bluuebunny/crossref_metadata_2025 huggingface dataset:
Land inventory and designation of the Kranji river riparian zone in Purwokerto city, Central Java
Authors: Sholichin M , Prayogo T B , Susilo H
Published: March 2024

River banks are virtual lines of the riverbed designated as river protection boundaries. This research aimed to inventory the Kranji Riverbank’s land condition and conduct a study to determine the width of the riparian zone. The methods used were field surveys, identification of land along the 11 km river, and analysis of flood discharge designs with a return period of 10 years. The results of an inventory along the river on the river land dominated the permanent building. There are 400 building units included in the repair zone on the Kranji River. Based on the planned flood analysis results with a return period of Q10 years of 38.11 m3/s, there are 160 flood points along the river. The width of the riparian zone in urban areas is 10 meters in East Purwokerto, while outside urban areas, it is 50 meters in Baturaden District. The benefit of the results of this research is the provision of initial data for coordinating with several other agencies in efforts to implement the Kranji River border in the future.
A GIS-based approach to determine the priority area for rainwater harvest in Kupang
Authors: Syarifuddin M , Masria  , Oktaviantoro D
Published: March 2024

Kupang, a pivotal economic and administrative hub in Nusa Tenggara Timur, Indonesia, faces recurring droughts resulting in crop failures, food insecurity, and health problems. Addressing this water crisis entails rainwater harvesting as a potential solution. This study establishes a comprehensive framework for prioritizing rainwater harvesting areas in Kupang. Using the weighted overlay method and open-source GIS software, our approach involves three stages: identifying drought and flood priority zones, defining suitability indicators, and quantifying the potential of rainwater harvesting systems. By leveraging climatological, geological, and hydrological information, we determine priority areas for drought and flood management. Our analysis of rainwater harvesting suitability integrates climatological information, land use and land cover mapping, runoff potential assessment, and water use index. Quantification of rainwater harvesting system requirements hinges on rooftop area and population data. The entire wards in Kupang are classified as high priorities for drought mitigation. Therefore, rainwater harvesting is a viable strategy for all wards. The most prioritized and in-demand wards, Oesapa, Sikumana, Lasiana, and Liliba, have the potential to install a minimum of 12,000 rainwater harvesting systems, each with a 1500-liter volume barrel.
Rainfall trend analysis to the change of flood discharge estimation in Bengawan Solo River
Authors: Nurhakim A , Widyaningrum D , Farid M , Prasetyo A , Moe I R , Chaidar A N , Hartanto I M , Sihombing Y I , Adityawan M B
Published: March 2024

Bengawan Solo Watershed is the largest watershed on Java Island, which also has fluctuating rainfall. The fluctuating rainfall may cause an alteration to the river discharge. The alteration can be analyzed through the SCS-CN model and Synder Unit Hydrograph. SCS-CN Java Island, which also has fluctuating rainfalis a well-known model in hydrological modeling that is commonly used because of its simplicity, stability, and predictability. Synder Unit Hydrograph is suitable for ungauged basins and may be used in watersheds about 25 km2 to 25.000 km2 (Sudhakar BS et al, 2015). The analysis and calibration were performed from the baseline data (2001-2022). The trend analysis was carried out by comparing the analysis results from data sequences with a ten-year range with the baseline data. According to the trend analysis, the rainfall design of the Bengawan Solo watershed has increased by approximately 4–6% in 2013–2022 compared to the baseline (2001-2022), which may lead to a 10% increase in flood design discharge in Bengawan Solo.
Analysis of factors affecting the intake gate operations of Gerokgak Reservoir for command areas of Subak Gede
Authors: Indrayana I B G , Nurrochmad F , Pratiwi E P A
Published: March 2024

Subak Gede in Gerokgak Village, Buleleng, practices traditional irrigation in Bali based on Tri Hita Karana principles. Subak sources water from Gerokgak Reservoir, where intake gate operations depend on three factors: the recent ten-day discharge (item 1), rainfall in command areas (item 2), and crop type (item 3). Quantification Analysis I simulated the intake gate from 2019 to 2022, comprising Models A to D, each using yearly data for its respective year (2019, 2020, 2021, 2022), and Model E using four years of data. Items 1 and 2 had high, moderate, and low categories; item 3 had paddy, palawija, paddy-palawija, and fallow categories. The simulation exhibited strong correlations between predicted and recorded discharge of every quantification model, with R-total > 0.6, varying for each sample year. Based on the analysis, the three items showed a different impact every year, depending on the item-category distribution and variation. Notably, due to its sample, quantification Model E excelled in predicting intake gate operations for other yearly data, including its own sample year.
Correlation between volume weight, porosity and moisture content in Central Kalimantan’s Peatlands
Authors: Novrianti  , Harisuseno D
Published: March 2024

Peat is determined by soil characteristics consisting of maturity, color, low PD, low BD, texture, and organic content, which are different from mineral soil types, which can store more water with relatively high porosity, can decrease if drought due to lack of peat wetting with fiber spaces blackish brown with a fine structure. The purpose of this study was to determine the physical and chemical properties of peat as a water storage container and to determine the correlation between volume weight, porosity, and water content. The method used is a descriptive method, Sieve analysis, using ring samples and eagle auger camp. Laboratory results show that the BD value is small, the PD value is small, the water content value is high, the peat has maturity levels of Sapric and Hemic, and the texture consists of coarse sand, medium sand, and fine sand > of dust, no silt or clay, has a relative ash content low, high organic matter. The correlation is that when the BD and PD values are low, high water content means high porosity, large water storage, drought easily during the dry season, so fires easily occur.
Characteristics of hydrogeological aquifer in potential lime stone by analysis pumping test in Campurdarat District, Tulungagung Regency, Indonesia
Authors: Chandrasasi D , Prasetyorini L , Yuliani E
Published: March 2024

Extraction of clean water from dug wells and drilled wells is a source of water that is obtained locally without buying, for example, clean water from the Drinking Water Company (PAM). Surface water and groundwater are generally used frequently, even though the utilization of groundwater is not optimal compared to surface water. One way to determine the potential of groundwater contained by aquifers or aquifer discharge is by pumping test wells. In this test, water is pumped to the surface through a test well dug into the designated aquifer. The purpose of this study is to determine the characteristics of hydrogeological aquifer of limestone by the pumping test analysis approach using the Theis and Cooper - Jacob methods in Campurdarat District, Tulungagung Regency. Pumping tests have been carried out on two observation and production wells with the results of the Theis method showing a transmissivity (T) of 73,193 m2/day, storage capacity (S) of 1,080×10-3 and hydraulic conductivity (K) of 1,220 m/day while Jacob shows a transmissivity (T) value of 71,682 m2/day, storage capacity (S) of 0.4512 and hydraulic conductivity (K) of 4,667 m/day. The Theis method was chosen because it has a relative error smaller than Jacob method, namely 29.77%.
Variable analysis for supporting reservoir impounding modeling
Authors: Rahmawati H R , Juwono P T
Published: March 2024

The impounding stage of the reservoir is a stage after the implementation of dam construction is finished. The process of reservoir impounding is started by closing the tunnel diversion gate and the elevation of the water level will be moving up slowly. The speed of the increasing reservoir water level elevation is affected by the dry season or rainy season, so it is arranged in such a way for obtaining the daily increase is not more than 1.0 m/day, due to dam safety. This research intends to build this modeling, at first by studying which variables are affecting in order to get the safe period of impounding. The methodology consists of a correlation analysis of inflow, outflow, and the ratio between storage volume and inflow volume to the optimal impounding equation. The statistical hydrology approach is used in this modeling that will assess the 7 observed reservoir impounding which is started from base elevation until Full Supply Level (FSL). This modeling will help in decision-making about the selection of the safe and optimal period of reservoir impounding. At the end of impounding, the reservoir will be full and it starts to be allocated regarding the utilization that has been designed.
Reservoir water budget estimation using satellite and ground measurement data
Authors: Wahyuni S , Berlian R.S , Widiarti W.Y , Wiswamitra K.A
Published: March 2024

Rising air temperatures, increased rainy runoff, reduced dry season runoff, and severe weather conditions have intensified floods and droughts, significantly affecting the reservoir water supply. The accuracy of reservoir water balance is crucial for meeting water needs. The study compares satellite data and ground measurements to analyze the water budget of Sutami Reservoir in Indonesia. Satellite data collected included precipitation (Tropical Rainfall Measuring Mission-TRMM) and evaporation (Global Land Data Assimilation System-GLDAS). The water balance approach was utilized to analyze the water budget. The suitability tests used were Root Mean Square Error (RMSE), Nash-Sutcliffe Efficiency (NSE), Correlation Coefficient (CC), and Relative Error (RE). The study revealed that the data from TRMM and GLDAS satellites closely resembled ground measurements. The reservoir water balance analysis revealed that satellite data aligns with ground measurements, indicating water shortages in the dry season and excess water in the rainy season. Satellite data is particularly beneficial for watershed management in areas lacking ground measurement equipment, as it can be analyzed for various purposes.
Performance assessment of existing canal-blocking in restoration management of peatland conservation
Authors: Yakubson  , Sumiadi
Published: March 2024

The aim of this research is to assess existing results of the canal-blocking peatland conservation due to the classification of 5 canal-blocking types on peatland conservation as the management of restoration in the peatland area of Block-C ex-PLG. The low water levels (>40 cm from the surface) during the dry season make dry peatlands susceptible to fires. The back wetting of peatland is the early effort in preventing the peatland fire, which can be carried out on a wide scale by exploiting the available canal network through the overall and integrated canal blocking in unity of peatland hydraulics. The canal blocking due to the five types of canal blocking classification, which is intended to back the discussion of peatland, can give the ecology and society economic impacts that include supporting the natural vegetation recovery, preparation of water supply along season on the peatland hydrologic unity, and to be preventing drought and also the fire that are often happened in the dry season. Land use is suggested based on customization: agriculture and plantation in designated areas, adaptive vegetation in limited plantation zones, and protected areas restored to serve as safeguarded vegetation zones.
Protective Measures for Scouring Effects in Serayu Micro Hydro Integrated Barrage
Authors: Zulfan J , Wardhana M S , Saputro C I , Ginting B M
Published: March 2024

Adding a new micro hydropower component to an established barrage, such as the Serayu Barrage in Central Java Province, poses significant structure risks and potentially compromises the stability of the structures. To mitigate these negative impacts, physical modeling was conducted at our hydraulic laboratory to accurately replicate 600 meters of the Serayu River, including the 110-meter-wide Serayu Barrage structure at a scale of 1:40. Multiple scenarios were examined to simulate hydrodynamic conditions and sediment transport along the barrage structure. Notably, downstream scouring conditions were identified as a crucial parameter affecting the structure’s stability. Results obtained using a design discharge of 2,470 m3/s revealed concerning findings, with an observed 4 to 6 meters deep scouring downstream near the end sill of the weir. Immediate mitigation measures using riprap are imperative to prevent further damage to the weir structure. This paper investigates several configurations for riprap protection to address the scouring problems. After implementing a full riprap arrangement downstream of the end sill, the scouring depth was reduced significantly and pushed far downstream. Looking at it from an economic standpoint, placing a full riprap configuration for downstream protection is a more financially efficient option over an extended period.
Identification of the characteristics of the physical vulnerability level of the Kendari Bay coastal landscape to tidal floods using the Quantum Geographic Information System
Authors: Hadini L O , Hidayat A , Khairisa N H , Nurgiantoro  , Aba L
Published: March 2024

Kendari City has a coastal stretch that runs into the sea and is feared to be vulnerable to tidal floods. This study aims to identify the tidal flood vulnerability of the coastal landscape of Kendari City, especially in terms of its relationship to the characteristics of the physical aspects of the landscape, distribution mapping, and the extent of tidal flood vulnerability areas in coastal areas. The research method uses spatial descriptive analytics to explain the tidal flood phenomenon in relation to physical aspects of the coastal landscape such as topography, distance from the beach, distance from rivers, and land use aspects. The data collected consists of primary data in the form of observation data on the physical aspects of coastal areas and secondary data in the form of satellite image data and data from related agencies. The analysis technique for describing tidal flood vulnerability uses buffer and overlay analysis, assisted by the QGIS application. The results of the research showed that the level of physical vulnerability to tidal flooding was obtained by three vulnerability classes and their areas: low physical vulnerability at 17,096.82 ha, medium physical vulnerability at 8,169.69 ha, and high physical vulnerability at 1,722.17 ha.
Experimental effect of wind and heavy rain on increased splash erosion using rainfall simulator
Authors: Fidari J S , Zahira N A , Hadiansyah M S N , Fitria R R , Hartoyo R P
Published: March 2024

To investigate the erosion process that occurs, rainfall simulation is used with a model scale for natural rain events in laboratory conditions. The calculation of erosion and any soil erosion with a slope setting of 5% was carried out experimentally on a laboratory scale using a rain simulator and adding wind using a 2-inch snail blower. Experiments carried out in the laboratory included erosion tests driven by rain and erosion tests by rain, which were given additional wind variables. Rain intensity used for testing is using discharge 1 litre/minute,1.5 litre/minute, and 2 litre/minute as a representative variation of rainfall. The occurrence of rain and wind simultaneously within a certain period will cause greater loss of soil. Although many studies have been conducted on the effects of rain and the combined effects of wind on soil erosion, only a limited number of studies have focused on the combination of the two variables that occur together. The results showed that in the applied rain intensity and wind factor, the collision of the kinetic energy of the rain driven by the wind resulted in higher erosion when compared to that without the influence of the wind.
Recommendation of excavation method and support system based on rock mass classification of the Matenggeng Dam Tunnel, Cilacap, Central Java
Authors: Firdausi A A , Setianto A , Indrawan I G B
Published: March 2024

The Matenggeng Dam is situated in Matenggeng village, Dayeuhluhur, Cilacap district, Central Java. It features a diversion channel equipped with a tunnel that has a diameter of five meters and is formed like a horseshoe. Therefore required engineering geological analysis for tunnel planning. The purpose of this study is to ascertain the tunneling technique and the corresponding support systems. This study will provide suggestions and input before and during the construction. This research uses rock mass classification and the Point Load Test for several samples. Tunneling method and support systems using empirical method Rock Mass Rating (RMR) and Geological Strength Index (GSI). The study location is composed of sandstone, conglomerate, andesite, and siltstone with alluvium deposits in Cijolang River area. Classification of rock masses is fair to good rock. The GSI and RMR analyses suggest that the excavation technique uses hammer and blasting methodologies and a max stand-up time without support of 20 to 144 hours. The tunneling method uses top heading and bench and support systems using rock bolts, wire mesh, shotcrete, and steel sets.
Indigenous community governance in marine conservation: A bibliometric analysis
Authors: Sejati A A , Sudarmo  , Haryanti R H
Published: March 2024

Maintaining marine sustainability and biodiversity requires support and cooperation from the government, stakeholders, and community. Indigenous communities have the right to restoration and protection of the environment and productive capacity of land, territory, sea, and all their natural resources. Research on community governance has been carried out by many researchers with increasingly developing topics. Including topics about indigenous peoples and natural resource conservation. This research aims is to determine the development of research trends regarding community governance of indigenous communities in marine conservation. The data source is literature in the Scopus database and the data analysis uses bibliometric analysis of indigenous community governance in marine conservation publications. The results are the research of indigenous communities governance in marine conservation from the first publication in 2006 has tended to increase. Although in certain years it has decreased or there have been no publications at all. The research become an interesting topic because it related with environmental science and indigenous communities have a big role in implementing marine conservation. This conservation has been going for a long time and passed down from generation to generation. The recommendation of this research is legal recognition for indigenous peoples to protect their rights.
Vis/NIR reflectance spectroscopy for non-destructive diagnosis of Fusarium spp. infection in postharvest potato tubers (Solanum tuberosum)
Authors: Prasetyo E W , Amanah H Z , Farras I , Pahlawan M F R , Masithoh R E
Published: March 2024

Conventional methods of detecting Fusarium spp. infection, which causes significant economic losses in potato production, are time-consuming and expensive. This study explored rapid and non-destructive detection techniques using visible/near-infrared (Vis/NIR) spectroscopy. Potato seeds of the Granola L variety were intentionally infected with Fusarium spp. by fungal inoculation, then stored at 12°C, 25°C, and a combination of both. Healthy potatoes were stored under the same conditions in containers for 30 days and monitored every five days. Principal component analysis-linear discriminate analysis (PCA-LDA) was used to classify potato tubers based on their infection status. PCA-LDA analysis revealed significant spectral differences between healthy and infected potato seeds across all storage temperatures. Calibration reliability values were 95.87% (for samples stored at 12°C), 97.52% (stored at 25°C), and 98.35% (for the combination of 12°C and 25°C). Similar trends were observed for accuracy: 91.96% (12°C), 98.29% (25°C), and the highest accuracy of 98.65% for the combined temperature. These techniques facilitate rapid identification of infections, aiding farmers and producers in implementing more efficient preventive actions, resulting in decreased crop losses and waste products and enhanced productivity in the agricultural sector.
Household food waste in Surakarta City, Indonesia: Quantity, global warming potential (GWP), and management
Authors: Rohmah M N , Setyono P , Utami T
Published: March 2024

Households represent one of the main contributors to food waste in urban areas. Surakarta is one of the cities in Indonesia where a significant portion of household food waste is disposed of in landfill sites. The piles of food waste can become an environmental issue if left unmanaged, as they generate greenhouse gas emissions that contribute to global warming. The aim of this research is to determine the quantity, emission estimations, and management of household food waste in Surakarta City. A total of 151 household samples had their food waste collected over a period of 7 days. The method for measuring the quantity of food waste involved direct measurements using a scale, calculating food waste emissions using the GWP formula, and collecting management data through a questionnaire. The research results indicate that, on average, households dispose of 0.499 kg/week of food waste and estimate food waste emissions to be 0.789 kg CO2e/week. In addition to being discarded, some food waste is managed as animal feed and fertilizer. Implementing proper and sustainable management can lead to a reduction in the quantity of food waste sent to landfills.
Bioremediation to Overcome Microplastic Contamination in The Water Environment
Authors: Khoiriyah Siti , Dian Syaputra Mei
Published: March 2024

Microplastics are a global environmental issue that is receiving increasing attention. Microplastic particles, which are plastic fragments measuring less than 5 mm, are widely distributed worldwide and have negative impacts on the environment, living organisms, and human health. Bioremediation is one method to address this problem, using living organisms to remove microplastics from the environment. Bioremediation involves the use of living organisms, such as bacteria, algae, worms, and other organisms, to clean up or degrade microplastics that are widely dispersed in the environment. This article explains the concept and role of bioremediation in addressing microplastic contamination, the factors influencing its effectiveness, and the advantages and challenges of using bioremediation. This article is a systematic literature review. The data used in this research consist of 23 scientific articles, with 21 indexed in Scopus and 2 indexed in Google Scholar. Through this article, it is hoped to obtain comprehensive insights into the future potential of sustainable bioremediation technology in addressing the issue of microplastic contamination in aquatic environments.
Substantiating the rational parameters for a complicated non-transport system when mining low-thickness fireclay deposits
Authors: Chebanov Maksym , Sobko Borys , Petlovanyi Mykhailo
Published: March 2024

The paper examines a complicated non-transport system for mining a gently sloping fireclay deposit using ESH-10/70 dragline excavators. The research purpose is to substantiate the technological scheme of stripping operations and determine their parameters to reduce the strip-mining costs. Theoretical research is performed using the following methods: methods of scientific analysis of theoretical research, as well as practices of project and production organizations; mining-geometric calculations; variant method for comparing and selecting a mining system. As a result, the dependence of the excavator block mining velocity on the entry way width has been determined, which makes it possible to study the relationship between mining and stripping equipment in time. The change in the re-excavation coefficient depending on the width of the dragline excavator entry way has been studied and its rational value has been determined. The practical value of the research results is in the substantiation of an effective system for mining a gently sloping fireclay deposit.
Germanium resource provision from mineral deposits in Ukraine
Authors: Lozhnikov Oleksii , Pavlychenko Artem , Shustov Oleksandr , Dereviahina Nataliia
Published: March 2024

The article is devoted to determining the resource potential of Ukraine in supplying industry with germanium. Statistical information on the potential content of germanium in various types of mineral raw materials located on the territory of Ukraine is summarized. The trends of the world market of germanium consumption in industry have been established. The value of the average content of germanium in coal deposits of the Lviv-Volynsky and Donetsky basins is given. It has been established that the greatest potential for germanium extraction is found in lignite deposits, the content of the valuable mineral in which can be ten times higher than that of hard coal. According to the results of research, germanium is found in the condition standards in ferruginous quartzites of the Annivske deposit of Kryvbas, Horishno-Plavnenske, Lavrykivske and Bilanivske deposits of the Kremenchuk district. The average content of germanium in ore deposits formed from magnetite, hematite, ribeckite, etc. was also determined. The approximate resource availability of germanium contained in deposits of coal, ore and non-ore raw materials of Ukraine was determined.
Research of land-saving schemes of mining the horizontal sedimentary mineral deposits
Authors: Adamchuk Andrii , Pavlychenko Artem , Shustov Oleksandr , Bondarenko Andrii
Published: March 2024

Technological mining transport schemes of open development of horizontal sedimentary deposits are considered. Various land-saving technological schemes for transportation of minerals in the absence of a capital trench have been developed. The dependence of the mineral transportation cost on the production capacity of the mine for the developed schemes was established. The research has been carried out for conditions of surface mining manganese deposits of Nikopol Basin. Transport schemes using mobile steeply inclined conveyor are offered. The developed technological solutions for the conditions of surface mining of deposits of the Nikopol manganese ore basin allow not only to reduce the amount of disturbed land, but also to reduce the cost of minerals by reducing its transportation distance by 2 km. The proposed transport schemes will make it possible to obtain an economic effect in the amount of 1–3 million UAH.
GATE Monte Carlo approach to heterogeneity dose distribution in small fields used in radiation therapy
Authors: Elcadi Z A , El Moussaoui M , Aouadi S , Sukumaran R , Hammoud R , Al-Hammadi N , Toufique Y , Bouhali O
Published: March 2024

The Accurate dosage prediction in Radiation Therapy is challenging, prompting a need for precision beyond conventional clinical Treatment Planning Systems (TPS). Monte Carlo-based methods are sought for their superior accuracy. The aim of this study is to compare dose distributions between the ACUROS algorithm and the GATE platform in various tissue densities and field sizes, focusing on smaller fields. This study was initiated with a homogeneous validation of the TrueBeam STX system, using measurements obtained from the Centre Hospitalier Interregional Edith Cavell (CHIREC) in Brussels. The validation compared dosimetric functions (Percentage Depth Dose (PDD), Dose profile (DP) and Collimator scatter fraction (CSF)) employing the GAMMA index with a 2% / 2 mm criterion tolerance. Following this, heterogeneous studies examined dose distributions between the ACUROS algorithm and the GATE platform in various tissue densities and field sizes, with a specific focus on smaller fields. Simulations were conducted using both platforms on chest phantoms with heterogeneous slabs representing bone, lung, and heart, each housing a central tumor. The impact of electronic equilibrium on tumors for different small field sizes was evaluated. Results showed a remarkable 99% agreement between measurements and GATE calculations in the homogeneous validation of the TrueBeam STX system. However, in heterogeneous studies, ACUROS consistently overestimated lung doses by up to 8% compared to GATE simulation, especially evident with a flattening filter and smaller beam sizes at density interfaces. This highlights significant dose estimation discrepancies between ACUROS and GATE, emphasizing the need for precise calculations. The findings support exploring Monte Carlo-based methods for enhanced accuracy in Radiation Therapy treatment planning.
Rotor fault characterization study by considering normalization analysis, feature extraction, and a multi-class classifier
Authors: Barstuğan Mücahid , Arabacı Hayri
Published: March 2024

Background. Rotor faults are the most common malfunctions encountered, especially during the manufacturing stage, in asynchronous motors. These faults cause vibration in the motor torque and a decrease in efficiency. In recent years, the detection of rotor faults has been done using motor current. The reflection of rotor faults on motor current depends on slip, and therefore, the effect increases as the current grows. Good results are achieved in fault detection at nominal loads. However, especially when motor manufacturers are considered, testing the motor by loading it requires expensive testing equipment and long-term test procedures. Therefore, the detection of faults in the motor at no load is emphasized. However, since the effect of the fault decreases when the motor is at no load, fault detection becomes difficult. Generally, small-level faults cannot be detected. Objective. This study focuses on fault detection from the motor current at no load. The development current at no load was used to eliminate the negative effects of slip. However, since the slip is not constant, the change in frequency and amplitude values to be used as a feature makes the diagnosis difficult. Method. In this study, the spectrogram was used to evaluate the change during the start-up time. Thus, a standard dataset was determined for comparison. The texture properties of the spectrogram image were extracted using various methods. The extracted features were subjected to normalization analysis and classified using the k-NN algorithm. Results. In the classification phase, a classification accuracy of 98.66% was achieved using the k-NN method, and it was seen that the proposed method could be used for the detection of rotor faults. Conclusions. The study has successfully demonstrated that broken rotor bar faults in asynchronous motors can be diagnosed using the motor start-up data.
Measurement properties of the usual and fast gait speed tests in community-dwelling older adults: a COSMIN-based systematic review
Authors: Mehdipour Ava , Malouka Selina , Beauchamp Marla , Richardson Julie , Kuspinar Ayse
Published: March 2024

Objective

The gait speed test is one of the most widely used mobility assessments for older adults. We conducted a systematic review to evaluate and compare the measurement properties of the usual and fast gait speed tests in community-dwelling older adults.

Methods

Three databases were searched: MEDLINE, EMBASE and CINAHL. Peer-reviewed articles evaluating the gait speed test’s measurement properties or interpretability in community-dwelling older adults were included. The Consensus-based Standards for the selection of health Measurement Instruments guidelines were followed for data synthesis and quality assessment.

Results

Ninety-five articles met our inclusion criteria, with 79 evaluating a measurement property and 16 reporting on interpretability. There was sufficient reliability for both tests, with intraclass correlation coefficients (ICC) generally ranging from 0.72 to 0.98, but overall quality of evidence was low. For convergent/discriminant validity, an overall sufficient rating with moderate quality of evidence was found for both tests. Concurrent validity of the usual gait speed test was sufficient (ICCs = 0.79–0.93 with longer distances) with moderate quality of evidence; however, there were insufficient results for the fast gait speed test (e.g. low agreement with longer distances) supported by high-quality studies. Responsiveness was only evaluated in three articles, with low quality of evidence.

Conclusion

Findings from this review demonstrated evidence in support of the reliability and validity of the usual and fast gait speed tests in community-dwelling older adults. However, future validation studies should employ rigorous methodology and evaluate the tests’ responsiveness.
polyGBLUP: a modified genomic best linear unbiased prediction improved the genomic prediction efficiency for autopolyploid species
Authors: Song Hailiang , Zhang Qin , Hu Hongxia
Published: March 2024

Given the universality of autopolyploid species in nature, it is crucial to develop genomic selection methods that consider different allele dosages for autopolyploid breeding. However, no method has been developed to deal with autopolyploid data regardless of the ploidy level. In this study, we developed a modified genomic best linear unbiased prediction (GBLUP) model (polyGBLUP) through constructing additive and dominant genomic relationship matrices based on different allele dosages. polyGBLUP could carry out genomic prediction for autopolyploid species regardless of the ploidy level. Through comprehensive simulations and analysis of real data of autotetraploid blueberry and guinea grass and autohexaploid sweet potato, the results showed that polyGBLUP achieved higher prediction accuracy than GBLUP and its superiority was more obvious when the ploidy level of autopolyploids is high. Furthermore, when the dominant effect was added to polyGBLUP (polyGDBLUP), the greater the dominance degree, the more obvious the advantages of polyGDBLUP over the diploid models in terms of prediction accuracy, bias, mean squared error and mean absolute error. For real data, the superiority of polyGBLUP over GBLUP appeared in blueberry and sweet potato populations and a part of the traits in guinea grass population due to the high correlation coefficients between diploid and polyploidy genomic relationship matrices. In addition, polyGDBLUP did not produce higher prediction accuracy than polyGBLUP for most traits of real data as dominant genetic variance was not captured for these traits. Our study will be a significant promising method for genomic prediction of autopolyploid species.
BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering
Authors: Matzko Richard Oliver , Konur Savas
Published: March 2024

Motivated by the need to parameterize ongoing multicellular simulation research, this paper documents the culmination of a ChatGPT augmented software engineering cycle resulting in an integrated visual platform for efficient cytohistological RNA-seq and bioregulatory network exploration. As contrasted to other systems and synthetic biology tools, BioNexusSentinel was developed de novo to uniquely combine these features. Reactome served as the primary source of remotely accessible biological models, accessible using BioNexusSentinel’s novel search engine and REST API requests. The innovative, feature-rich gene expression profiler component was developed to enhance the exploratory experience for the researcher, culminating in the cytohistological RNA-seq explorer based on Human Protein Atlas data. A novel cytohistological classifier would be integrated via pre-processed analysis of the RNA-seq data via R statistical language, providing for useful analytical functionality and good performance for the end-user. Implications of the work span prospects for model orthogonality evaluations, gap identification in network modelling, prototyped automatic kinetics parameterization, and downstream simulation and cellular biological state analysis. This unique computational biology software engineering collaboration with generative natural language processing artificial intelligence was shown to enhance worker productivity, with evident benefits in terms of accelerating coding and machine-human intelligence transfer.

Availability and implementation

BioNexusSentinel project releases, with corresponding data and installation instructions, are available at https://github.com/RichardMatzko/BioNexusSentinel.
Advancing entity recognition in biomedicine via instruction tuning of large language models
Authors: Keloth Vipina K , Hu Yan , Xie Qianqian , Peng Xueqing , Wang Yan , Zheng Andrew , Selek Melih , Raja Kalpana , Wei Chih Hsuan , Jin Qiao , Lu Zhiyong , Chen Qingyu , Xu Hua
Published: March 2024

Motivation

Large Language Models (LLMs) have the potential to revolutionize the field of Natural Language Processing, excelling not only in text generation and reasoning tasks but also in their ability for zero/few-shot learning, swiftly adapting to new tasks with minimal fine-tuning. LLMs have also demonstrated great promise in biomedical and healthcare applications. However, when it comes to Named Entity Recognition (NER), particularly within the biomedical domain, LLMs fall short of the effectiveness exhibited by fine-tuned domain-specific models. One key reason is that NER is typically conceptualized as a sequence labeling task, whereas LLMs are optimized for text generation and reasoning tasks.

Results

We developed an instruction-based learning paradigm that transforms biomedical NER from a sequence labeling task into a generation task. This paradigm is end-to-end and streamlines the training and evaluation process by automatically repurposing pre-existing biomedical NER datasets. We further developed BioNER-LLaMA using the proposed paradigm with LLaMA-7B as the foundational LLM. We conducted extensive testing on BioNER-LLaMA across three widely recognized biomedical NER datasets, consisting of entities related to diseases, chemicals, and genes. The results revealed that BioNER-LLaMA consistently achieved higher F1-scores ranging from 5% to 30% compared to the few-shot learning capabilities of GPT-4 on datasets with different biomedical entities. We show that a general-domain LLM can match the performance of rigorously fine-tuned PubMedBERT models and PMC-LLaMA, biomedical-specific language model. Our findings underscore the potential of our proposed paradigm in developing general-domain LLMs that can rival SOTA performances in multi-task, multi-domain scenarios in biomedical and health applications.

Availability and implementation

Datasets and other resources are available at https://github.com/BIDS-Xu-Lab/BioNER-LLaMA.
Hyperbaric Oxygen Enabled a Transition to Oral Steroids in an Acute Severe Ulcerative Colitis Flare
Authors: Hennessey Megan M , Zelman Sara R , Hannigan Pam M , Wilkinson Kimberly B , Siegel Corey A , Buckey Jay C
Published: March 2024

Background

Ulcerative colitis (UC) is characterized in part by a dysregulated response to tissue hypoxia. While intravenous (IV) steroids are the mainstay of treatment for acute severe UC (ASUC), up to one-third of patients are refractory to steroids alone and require rescue therapy.

Case Description

A 71-year-old female with extensive UC on infliximab presented with abdominal pain and more than 10 bloody bowel movements per day. Her infliximab concentration was undetectable with a positive antibody level. Flexible sigmoidoscopy on hospital day (HD)1 showed Mayo 3 colitis; biopsies for CMV were negative. She was started on hydrocortisone IV with improvement in her CRP from 56 to 40 mg/L. She also received 1 dose of vedolizumab. Hyperbaric treatments were offered but declined. By HD5, she was clinically improved, with a CRP of 9 mg/L. She was transitioned from IV to oral steroids. After starting oral steroids her symptoms relapsed, her CRP increased from 9 to 48 mg/L, and IV steroids were reinitiated on HD6. Hyperbaric medicine was reconsulted and she completed 5 hyperbaric oxygen (HBO2) treatments (HD 7–11) with prompt reduction in CRP, stool frequency, and bleeding. After 3 HBO2 treatments, she transitioned successfully from IV to oral steroids on HD9.

Conclusions

This case demonstrates the potential of HBO2 therapy to help UC patients transition successfully from IV to oral steroids who were previously refractory to de-escalation. HBO2 therapy may be considered as an adjunctive treatment for patients with ASUC to potentiate the effects of standard therapies and avoid progression to colectomy.
Influence of angiotensin II on the gut microbiome: modest effects in comparison to experimental factors
Authors: R Muralitharan Rikeish , Nakai Michael E , Snelson Matthew , Zheng Tenghao , Dinakis Evany , Xie Liang , Jama Hamdi , Paterson Madeleine , Shihata Waled , Wassef Flavia , Vinh Antony , Drummond Grant R , Kaye David M , Mackay Charles R , Marques Francine Z
Published: March 2024

Aims

Animal models are regularly used to test the role of the gut microbiome in hypertension. Small-scale pre-clinical studies have investigated changes to the gut microbiome in the angiotensin II hypertensive model. However, the gut microbiome is influenced by internal and external experimental factors, which are not regularly considered in the study design. Once these factors are accounted for, it is unclear if microbiome signatures are reproduceable. We aimed to determine the influence of angiotensin II treatment on the gut microbiome using a large and diverse cohort of mice and to quantify the magnitude by which other factors contribute to microbiome variations.

Methods and results

We conducted a retrospective study to establish a diverse mouse cohort resembling large human studies. We sequenced the V4 region of the 16S rRNA gene from 538 samples across the gastrointestinal tract of 303 male and female C57BL/6J mice randomized into sham or angiotensin II treatment from different genotypes, diets, animal facilities, and age groups. Analysing over 17 million sequencing reads, we observed that angiotensin II treatment influenced α-diversity (P = 0.0137) and β-diversity (i.e. composition of the microbiome, P < 0.001). Bacterial abundance analysis revealed patterns consistent with a reduction in short-chain fatty acid producers, microbial metabolites that lower blood pressure. Furthermore, animal facility, genotype, diet, age, sex, intestinal sampling site, and sequencing batch had significant effects on both α- and β-diversity (all P < 0.001). Sampling site (6.8%) and diet (6%) had the largest impact on the microbiome, while angiotensin II and sex had the smallest effect (each 0.4%).

Conclusion

Our large-scale data confirmed findings from small-scale studies that angiotensin II impacted the gut microbiome. However, this effect was modest relative to most of the other factors studied. Accounting for these factors in future pre-clinical hypertensive studies will increase the likelihood that microbiome findings are replicable and translatable.
Spondyloarthritis in First-Degree Relatives and Spouses of Patients with Inflammatory Bowel Disease: A Nationwide Population-based Cohort Study from Sweden
Authors: Shrestha Sarita , Brand Judith S , Osooli Mehdi , Eriksson Carl , Schoultz Ida , Askling Johan , Jess Tine , Montgomery Scott , Olén Ola , Halfvarson Jonas
Published: March 2024

Background and Aims

Register-based research suggests a shared pathophysiology between inflammatory bowel disease [IBD] and spondyloarthritis [SpA], but the role of familial [genetic and environmental] factors in this shared susceptibility is largely unknown. We aimed to compare the risk of SpA in first-degree relatives [FDRs] and spouses of IBD patients with FDRs and spouses of matched, population-based, reference individuals.

Methods

We identified 147 080 FDRs and 25 945 spouses of patients with incident IBD [N = 39 203] during 2006–2016, and 1 453 429 FDRs and 258 098 spouses of matched reference individuals [N = 390 490], by linking nationwide Swedish registers and gastrointestinal biopsy data. Study participants were followed 1987–2017. Cox regression was used to estimate hazard ratios [HRs] of SpA.

Results

During follow-up, 2430 FDRs of IBD patients [6.5/10 000 person-years] and 17 761 FDRs of reference individuals [4.8/10 000 person-years] were diagnosed with SpA, corresponding to an HR of 1.35 [95% CI:1.29, 1.41]. In subgroup analyses, the increased risk of SpA was most pronounced in FDRs of Crohn’s disease patients [HR = 1.44; 95% CI:1.34,1.5 6] and of IBD patients aged <18 years at diagnosis [HR = 1.46; 95% CI: 1.27, 1.68]. IBD patients’ spouses also had a higher SpA rate than reference individuals’ spouses, but the difference was less pronounced [4.3 vs 3.5/10 000 person-years; HR = 1.22; 95% CI:1.09, 1.37]. No subgroup-specific risk pattern was identified among spouses.

Conclusions

The observed shared familial risks between IBD and SpA support shared genetic factors in their pathogenesis. However, spouses of IBD patients were also at increased risk for SpA, reflecting the influence of environmental exposures or similarities in health-seeking patterns.
Multireceptor phage cocktail against Salmonella enterica to circumvent phage resistance
Authors: Martinez-Soto Carlos E , McClelland Michael , Kropinski Andrew M , Lin Janet T , Khursigara Cezar M , Anany Hany
Published: March 2024

Non-Typhoidal Salmonella (NTS) is one of the most common food-borne pathogens worldwide, with poultry products being the major vehicle for pathogenesis in humans. The use of bacteriophage (phage) cocktails has recently emerged as a novel approach to enhancing food safety. Here, a multireceptor Salmonella phage cocktail of five phages was developed and characterized. The cocktail targets four receptors: O-antigen, BtuB, OmpC, and rough Salmonella strains. Structural analysis indicated that all five phages belong to unique families or subfamilies. Genome analysis of four of the phages showed they were devoid of known virulence or antimicrobial resistance factors, indicating enhanced safety. The phage cocktail broad antimicrobial spectrum against Salmonella, significantly inhibiting the growth of all 66 strains from 20 serovars tested in vitro. The average bacteriophage insensitive mutant (BIM) frequency against the cocktail was 6.22 × 10−6 in S. Enteritidis, significantly lower than that of each of the individual phages. The phage cocktail reduced the load of Salmonella in inoculated chicken skin by 3.5 log10 CFU/cm2 after 48 h at 25°C and 15°C, and 2.5 log10 CFU/cm2 at 4°C. A genome-wide transduction assay was used to investigate the transduction efficiency of the selected phage in the cocktail. Only one of the four phages tested could transduce the kanamycin resistance cassette at a low frequency comparable to that of phage P22. Overall, the results support the potential of cocktails of phage that each target different host receptors to achieve complementary infection and reduce the emergence of phage resistance during biocontrol applications.