bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief review on the implementation of charging stations for electric buses
Authors: Yánez A.H , González Cindy Franco , Yánez B. E.R. , Moreira B. Karem , Alvear D. Josselin 
Published: December 2024

Abstract
The transition to Battery Electric Vehicles (BEVs) is crucial for addressing climate change, as BEVs have the potential to reduce carbon mitigation costs within climate policy frameworks, thereby increasing economic, social, and ecological benefits. Moreover, the electrification of transportation plays a vital role in the decarbonisation of energy infrastructures and the integration of renewable energy sources into the grid, significantly contributing to global climate action efforts. The systematic review employed a rigorous search protocol to carefully compile academic sources from reputable international scientific databases, with a particular focus on articles from SJR-Scopus and Web of Science. This approach ensured comprehensive interdisciplinary coverage and strong representation within the relevant field, thereby enhancing the credibility and reliability of the review. The paper investigates the establishment of charging stations for electric buses across Latin America, shedding light on sustainability strategies, economic viability, and the impact of governmental policies on advancing public transport electrification. It emphasizes the importance of battery technology, charging infrastructure, and energy management for the effective deployment of electric buses. Additionally, it highlights the challenges and benefits associated with electrified transportation, including energy efficiency, environmental benefits, and economic impacts. The study showcases successful electric bus initiatives in cities such as Quito, Buenos Aires, Bogotá, and Santiago, emphasizing the collaborative efforts between local and international companies to improve air quality and reduce greenhouse gas emissions.
Fish diversity of siluridae from Central Mahakam East Kalimantan Province, Indonesia
Authors: Haryono  , Gustiano R , Jusmaldi  , Nasution S H , Wahyudewantoro G , Yulianto  , Rusdianto  
Published: December 2024

Abstract

Siluridae is a large family with varying species and sizes. Besides, many species of Siluridae are endemic and endangered. The Mahakam River in East Kalimantan is an important habitat for Siluridae, but the threat is increasing especially the construction of the New State Capital (IKN). The aims of this study were to find out the diversity of silurids from Mahakam watershed, knowing the potential and taxonomic status, also conservation status. To achieve this goal, a survey was carried out in Kutai Kartanegara Regency which is included in the Central Mahakam in June 2023. Sampling used gill nets with mesh size of 0.5-1.0 inches. Fish caught is preserved in a plastic bag containing 10% formalin solution which is equipped with a label containing the important information. Then, it is deposited in the Museum Zoologicum Bogoriense (MZB) for processing that immersing in running water, sorting, and storing in a collection bottle containing 70% alcohol solution. The next stage to identified using books and related references. Morphometric covering 20 characters, then analysis using discriminant methods. The results were caught 37 individuals from six species, namely Kryptopterus bicirrhis, Kryptopterus limpok, Ompok hypophthalmus. Ompok miostoma, Phalacronotus apogon, and Phalacronotus micronemus. Based discriminant analysis showed the six species are completely separated (100%) with the main characters viz. HL, PDL, PEL, DFH, DFBL, and PFBL. Two genera are Kryptopterus and Ompok formed group separated from Phalacronotus. All species in this study are potential as consume fish, but Kryptopterus bichirrhis has possible to develop as ornamental fish. The conservation status is mostly Least Concern (LC), except Ompok miostoma is Near Threatened (NT).
Assessment of heavy metals contamination and sediment quality in the Upstream Citarum Watershed
Authors: Yustiawati  , Mulyaningsih T R , Yusuf S , Subehi L , Nugraha M F I , Julzarika A , Imroatushshoolikhah  , Sofiyudin H A , Akhdiana I 
Published: December 2024

Abstract
Anthropogenic activities such as agriculture, industry, and settlements along the Citarum watershed tend to release a number of wastes into the aquatic environment, which then causes contamination of water and river sediments, such as heavy metal contamination. In the aquatic environment, sediment quality is one of the indicators for assessing the level of pollution. The aim of this study is to determine the content of heavy metals (As, Co, Cr, Zn) in sediments and to determine the quality of sediments in the upstream segment of the Citarum watershed using various indices. The sediment samples were collected from 10 sampling sites of Citarum watershed, in March and September 2022. Heavy metal concentrations were determined using the neutron activation analysis technique. Enrichment Factor (EF), Geo-accumulation index (I-geo), Pollution Load Index (PLI), Contamination Factor (EF) and Ecological risk Factor (Er) were calculated to evaluate pollution level of sediment in Citarum watershed. Arsenic enrichment was detected in Situ Cisanti (Stations 1 and 3) at moderate levels, however, there was no enrichment of Zn, Cr, Co, and As in the other sampling points. According to the I-geo, PLI, CF, and Er values, various sampling stations within the Citarum watershed have been found to be contaminated with As, Cr, and Co at different levels, ranging from low to high. However, the Ecological Risk Factor assessment suggests that all the sampling stations pose a low risk in terms of ecological impact.
Abundance of periphyton on some types of plastic waste in Singkarak Lake West Sumatera
Authors: Suryono T , Henny C , Yoga G P , Rahmadya A 
Published: December 2024

Abstract
This research was carried out on the distribution and abundance of periphyton on several types of plastic in the waters of Singkarak Lake in September 2022 at three main inlets, namely the Sumpur, Paninggahan, and Sumani Rivers, as well as one outlet, namely Batang Ombilin. Periphyton was taken from several types of plastic waste submerged in the water of Singkarak Lake with an area of 16 cm2 in 3 repetitions. The surface of the plastic sample was scrubbed using a brush, then placed in a plankton bottle, then preserved using Lugol’s solution, and two drops of 4% formalin were added. Water quality, such as temperature, dissolved oxygen, pH, conductivity, nitrate, orthophosphate, total dissolve solid, turbidity, and chlorophyll, are also taken to determine environmental conditions. The composition and abundance of periphyton found in samples of several types of plastic consisted of the Bacillariophyta class ranging from 56-59.2%, then the Chlorophyta class had an abundance of between 28.5 - 34.3%, the Cyanophyta class ranged from 7.2 - 10.5% meanwhile, the Chrysophyta class is only found in 4.6% of plastic drinking glasses. The Xanthophyta class is only found in clear white plastic at 4.4%. The results of CCA ordination with MVSP software show that the periphyton abundance is distributed centrally. This indicates that the abundance of periphyton found in several types of plastic waste in the waters of Lake Singkarak is similar and there is no dominance of certain types of periphyton.
Assessment of soil erosion severity zones for prioritization of sedimentation control measures at Mahakam Cascade Lake in East Kalimantan, Indonesia
Authors: Apip  , Fakhrudin M 
Published: December 2024

Abstract
Because of high sedimentation, Mahakam Cascade Lake’s sustainability functions are at risk. Surface soil erosion in its internal catchment area (51,571 km2) is the primary source of sediment. In order to control erosion, it is necessary to choose high-priority areas. This research aims to develop priority control zones based on the level of soil erosion in the lake’s catchment area. The distributed simulation model for rainfall, runoff, and sediment served as the main methodology to accomplish this. The model’s output includes spatial information on the five classes of soil erosion rates (very light, light, medium, heavy, and very heavy). We then establish the priorities for erosion control areas based on the erosion rate criteria. We determined that an area meeting the criteria for a very heavy erosion rate class (> 250 tons/ha) is the primary control priority within the catchment. The mapping results show that 26 sub-districts and 4 regencies administratively distribute the main control priority area. Each sub-district has a different total area for priority areas, and there are 8 sub-districts with a combined potential priority area of more than 300 km2. In general, mapping soil erosion severity zones can serve as a guide for more effective erosion control.
Evaluation of floating water intake on the Citarum river for industrial needs in the Purwakarta industrial area, West Java
Authors: Prayogo T , Hidayat N , Riyadi A , Zaidan M , Syaefudin  , Widodo L , Widiatmoko N , Tresnadi H , Kusumastuti E , Rosadi AHY , Budiman B , Mujianto  
Published: December 2024

Abstract
Water is a vital resource for all living organisms, including industrial processes. To ensure the uninterrupted operation of industrial processes, it is crucial to provide adequate amounts of clean water of appropriate quality. Floating water intakes are designed to extract surface water from dams or rivers, which may experience significant fluctuations in water levels. The enhancement of industrial capacity and the maintenance of pump houses in the sector necessitate the implementation of a comprehensive planning, construction, and supervisory system to regulate and utilize the water resources of the Citarum River. In order to meet the requirements of the industry, it is essential to ensure the continuous functioning of the relevant processes. The objective of this study is to assess the floating water intake in the vicinity of the Pump House. This will be achieved through the utilisation of a topographical survey and a depth probe of the Citarum River. The Citarum River at the floating water intake location exhibits a depth range of 5 to 7.5 meters, while the terrain surrounding the pump house demonstrates a height range of 27,255 to 29,876 meters, as evidenced by the findings of the study. Furthermore, the elevation of the Citarum river bed at this location varies from 19.5 to 22 meters.
Study of the effectiveness of wasted container bags in SMART floating net cage culture system
Authors: Warsa A , Tjahjo D W H , Astuti L P 
Published: December 2024

Abstract
A floating net cage (FNC) aquaculture program is one of the attempts to maximize the Jatiluhur Reservoir’s use. The community surrounding the waters benefits economically from the FNC activity. However, there is a chance that the pollution from this activity will deteriorate the quality of the water. sources of pollution from fish faeces and uneaten feed in aquaculture operations. To lower the pollution load, an environmentally friendly FCC technology is therefore required. A technology that is applicable is SMART Floating Net Cages. An adaptation of aquaponics, the Smart FNC can be used in open water, such as a lake or reservoir. There is a container for uneaten feed and plant filtration included into the Smart FNC. Determining approximately the amount of feed storage remaining in the container is the objective of the research. This study was carried out in Jatiluhur Reservoir using a double net cage from February to May of 2021. The lower net measures 14x7x6 m, and the upper net includes two plots of 7x7x3 m. 200 kilograms of nile tilapia (Oreochromis niloticus), with an average weight of 49.0 g, were reared in the lower net, whereas 150 kg of common carp (Cyprinus carpio) weighed an average of 13.5 g in the upper net. Fish reared for carp will be fed to ensure they are satisfied, but Nile tilapia only consume leftover food from common carp rearing. At the end of reared, the wasted feed remaining in the storage bag is thoroughly sucked up and dried. The remaining feed was wasted as much as 255 kg with a waste storage bag efficiency of 38.6%.
Design and performance characterisation of 10 nm negative capacitance double gate MOSFET (NCDGMOSFET)
Authors: Prakash Neeraj Nayan , Tripathi Suman Lata , Saxena Sobhit 
Published: December 2024

Abstract
The major focus on any transistor-level design is to minimize the effects on switching speed and power consumption at smaller dimensions, which are crucial in VLSI design for low power applications. In this work, a double gate MOSFET design is proposed with p+ pocket in the channel region at 10 nm technology node. Further a ferroelectric material HfO2FE is also introduced between gate and oxide layer resulting a negative capacitance double gate MOSFET (NCDGMOSFET). Ferroelectric material shows negative capacitance that limits the subthreshold slope with dimension scaling. Increased gate control and high switching speed in NCDGMOSFET with lightly doped n-channel, is a promising transistor option for low-power high performance IC design. The proposed device design is characterised with different pocket dimensions for gate and drain voltage ranges from 0 V to 1.5 V. The contact resistance of drain and source is also varied to observe device ON/OFF performances. The electrostatic behaviour of the device is also analysed via observation of electric field and potential variations at different bias conditions. Adding a p+ pocket in the NCDGMOSFET structure further enhances the performance by modifying the channel properties with subthreshold slope and DIBL vales of 76 mV decade−1 and 36 mV/V respectively. This modification also leads to improved barrier to subthreshold conduction during the Ioff state of the transistor, while minimally impacting the Ion state. The proposed device design and performance analysis are conducted through TCAD 2D/3D device simulation software by Cogenda.
Evaluating machine learning models for supernova gravitational wave signal classification
Authors: Abylkairov Y Sultan , Edwards Matthew C , Orel Daniil , Mitra Ayan , Shukirgaliyev Bekdaulet , Abdikamalov Ernazar 
Published: December 2024

Abstract
We investigate the potential of using gravitational wave (GW) signals from rotating core-collapse supernovae to probe the equation of state (EOS) of nuclear matter. By generating GW signals from simulations with various EOSs, we train machine learning models to classify them and evaluate their performance. Our study builds on previous work by examining how different machine learning models, parameters, and data preprocessing techniques impact classification accuracy. We test convolutional and recurrent neural networks, as well as six classical algorithms: random forest, support vector machines, naïve Bayes(NB), logistic regression, k-nearest neighbors, and eXtreme gradient boosting. All models, except NB, achieve over 90 per cent accuracy on our dataset. Additionally, we assess the impact of approximating the GW signal using the general relativistic effective potential (GREP) on EOS classification. We find that models trained on GREP data exhibit low classification accuracy. However, normalizing time by the peak signal frequency, which partially compensates for the absence of the time dilation effect in GREP, leads to a notable improvement in accuracy. Despite this, the accuracy does not exceed 70 per cent, suggesting that GREP lacks the precision necessary for EOS classification. Finally, our study has several limitations, including the omission of detector noise and the focus on a single progenitor mass model, which will be addressed in future works.
Experimental analysis of genetic and environmental interactions on leaf elongation and reproductive development in Lolium perenne
Authors: Rouet Simon , Durand Jean-Louis , Troux Alice , Barillot Romain 
Published: December 2024

Abstract
Perennial grasses’ reproductive phenology profoundly impacts plant morphogenesis, biomass production, and perenniality in natural ecosystems and cultivated grasslands. Complex interactions between vegetative and reproductive development complicate grass phenology prediction for various environments and genotypes. This work aims to analyse genetic × environment interactions effects on tiller growth and reproductive development in Lolium perenne. Three perennial ryegrass cultivars, Bronsyn, Carvalis, and Tryskal, were grown from seedling to heading under four inductive conditions. T0 plants were continuously exposed to high temperatures and long days (HT–LD). T1, T2, and T3, plants were initially exposed to low temperatures and short days (LT–SD) for 9 weeks. Then, T1 plants were immediately transferred to high temperatures and long days (HT–LD). Before their exposure to HT–LD, T2, and T3 plants were first transferred to high temperatures and short days (HT–SD) for 3 and 6 weeks, respectively. Leaf length, leaf emergence, and heading were regularly monitored. Floral transition and heading only occurred in T1, T2, and T3, i.e. after successive exposure to low temperature and long photoperiod. Bronsyn had higher heading earliness and proportion of reproductive tillers than Carvalis and Tryskal. The duration of HT–SD exposure affected the final number of leaves and spikelets. The rate of leaf and spikelet production significantly increased once plants were exposed to LD. Our results suggest an additive effect of the photoperiod and floral transition on leaf elongation rate. These findings enhance our understanding of the genetic × environment interactions on the vegetative and reproductive development in perennial ryegrass.
QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data
Authors: Li Manci , Bryant Damani N , Gresch Sarah , Milstein Marissa S , Christenson Peter R , Lichtenberg Stuart S , Larsen Peter A , Oh Sang-Hyun 
Published: December 2024

Abstract

Motivation
Fluorophore-assisted seed amplification assays (F-SAAs), such as real-time quaking-induced conversion (RT-QuIC) and fluorophore-assisted protein misfolding cyclic amplification (F-PMCA), have become indispensable tools for studying protein misfolding in neurodegenerative diseases. However, analyzing data generated by these techniques often requires complex and time-consuming manual processes. In addition, the lack of standardization in F-SAA data analysis presents a significant challenge to the interpretation and reproducibility of F-SAA results across different laboratories and studies. There is a need for automated, standardized analysis tools that can efficiently process F-SAA data while ensuring consistency and reliability across different research settings.

Results
Here, we present QuICSeedR (pronounced as “quick seeder”), an R package that addresses these challenges by providing a comprehensive toolkit for the automated processing, analysis, and visualization of F-SAA data. Importantly, QuICSeedR also establishes the foundation for building an F-SAA data management and analysis framework, enabling more consistent and comparable results across different research groups.

Availability and implementation
QuICSeedR is freely available at: https://CRAN.R-project.org/package=QuICSeedR. Data and code used in this manuscript are provided in Supplementary Materials.
FuncFetch: an LLM-assisted workflow enables mining thousands of enzyme–substrate interactions from published manuscripts
Authors: Smith Nathaniel , Yuan Xinyu , Melissinos Chesney , Moghe Gaurav 
Published: December 2024

Abstract

Motivation
Thousands of genomes are publicly available, however, most genes in those genomes have poorly defined functions. This is partly due to a gap between previously published, experimentally characterized protein activities and activities deposited in databases. This activity deposition is bottlenecked by the time-consuming biocuration process. The emergence of large language models presents an opportunity to speed up the text-mining of protein activities for biocuration.

Results
We developed FuncFetch—a workflow that integrates NCBI E-Utilities, OpenAI’s GPT-4, and Zotero—to screen thousands of manuscripts and extract enzyme activities. Extensive validation revealed high precision and recall of GPT-4 in determining whether the abstract of a given paper indicates the presence of a characterized enzyme activity in that paper. Provided the manuscript, FuncFetch extracted data such as species information, enzyme names, sequence identifiers, substrates, and products, which were subjected to extensive quality analyses. Comparison of this workflow against a manually curated dataset of BAHD acyltransferase activities demonstrated a precision/recall of 0.86/0.64 in extracting substrates. We further deployed FuncFetch on nine large plant enzyme families. Screening 26 543 papers, FuncFetch retrieved 32 605 entries from 5459 selected papers. We also identified multiple extraction errors including incorrect associations, nontarget enzymes, and hallucinations, which highlight the need for further manual curation. The BAHD activities were verified, resulting in a comprehensive functional fingerprint of this family and revealing that ∼70% of the experimentally characterized enzymes are uncurated in the public domain. FuncFetch represents an advance in biocuration and lays the groundwork for predicting the functions of uncharacterized enzymes.

Availability and implementation
Code and minimally curated activities are available at: https://github.com/moghelab/funcfetch and https://tools.moghelab.org/funczymedb.
Understanding climate change response of plant–insect herbivore interactions from ecological traits
Authors: Chang Xinyue , Yang Yuchen , Ashton Louise A , Pang Hong , Xing Shuang 
Published: December 2024

Abstract
The interactions between plants and insect herbivores play crucial roles in ecosystem functions and services. Ongoing climate change can affect these interactions through different mechanisms either directly or indirectly. In this review, we outline key ecological traits through which organisms respond to climate change. These include morphology, physiology, and chemistry for plants, and morphology, physiology, and behaviour for insects. We highlight how the responses of those traits to a changing climate might consequently affect herbivory. We propose key ecological questions that need to be addressed for each perspective of plant and insect traits, and we suggest novel approaches for answering these questions. Looking forwards, we outline fruitful areas for exploration of the ecological mechanisms underlying how plant–insect herbivore interactions might respond to climate changes from trait-based approaches.