bluuebunny/crossref_metadata_2025 huggingface dataset:
Target strength of Nile tilapia (Oreochromis niloticus) from 200 kHz calibrated fish finder and scientific echosounder: laboratory measurement and modeling
Authors: Dwinovantyo A , Solikin S , Triwisesa E , Triyanto T
Published: October 2023

Target strength (TS) values from laboratory measurement and TS values from the model were measured and calculated from Nile tilapia (Oreochromis niloticus). Nile tilapia is one of the fastest growing aquaculture species, the fourth most produced fish globally, easily available in various sizes and lengths, and more importantly, it has a one-chambered swimbladder, which is suitable for TS measurement and modeling. The most common technique of measuring fish TS is utilizing a scientific echosounder. However, this instrument has a low implementation for small-scale fisheries due to its relatively high cost compared to the conventional fish finder. Thus, the objective of this study is to offer a solution that considers the instrument’s cost and usefulness using calibrated fish finder and scientific echosounder. TS values were produced by the two instruments that later being examined with TS from the Kirchhoff-ray mode (KRM) model to validate the result. Two single-beam echosounder instruments (Furuno FCV-628 fish finder and Simrad EK15 scientific echosounder) operated at a frequency of 200 kHz were used to assess the TS values for 30 samples of living Nile tilapia whose total length (TL) was in a range of 6 to 26 cm. In conclusion, statistically, the results showed no significant differences in TS measurement between the two instruments compared to TS values from the model. The TS values from the KRM model agreed well based on the regression analysis with the TS values from both instruments in the laboratory measurement.
Preliminary study on restoration of tropical seagrass ecosystem through utilization of Enhalus acoroides seedling in Bintan Island, Indonesia
Authors: Nugraha A H , Addini I , Halim M , Darus R F
Published: October 2023

There has been a global decline in the area of seagrass ecosystems caused by the increasing number of human activities in coastal areas. It is suspected that the decline in the area of seagrass beds in Indonesia is 2%-5% per year. It takes an effort that can be used to restore the condition of seagrass beds. So far, efforts have been made to do seagrass transplants. There is a weakness in the transplant method, namely the reduction of seagrass stands in the origin (donor) area. Another effort that can be used is planting seagrass using seagrass seeds derived from seedlings. Seagrass seeds come from the seagrass, Enhalus acoroides, which is found throughout the year in the waters of Bintan Island. Furthermore, the seeds obtained will be sown for three months in the laboratory. Generally, the survival rate of seagrass seeds during the seedling process has a value of more than 90%, which is very good. Furthermore, the seeds produced from the nursery process are planted in the field. In this experimental study, 25 seedlings were planted. Seedlings were planted directly into the substrate at a depth of 10 cm (sprig method). During the four-month observation period, the survival rate declined to 20%. Several factors that affect the survival rate include the condition of the aquatic environment and human activities around it.
The Utilization of Seasonal Variation of Ocean Wave Characteristics Identification in Monitoring the Chlorophyll-a Distribution in South Sulawesi
Authors: Islami M F , Jasruddin  , Sujiono E H
Published: October 2023

South Sulawesi is one of Indonesia’s provinces with various forms of waters around its territory, such as the sea, strait, the Spermonde archipelago, and bay. This geographical condition makes it interesting to examine what phenomena can affect the characteristics and variability of ocean waves in each type to increase efficiency and effectiveness in carrying out activities in the waters, especially fishing. By utilizing the BMKG Ina-Waves wave model and NASA’s Aqua MODIS satellite image, the characteristics and variations of ocean waves and the level of fertility of the waters around South Sulawesi Province can be seen. Based on the climatological analysis of wind, ocean waves, and the distribution of chlorophyll-a in this study, the results showed that the Asian and Australian monsoon phenomena greatly influenced these three parameters. The monsoon winds increase the average wave height and affect the distribution of chlorophyll-a concentrations in the waters of South Sulawesi and its surroundings. Efficiency and effectiveness of fishing at sea are carried out during the transition season in the coastal waters of South Sulawesi so that the risk of sea accidents can be minimized.
Estimation of diffuse coefficient attenuation (Kd
490) using sentinel 2A in Panggang Island and its Surrounding Water
Authors: Tiarasani A , Siregar V P , Gaol J L
Published: October 2023

In marine remote sensing areas, the intensity of the light that enters the water column will decrease exponentially with increasing depth due to scattering and absorption. The process of reducing intensity is called the attenuation process. This process became a limiting factor in detecting objects at the bottom and water column using a remote sensing method that depends on light intensity. Diffuse attenuation coefficient (Kd
) is an important optical property of seawater because it provides information on water clarity and the level of light attenuation. This research analyzed the Kd and its variability from in situ measurement and Sentinel-2 level 2A MSI (Multi Spectral Imagery) data in Karang Lebar, Panggang Island, and Air Island, in Seribu Island, North Jakarta. We determined the Kd
(490) value using several algorithms. The result showed that Kd
(490) in situ and from the model has a good correlation (r = 0.75 – 0.86).
Mapping reef terrain roughness and benthic habitat complexity in the Pamegaran Island, Kepulauan Seribu National Marine Park
Authors: Batubara S R , Agus S B , Sunuddin A
Published: October 2023

The formation of coral cays in the Kepulauan Seribu Marine Parks, Jakarta Special Capital Region, is the result of patch reef evolution which linked to the geology of sediment accretion, including the ecology of coral growth and competition of benthic community. This study aims to map the level of reef complexity in Pamegaran Island using Benthic Terrain Modeler. Field observation to monitor benthic communities in four stations at 3- and 5- meter depth was combined with SPOT-7 image processing to evaluate in situ rugosity, 3-dimensional bathymetry and benthic habitat classification. The results of this study revealed low degree of terrain complexity as results of habitat degradation and dominant benthic class of sand. Classification of reef benthic habitat resulted in five classes, namely sand (Sd= 126.65 ha), seagrass (Sg= 35.29 ha), bare rubble (Rb= 32.68 ha), reefs dominated by dead corals (DC=3.16 ha) and dead coral with algae (DA= 20.50 ha); with 67.21% score of overall accuracy (OA). In situ rugosity at 5 m was higher than 3 m, as result of higher coverage of live corals particularly in the east site. Similar profile was shown for rugosity index, which reflects ratio between surface to planar area and seafloor gradient along the reef slope. Finally, positive correlation between reef surface and in situ rugosity implies the importance of live coral communities in supporting complex terrain and benthic habitat in the patch reef environment.
Distribution of heavy metals in water and sediment at the Bojonegara nearshore of Banten Bay, Indonesia
Authors: Sari J E W , Prartono T , Sulistiono
Published: October 2023

Heavy metals released to a nearshore environment may vary due to contaminant sources and the seasonally coastal processes. This study revealed how the seasonal variability and potential sources controlled the distribution pattern of several heavy metals and the level of water quality in Bojonegara nearshore of Banten Bay. The water and sediment samples were collected once in January, February, August, September, and October 2020 at six stations representing the river and sea. Heavy metal was determined using the APHA procedure. Cu was detected in August-October, ranging from <0.002 – 0.008 mg/L. The concentrations of Cu, Cd, and Pb in the sediment were detected, varying from <0.02 to 3.90 mg/kg, <0.02-1.68 mg/kg, and <0.02-6.71 mg/kg, respectively. The concentrations of the concerned metals in sediment vary, and their distribution pattern change seasonally. These metals in water and sediments were still safe for the environment and marine biota. This study suggests how contaminant sources and coastal processes could control the contaminant level. In addition, potential sources of heavy metal merely derived from onshore of the Bojonegara, but it could be derived from advection from other areas through the coastal processes.
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

This 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

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

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

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

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

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

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

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

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

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

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

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 (<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, <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

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

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

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/.
ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations
Authors: Schäfer Richard A , Guo Qingxiang , Yang Rendong
Published: October 2023

Motivation

Neoantigens, tumor-specific protein fragments, are invaluable in cancer immunotherapy due to their ability to serve as targets for the immune system. Computational prediction of these neoantigens from sequencing data often requires multiple algorithms and sophisticated workflows, which are currently restricted to specific types of variants, such as single-nucleotide variants or insertions/deletions. Nevertheless, other sources of neoantigens are often overlooked.

Results

We introduce ScanNeo2 an improved and fully automated bioinformatics pipeline designed for high-throughput neoantigen prediction from raw sequencing data. Unlike its predecessor, ScanNeo2 integrates multiple sources of somatic variants, including canonical- and exitron-splicing, gene fusion events, and various somatic variants. Our benchmark results demonstrate that ScanNeo2 accurately identifies neoantigens, providing a comprehensive and more efficient solution for neoantigen prediction.

Availability and implementation

ScanNeo2 is freely available at https://github.com/ylab-hi/ScanNeo2/ and is accompanied by instruction and application data.
Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta–brain axis
Authors: Kinkade Jessica A , Seetharam Arun S , Sachdev Shrikesh , Bivens Nathan J , Phinney Brett S , Grigorean Gabriela , Roberts R Michael , Tuteja Geetu , Rosenfeld Cheryl S
Published: October 2023

The fetal brain of the mouse is thought to be dependent upon the placenta as a source of serotonin (5-hydroxytryptamine; 5-HT) and other factors. How factors reach the developing brain remains uncertain but are postulated here to be part of the cargo carried by placental extracellular vesicles (EV). We have analyzed the protein, catecholamine, and small RNA content of EV from mouse trophoblast stem cells (TSC) and TSC differentiated into parietal trophoblast giant cells (pTGC), potential primary purveyors of 5-HT. Current studies examined how exposure of mouse neural progenitor cells (NPC) to EV from either TSC or pTGC affect their transcriptome profiles. The EV from trophoblast cells contained relatively high amounts of 5-HT, as well as dopamine and norepinephrine, but there were no significant differences between EV derived from pTGC and from TSC. Content of miRNA and small nucleolar (sno)RNA, however, did differ according to EV source, and snoRNA were upregulated in EV from pTGC. The primary inferred targets of the microRNA (miRNA) from both pTGC and TSC were mRNA enriched in the fetal brain. NPC readily internalized EV, leading to changes in their transcriptome profiles. Transcripts regulated were mainly ones enriched in neural tissues. The transcripts in EV-treated NPC that demonstrated a likely complementarity with miRNA in EV were mainly up- rather than downregulated, with functions linked to neuronal processes. Our results are consistent with placenta-derived EV providing direct support for fetal brain development and being an integral part of the placenta–brain axis.
Should we enlarge the indication for kidney biopsy in diabetics? The con part
Authors: Ortiz Alberto
Published: October 2023

Diabetes is the most common cause of chronic kidney disease (CKD), a condition found in 850 million persons and projected to become the fifth global cause of death by 2040. Research is needed that examines kidney tissue to characterize distinct phenotypes in patients with diabetes mellitus (DM) and CKD so as to identify non-invasive biomarker signatures and develop targeted therapeutic approaches. However, from a routine care point of view, kidney biopsy is likely overused in patients with CKD and DM, as most biopsy results are not expected to be associated with a therapeutic approach that differs from standard kidney protection with triple or quadruple therapy (renin–angiotensin system blockade, sodium-glucose cotransporter 2 inhibitors, nonsteroidal mineralocorticoid receptor antagonists and glucagon-like peptide-1 receptor agonists). Moreover, expanding the kidney biopsy criteria will increase the absolute number of complications from kidney biopsies, which may reach 27 000 to 108 000 deaths of persons that would derive little benefit from kidney biopsy if all people with DM and severe CKD were biopsied globally. Finally, limited resources should be optimally allocated. The cost of one kidney biopsy can fund 7000 semiquantitative urinary albumin:creatinine ratio assessments that could identify earlier stages of the disease and allow treatment that prevents progression to a stage at which kidney biopsy may be considered.
Kidney biopsy in diabetic kidney disease. Yes, but in very selected cases
Authors: Zoccali Carmine
Published: October 2023

The debate on kidney biopsy in diabetic kidney disease (DKD) is multifaceted. Loreto Gesualdo and colleagues argue for its broader application, claiming that biopsies can offer precise diagnostic data and guide personalized treatment plans. On the other hand, Alberto Ortiz opposes this, citing insufficient evidence, resource constraints and potential risks. He suggests that alternative diagnostic methods, such as advanced imaging techniques and serological markers, will obviate the need for biopsy in most patients. Both sides agree on the need for individualized patient care, and open discussions between healthcare providers and patients about the procedure's risks and benefits. The application of kidney biopsy in these patients needs to consider clinical evidence, practical limitations and patient preferences, and demands a balanced, case-by-case approach. Overall, this moderator believes that, although fundamental in clinical research, kidney biopsy in DKD is infrequently needed.
Organ perfusion pressure at admission and clinical outcomes in patients hospitalized for acute heart failure
Authors: Bocchino Pier Paolo , Cingolani Marco , Frea Simone , Angelini Filippo , Gallone Guglielmo , Garatti Laura , Sacco Alice , Raineri Claudia , Pidello Stefano , Morici Nuccia , De Ferrari Gaetano Maria
Published: October 2023

Aims

Hypoperfusion portends adverse outcomes in acute heart failure (AHF). The gradient between end-organ inflow and outflow pressures may more closely reflect hypoperfusion than mean arterial pressure (MAP) alone. The aim of this study was to investigate organ perfusion pressure (OPP), calculated as MAP minus central venous pressure (CVP), as a prognostic marker in AHF.

Methods and results

The Sodium NItroPrusside Treatment in Acute Heart Failure (SNIP)-AHF study was a multicentre retrospective cohort study of 200 consecutive patients hospitalized for AHF treated with sodium nitroprusside. Only patients with both MAP and invasive CVP data available from the SNIP-AHF cohort were included in this analysis. The primary endpoint was to assess OPP as a predictor of worsening heart failure (WHF), defined as the worsening of signs and symptoms of heart failure leading to intensification of therapy at 48 h. One hundred and forty-six patients fulfilling the inclusion criteria were included [mean age: 61.1 ± 13.5 years, 32 (21.9%) females; mean body mass index: 26.2 ± 11.7 kg/m2; mean left ventricular ejection fraction: 23.8%±11.4%, mean MAP: 80.2 ± 13.2 mmHg, and mean CVP: 14.0 ± 6.1 mmHg]. WHF occurred in 14 (9.6%) patients. At multivariable models including hemodynamic variables (OPP, shock index, and CVP), OPP at admission was the best predictor of WHF at 48 h [OR 0.91 (95% confidence interval 0.86–0.96), P-value = 0.001] with an optimal cut-off value of 67.5 mmHg (specificity 47.3%, sensitivity 100%, and AUC 0.784 ± 0.054). In multivariable models, including univariable significant parameters available at first bedside assessment, namely New York Heart Association functional class, OPP, shock index, CVP, and left ventricular end-diastolic diameter, OPP consistently and significantly predicted WHF at 48 h.

Conclusion

In this retrospective analysis on patients hospitalized for AHF treated with sodium nitroprusside, on-admission OPP significantly predicted WHF at 48 h with high sensitivity.
Macroevolutionary Origins of Comparative Development
Authors: Riahi Ideen A
Published: October 2023

Advances in evolutionary theories (the Extended Synthesis) demonstrate that organisms systematically modify environments in ways that influence their own and other species’ evolution. This paper utilises these theories to examine the economic consequences of human dispersal from Africa. Evidence shows that early humans’ dispersal affected the adaptability of animal species to human environments and, through this, the extinction of large mammals during Homo sapiens’ out-of-Africa migration. Empirical analyses explore the variation in extinction rates as a source of exogenous pressure for cooperation and innovation among hunter-gatherers and examine the impact of extinction on long-run development. The results indicate that extinction affects economic performance by driving continental differences in biogeography, disease environments and institutions. Eurasia’s location along the out-of-Africa migratory path provided human and animal populations with co-evolutionary foundations for domestication and agriculture, which gave Eurasians technological and institutional advantages in comparative development.
Metataxonomic analysis of milk microbiota in the bovine subclinical mastitis
Authors: Alessandri Giulia , Sangalli Elena , Facchi Mario , Fontana Federico , Mancabelli Leonardo , Donofrio Gaetano , Ventura Marco
Published: October 2023

Subclinical mastitis is one of the most widespread diseases affecting dairy herds with detrimental effects on animal health, milk productivity, and quality. Despite its multifactorial nature, the presence of pathogenic bacteria is regarded one of the main drivers of subclinical mastitis, causing a disruption of the homeostasis of the bovine milk microbial community. However, bovine milk microbiota alterations associated with subclinical mastitis still represents a largely unexplored research area. Therefore, the species-level milk microbiota of a total of 75 milk samples, collected from both healthy and subclinical mastitis-affected cows from two different stables, was deeply profiled through an ITS, rather than a traditional, and less informative, 16S rRNA gene microbial profiling. Surprisingly, the present pilot study not only revealed that subclinical mastitis is characterized by a reduced biodiversity of the bovine milk microbiota, but also that this disease does not induce standard alterations of the milk microbial community across stables. In addition, a flow cytometry-based total bacterial cell enumeration highlighted that subclinical mastitis is accompanied by a significant increment in the number of milk microbial cells. Furthermore, the combination of the metagenomic and flow cytometry approaches allowed to identify different potential microbial marker strictly correlated with subclinical mastitis across stables.
Promoter-proximal introns impact recombinant amylase expression in Saccharomyces cerevisiae
Authors: Schwerdtfeger Kirstie S , Myburgh Marthinus W , van Zyl Willem H , Viljoen-Bloom Marinda
Published: October 2023

Consolidated bioprocessing (CBP) of starch requires recombinant Saccharomyces cerevisiae strains that produce raw starch-degrading enzymes and ferment the resultant sugars to ethanol in a single step. In this study, the native S. cerevisiae COX4 and RPS25A promoter-proximal introns were evaluated for enhanced expression of amylase genes (ateA, temA or temG_Opt) under the control of an S. cerevisiae promoter (ENO1P, TEF1P, TDH3P, or HXT7P). The results showed that different promoters and promoter-intron combinations differentially affected recombinant amylase production: ENO1P-COX4i and TDH3P-RPS25Ai were the best promoters for AteA, followed closely by HXT7P. The latter was also the best promoter for TemA and TemG production, followed closely by TDH3P-RPS25Ai for both these enzymes. Introducing promoter-proximal introns increased amylase activity up to 62% in Y294[ENO-COX-AteA] and Y294[TDH3-RPS-TemA], a significant improvement relative to the intron-less promoters. Strains co-expressing both an α-amylase and glucoamylase genes yielded up to 56 g/L ethanol from 20% w/v raw starch, with a higher carbon conversion observed with strains co-expressing TDH3P-RPS25Ai-temG_Opt than HXT7P-temG_Opt. The study showed that promoter-proximal introns can enhance amylase activity in S. cerevisiae and suggest that these alternative cassettes may also be considered for expression in more efficient ethanol-producing industrial yeast strains for raw starch CBP.
The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum
Authors: Lei Li , Gordon Sean P , Liu Lifeng , Sade Nir , Lovell John T , Rubio Wilhelmi Maria Del Mar , Singan Vasanth , Sreedasyam Avinash , Hestrin Rachel , Phillips Jeremy , Hernandez Bryan T , Barry Kerrie , Shu Shengqiang , Jenkins Jerry , Schmutz Jeremy , Goodstein David M , Thilmony Roger , Blumwald Eduardo , Vogel John P
Published: October 2023

Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.
Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha
Authors: Sandler George , Agrawal Aneil F , Wright Stephen I
Published: October 2023

The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction.