqiyuddin M W , Satria M B , Nugroho K C , Setioko W 
Published: October 2023

Abstract
Blue Swimming Crab (Portunus pelagicus) is high export value product from Indonesia that usually exported as pasteurized crabmeat in cans, and has high consumer demand. Blue swimming crab production still depends on wild catch, so that it will threaten the existence of them in the sea. The use of traps will cause almost all sizes of blue swimming crabs to be caught (accidentally) including those that are still small (not suitable for catching). This study aims to analyze the effectiveness of the escape vent in collapsible traps to reduce small catches of blue swimming crabs in the Pamekasan area. This research was carried out from August 2021 - January 2022 in the southern waters of Pamekasan. The method used is descriptive analysis and the effectiveness analysis of collapsible traps with a size (length x width) of escape vents is 4,5 x 3,5 cm. The study carried out 106 females and 85 males with a total weight of 22,908 kg and the carapace width ranged from 9,7 to 15,8 cm. The effectiveness of escape vents is 98,65%, which is the higher value (closer to 100%) the more benefits it will give to sustainability of blue swimming crabs in the Pamekasan area.
Measurement of live shrimp carapace length and its swimming speed in the cage culture using Multiple Object Tracking
Authors: Aprianto G N P , Jaya I , Iqbal M 
Published: October 2023

Abstract
The carapace length of live shrimp is one of the important parameters to monitor the growth of the shrimp from time to time in cage culture, while its swimming speed is one of the key indicators to understanding the behavior and health of the shrimp. To estimate live shrimp carapace length and its swimming speed, we recorded a live shrimp in the cage culture using an underwater video camera. The collected datasets then being preprocessed and labeled. Before measuring the carapace length of the shrimp, we used the You Only Look Once (YOLO) v5 algorithm with K-fold cross-validation to detect shrimp heads. The accuracy value obtained is 85.6%, recall 85.4%, precision 77.3%, and F1-score 81.1%. Then the multiple object tracking (MOT) DeepSORT method was used to measure the shrimp’s carapace length and its swimming speed. The measurement results showed that the average length of the shrimp was 13.5-14.8 pixels, and the average speed of the shrimp was 62-78 pixels/second. We obtained that there is a strong linear relationship between carapace length and swimming speed of shrimp, namely SS = 11.864 CL + 43.419, where CL and SS are carapace length and swimming speed, respectively, with R-square = 0.9095. In conclusion, the live shrimp carapace length and its swimming speed can be measured using YOLO v5 and MOT DeepSORT directly and accurately.
Rehabilitation of captive Indo-Pacific bottlenose dolphin (Tursiops aduncus) as a way to combat the effects of climate change
Authors: Josephine E C , Adriani  , Mujiyanto  
Published: October 2023

Abstract
Climate change caused by human industrialization is an unavoidable global problem which started in the 20th century. The high concentration of greenhouse gases has caused global warming, natural disaster, rising sea level, and threatened marine wildlife. It has been proven to decrease the survival rate of dolphins by 12%. This research aims to describe the behavior and assess the readiness to release rehabilitated Tursiops aduncus in Umah Lumba, Banyuwedang Bay, Bali, to boost the wild dolphin population. Visual observation was made on three individuals: Rambo, Rocky and Johnny, at Umah Lumba, Banyuwedang Bay Bali, on March 2021, who have been in the rehabilitation facility since September 2019. The three individuals can be identified by the physical characteristics of their head, mandible, and dorsal fin. The dolphins have developed nine wild-dolphin-like behaviors: respiratory, exploratory, resting, reproductive, social, predatory, spy-hopping, tail-clapping, and sneezing. This rehabilitation program is essential because it increases the population of wild dolphins by acclimating, adapting, and training former captive dolphins for release.
Smart hydroponic monitoring using Internet of Things (IoT’s) supported by hybrid solar system
Authors: Rahmat A , Wibowo G W 
Published: October 2023

Abstract
Aquaponics provides an alternative to farming on limited land by combining aquaculture and hydroponics in a symbiotic environment. Aquaponics practitioners usually only focus on techniques and the use of fertilizers. But over time, the need for science and technology has become an important factor in the application of more modern aquaponics based on the Internet of Things until the 4.0 revolution. Routine and intensive monitoring can certainly be an obstacle for aquaponics actors who have limited time and human resources. So we need an automation system that can be used for remote monitoring and control in real-time with a high level of mobility. The presence of solar energy leads to the use of hybrid power plants. A smart grid is a modern electric grid concept that has a high degree of flexibility, accessibility and efficiency. The pattern of gardening with hydroponics provides a solution for residents who live in urban areas because hydroponics is a way of planting with water media which is an alternative medium to replace soil. The use of IoT technology makes it easy because maintenance can be done by the system itself and monitoring and control of the hydroponic system can be done anywhere. A smartphone can be used as a device to monitor and control the system. Several studies related to this aquaponic monitoring and control system have also been carried out with various innovations, such as making an aquaponic system with IoT technology by integrating it on android applications and websites with several actuator controls. In this study, it was integrated between IoT-based aquaponic control systems and hybrid solar systems to accommodate power consumption. The system has been operating well and can control cultivated plants.
Spatial aggregation effects on the performance of machine learning metamodels for predicting transit time to baseflow
Authors: Soriano Jr Mario A , Maxwell Reed 
Published: October 2023

Abstract
Water transit time is the duration between the entry and exit of a parcel of water across a hydrologic system. It is a fundamental characteristic that links hydrologic transport, biogeochemical processing, and water quality, and it has broad implications for resource vulnerability and sustainability. Physically based models can accurately describe transit time distributions but require significant computational resources when applied to large regions at high resolutions. In this study, we evaluate the potential of machine learning metamodels to emulate physically based models for computationally efficient prediction of key metrics from transit time distributions. Transit times are computed from a continental scale, integrated hydrologic model coupled with particle tracking. The metamodeling approach is illustrated in the 280,000-sq km Upper Colorado River Basin, USA, a principal headwater basin that is under multiple stresses, including resource overallocation, water quality threats, and climate change impacts. We evaluate the effects of using different types of spatial aggregation in the metamodels, including regular grids, hydrologic units, and upstream watersheds. We found that metamodels using upstream watershed aggregation exhibited the best overall performance across our target predictions. Errors were more pronounced in metamodels that employed smaller spatial aggregation units compared to larger units, suggesting that additional predictors that capture the heterogeneity of topographic, climatic, and geologic properties are needed at these scales. We also found that predictor importance and input-output relations were remarkably consistent across spatial aggregation type and agree with previous findings documented from physically based models and tracer-based studies. Our results show the feasibility of developing machine learning metamodels for predicting transit times and demonstrate the necessity of multiscale analyses to probe the robustness of the findings.
Variability in opioid conversion calculators in critically ill children transitioned from fentanyl to hydromorphone
Authors: Casten Madison , Miller Jamie L , Neely Stephen B , Harkin Maura , Johnson Peter N 
Published: October 2023

Abstract

Purpose
Opioid conversion calculators (OCCs) are used to convert between opioids. The purpose of this study was to describe the variability in OCC results in critically ill children transitioned from fentanyl to hydromorphone infusions.

Methods
This was a descriptive, retrospective study. Seventeen OCCs were identified and grouped into 6 groups (groups 1-6) based on the equianalgesic conversions. The OCCs were used to calculate the hydromorphone rate in critically ill children (&lt;18 years) converted from fentanyl to hydromorphone. Information from a previous study on children stabilized on hydromorphone (defined as the first 24-hour period with no change in the hydromorphone rates, &lt;3 hydromorphone boluses administered, and 80% of State Behavior Scale scores between 0 and –1) were utilized. The primary objective was to compare the median hydromorphone rates calculated using the 17 OCCs. The secondary objective was to compare the percent variability of the OCC-calculated hydromorphone rates to the stabilization rate.

Results
Seventeen OCCs were applied to data on 28 children with a median age and hydromorphone rate of 2.4 years and 0.08 mg/kg/h, respectively. The median hydromorphone rate calculated using the 17 OCCs ranged from 0.06 to 0.12 mg/kg/h. Group 3 and group 6 OCCs resulted in a calculated hydromorphone rate that was higher than the stabilization rate in 96% and 75% of patients, respectively. Use of group 4 and group 5 OCCs resulted in a calculated hydromorphone rate that was lower than the stabilization rate in 64% and 75% of patients, respectively.

Conclusion
Given the considerable variability of OCCs, caution should be used when applying OCCs to critically ill children.
Latest knowledge on strigolactone biosynthesis and perception
Authors: Seto Yoshiya 
Published: October 2023

ABSTRACT
Strigolactones (SLs) are a class of terpenoid lactones initially identified as seed germination stimulants for root parasitic plants more than 50 years ago. Long after this initial discovery, SLs were re-characterized as the symbiotic signals for arbuscular mycorrhizal fungi that supply inorganic nutrients, such as phosphate, to their host plants. In 2008, SLs were found to be endogenous plant hormones that regulate shoot branching in plants. The discovery of SLs as a new class of plant hormones has significantly advanced research in this field. Studies over the past 15 years have elucidated almost the entire pathway of SL biosynthesis and the overall mechanism of its signaling. This review summarizes research on the SL biosynthetic pathway, and the current state of knowledge of the SL perception mechanism.
Bayesian linear mixed model with multiple random effects for prediction analysis on high-dimensional multi-omics data
Authors: Hai Yang , Ma Jixiang , Yang Kaixin , Wen Yalu 
Published: October 2023

Abstract

Motivation
Accurate disease risk prediction is an essential step in the modern quest for precision medicine. While high-dimensional multi-omics data have provided unprecedented data resources for prediction studies, their high-dimensionality and complex inter/intra-relationships have posed significant analytical challenges.

Results
We proposed a two-step Bayesian linear mixed model framework (TBLMM) for risk prediction analysis on multi-omics data. TBLMM models the predictive effects from multi-omics data using a hybrid of the sparsity regression and linear mixed model with multiple random effects. It can resemble the shape of the true effect size distributions and accounts for non-linear, including interaction effects, among multi-omics data via kernel fusion. It infers its parameters via a computationally efficient variational Bayes algorithm. Through extensive simulation studies and the prediction analyses on the positron emission tomography imaging outcomes using data obtained from the Alzheimer’s Disease Neuroimaging Initiative, we have demonstrated that TBLMM can consistently outperform the existing method in predicting the risk of complex traits.

Availability and implementation
The corresponding R package is available on GitHub (https://github.com/YaluWen/TBLMM).
Expanded utility of the R package, qgg, with applications within genomic medicine
Authors: Rohde Palle Duun , Fourie Sørensen Izel , Sørensen Peter 
Published: October 2023

Abstract

Summary
Here, we present an expanded utility of the R package qgg for genetic analyses of complex traits and diseases. One of the major updates of the package is, that it now includes Bayesian linear regression modeling procedures, which provide a unified framework for mapping of genetic variants, estimation of heritability and genomic prediction from either individual level data or from genome-wide association study summary data. With this release, the qgg package now provides a wealth of the commonly used methods in analysis of complex traits and diseases, without the need to switch between software and data formats.

Availability and implementation
The methodologies are implemented in the publicly available R software package, qgg, using fast and memory efficient algorithms in C++ and is available on CRAN or as a developer version at our GitHub page (https://github.com/psoerensen/qgg). Notes on the implemented statistical genetic models, tutorials and example scripts are available at our GitHub page https://psoerensen.github.io/qgg/.