bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrin-activating
Yersinia
protein Invasin sustains long-term expansion of primary epithelial cells as 2D organoid sheets
Authors: Wijnakker Joost J.A.P.M. , van Son Gijs J.F. , Krueger Daniel , van de Wetering Willine J. , Lopez-Iglesias Carmen , Schreurs Robin , van Rijt Fenna , Lim Sangho , Lin Lin , Peters Peter J. , Isberg Ralph R. , Janda Claudia Y. , de Lau Wim , Clevers Hans
Published: December 2024

Matrigel
®
/BME
®
, a basement membrane-like preparation, supports long-term growth of epithelial 3D organoids from adult stem cells [T. Sato
et al.
,
Nature
459
, 262–265 (2009); T. Sato
et al.
,
Gastroenterology
141
, 1762–1772 (2011)]. Here, we show that interaction between Matrigel’s major component laminin-111 with epithelial α6β1-integrin is crucial for this process. The outer membrane protein Invasin of
Yersinia
is known to activate multiple integrin–β1 complexes, including integrin α6β1. A C-terminal integrin-binding fragment of Invasin, coated on culture plates, mediated gut epithelial cell adhesion. Addition of organoid growth factors allowed multipassage expansion in 2D. Polarization, junction formation, and generation of enterocytes, goblet cells, Paneth cells, and enteroendocrine cells were stable over time. Sustained expansion of other human, mouse, and even snake epithelia was accomplished under comparable conditions. The 2D “organoid sheet” format holds advantages over the 3D “in gel” format in terms of imaging, accessibility of basal and apical domains, and automation for high-throughput screening. Invasin represents a fully defined, affordable, versatile, and animal-free complement to Matrigel
®
/BME
®
.
Angular dynamic model for fault detection of the outer raceway of the RV reducer main bearings under low-speed conditions
Authors: Wang Lin , Guo Yu , Shen Yankang
Published: December 2024

Because industrial robot joints typically operate at low speeds, conventional vibration-based fault detection techniques are unsuitable for detecting the fault of the main bearing in an industrial robot joint or rotary vector (RV) reducer. This study aims to assist in the development of the instantaneous angular speed (IAS) based main bearing fault detection method by investigating the angular response patterns caused by RV reducer main bearings with spall on the outer raceway under low-speed conditions. This study establishes an angular dynamic model to explain the IAS jitters caused by the main bearing with spall on the outer raceway under low-speed conditions. First, the radial and axial deformations arising from the contact between the roller and raceway were analyzed using Hertz contact theory. Subsequently, formulas for the induced tangential force and moment generated by the contact deformation were derived, considering the additional displacement and torque resulting from the impact force. The IAS jitters reveal the torque changes associated with the spall under low-speed conditions, enabling the estimation of the spall size by determining the start and end points of the IAS jitters. The model contribute to developing IAS-based main bearing fault detection methods for industrial robot joints.
VSPNet: a vehicle speed prediction model incorporating transformer and BiLSTM
Authors: Zhu Qinglin , Chen Dehui , Wang Zhangu , Lv Baibing , Zhao Ziliang , Zhao Jun
Published: December 2024

In recent years, with the increasing adoption of hybrid vehicles, energy management strategies have become a prominent research focus. Accurate vehicle speed prediction (VSP) is a critical prerequisite for achieving optimal results in predictive energy management strategies. However, existing speed prediction algorithms fail to fully leverage vehicle data to enhance prediction accuracy. Therefore, a novel VSP Net (VSPNet) is proposed in this study. Firstly, we constructed a combined cycle condition for model training through comprehensive analysis and analyzed the vehicle feature parameters through the random forest algorithm and Pearson correlation analysis to select the best input feature parameters. Then a VSPNet speed prediction model is proposed based on the Transformer model. In the encoder part, firstly, by assigning weights to the input feature parameters and incorporating the temporal attention mechanism, the model is made to make better use of the input features from two dimensions, and at the same time the Transformer model’s encoder based on positional coding combined with Bi-directional Long Short-Term Memory belonging to recurrent neural networks, which is used as a decoder to better catch and handle long-term dependencies in sequence data. Finally, a comparative experiment between VSPNet and the classical speed prediction models was carried out. The proposed VSPNet model reduces the root mean square error (RMSE) by 37%, 22%, and 20% and mean absolute error (MAE) by 39%, 25, and 24% compared to the LSTM model for the prediction time horizons of 3, 5, and 8 s. The RMSE is reduced by 47%, 28%, and 7%, and the MAE is reduced by 47%, 30%, and 9% compared to the Transformer model for the prediction time horizons of 3, 5, and 8 s. The experimental results demonstrate the superiority of this speed prediction model.
Optimized multi-line laser calibration based on innovative 3D target for high-precision vision systems
Authors: Yang Ziyi , Yang Pei , Wu Qiang , Zhang Jin , Xia Haojie
Published: December 2024

To achieve high-precision calibration of multi-line structured light vision measurement systems, this paper proposes a novel multi-line laser calibration method based on an encoded 3D target. Unlike traditional calibration methods that rely on 2D and 3D targets, the proposed method eliminates the need for multiple adjustments of target pose and multiple image captures, enabling rapid calibration of multiple laser lines in a single shot. The encoded 3D target designed in this study includes several flexible, adjustable planar coded feature boards, rendering it adaptable to different multi-line laser spacings and enhancing its applicability and practicality. Furthermore, this study introduces reverse reprojection constraints to optimize the proposed calibration method. This optimization enhances the precision of the light plane parameters and corrects the camera parameters. Comparative experiments with other light plane calibration methods confirm the effectiveness and superiority of the proposed method in terms of measurement accuracy.
Continuous implicit neural representation for arbitrary super-resolution of system matrix in magnetic particle imaging
Authors: Miao Zhaoji , Zhang Liwen , Tian Jie , Yang Guanyu , Hui Hui
Published: December 2024

Objective. Magnetic particle imaging (MPI) is a novel imaging technique that uses magnetic fields to detect tracer materials consisting of magnetic nanoparticles. System matrix (SM) based image reconstruction is essential for achieving high image quality in MPI. However, the time-consuming SM calibrations need to be repeated whenever the magnetic field’s or nanoparticle’s characteristics change. Accelerating this calibration process is therefore crucial. The most common acceleration approach involves undersampling during the SM calibration procedure, followed by super-resolution methods to recover the high-resolution SM. However, these methods typically require separate training of multiple models for different undersampling ratios, leading to increased storage and training time costs. Approach. We propose an arbitrary-scale SM super-resolution method based on continuous implicit neural representation (INR). Using INR, the SM is modeled as a continuous function in space, enabling arbitrary-scale super-resolution by sampling the function at different densities. A cross-frequency encoder is implemented to share SM frequency information and analyze contextual relationships, resulting in a more intelligent and efficient sampling strategy. Convolutional neural networks (CNNs) are utilized to learn and optimize the grid sampling process in INR, leveraging the advantage of CNNs in learning local feature associations and considering surrounding information comprehensively. Main results. Experimental results on OpenMPI demonstrate that our method outperforms existing methods and enables calibration at any scale with a single model. The proposed method achieves high accuracy and efficiency in SM recovery, even at high undersampling rates. Significance. The proposed method significantly reduces the storage and training time costs associated with SM calibration, making it more practical for real-world applications. By enabling arbitrary-scale super-resolution with a single model, our approach enhances the flexibility and efficiency of MPI systems, paving the way for more widespread adoption of MPI technology.
Effect of calcination temperature on the physicochemical properties of natural hydroxyapatite derived from Catla fish bone
Authors: Bee Soo-Ling , Noor Siti Noor Fazliah Mohd , Ul-Hamid Anwar , Hamid Zuratul Ain Abdul
Published: December 2024

The aim of this research is to investigate the effect of calcination temperature on the crystallinity and composition of hydroxyapatite derived from Catla bone waste using thermal calcination approach. To achieve this, bone waste was first cleaned and then thermally treated at varying calcination temperatures (650°C, 750°C, and 900°C) to yield hydroxyapatite. XRD and FTIR analyses revealed that elevating the calcination temperature leads to higher crystallinity and a reduction in carbonate content within the hydroxyapatite structure. FTIR analysis also revealed that calcination of Catla bone from 650 to 750 ·C will form B-type carbonated hydroxyapatite. Nonetheless, a biphasic calcium phosphate mixture, which is ascribed to the decomposition of hydroxyapatite phase into tricalcium phosphate was observed for product sintered at 900 ·C. Meanwhile, EDS analysis revealed the existence of trace elements, including Mg, K, Na, Si, and Sr within the crystal structure of all calcined products, irrespective of the employed calcination temperature. In conclusion, a calcination temperature of 650 °C emerged as the optimal choice for HAp extraction from Catla fish bone. This temperature not only maintained lower crystallinity but also preserved carbonate content, yielding single-phase HAp with properties well-suited for bone tissue engineering application.
Experimental Investigations on Mechanical Properties of Virgin and Recycled High-Density Polyethylene (HDPE) for the Blown Film Extrusion
Authors: Zulbakri ML , Abdullah MK , Amin AAM , Shuib RK , Abdul Hamid ZA , Idroas MY , Majid MFMA
Published: December 2024

This paper presents an experimental investigation of the mechanical properties when blending virgin and recycled high-density polyethylene (HDPE) for blown film extrusion. The investigation has been made to ensure the films meet or surpass the standards and specifications of commercial HDPE films. A sample with uniform film thickness was produced for both materials before mechanical testing using a universal testing machine. The films were cut into dumbbell shapes in machine and transverse directions, followed by a tensile test of ASTM D638 Type IV standard with a crosshead speed of 50 mm/min and 50 mm gauge length. Results such as tensile strength, elongation at break, and tensile modulus were obtained. The mechanical properties of films made from virgin HDPE and recycled HDPE were compared in various mixture ratios and with those of commercial HDPE film. The results indicate that the mechanical properties of the 8:2 mixture of virgin and recycled HDPE films perform better than the 9:1 or 7:3 mixture, which also outperforms those of commercial HDPE films, with higher tensile strength and elongation at break.
Anodic Porous NiO Film Formation for the Hexavalent Chromium Removal under Ultraviolet Irradiation
Authors: Rosli Siti Azlina , Alias Nurhaswani , Misran Halina , Matsuda Atsunori , Tan Wai Kian , Kawamura Go , Razak Khairunisak Abdul , Lockman Zainovia
Published: December 2024

Anodic porous nickel oxide (NiO) was grown by anodization of Ni in ethylene glycol (EG) added to NH4F at 60 V in a two-step anodic process. The first process produced hydrated anodic film which was removed before the foil was subjected to a second anodic process. This led to the formation of porous structure with pore diameters of ∼ 90-180 nm. Formation of porous structure was done as to provide a larger specific surface area that can increase the removal efficiency of the hexavalent chromium. The as-anodized anodic film was then annealed at 300 °C to improve the adhesion of nickel oxides porous to substrates before being used as a photocatalyst to reduce Cr(VI) in a synthetic wastewater under ultraviolet (UV) irradiation. Porous NiO showed a good photocatalyst performance in reducing Cr(VI) to Cr(III) with 60% reduction after 150 min. However, with the addition of ethylenediaminetetraacetic acid (EDTA), 100% reduction was achieved after 120 min indicating that EDTA is required as holes scavengers.
LCO(1-0) – LFIR Correlation at Sub-Kiloparsec Scale in Nearby Spiral Galaxy NGC 1068
Authors: Azeez Jazeel H. , Umar Roslan
Published: December 2024

The impetus for researching the LCO(1-0)-LFIR connection at sub-kpc levels comes from the opportunity to improve our knowledge of the intricate processes regulating star formation, molecular gas dispersion, and galaxies’ overall evolution. We use a high spatial resolution 12CO(1–0) line emission data from the Atacama Large Millimeter/Submillimeter Array (ALMA) for the galaxy NGC 1068 (commonly known as M77) at a distance of 14.4 Mpc as well as Herschel 160 μm data for the same galaxy at (∼ 210 pc) scale. 31 regions were targeted across the gaseous disc of NGC 1068 (C and R1- R30). We measured the luminosity of CO(1-0) molecular gas and FIR luminosity in these regions. The relation between LCO(1-0) and LFIR has been studied in the upper and lower arms of this galaxy with a high spatial resolution. Using the Pearson Correlation test, the results indicate that a high positive correlation exists between the LFIR and the LCO(1-0) in the lower arm of this galaxy with correlation coefficient r = 0.86 and probability p = 99.99%, while a moderate correlation exists in the upper arm with correlation coefficient r = 0.45 and probability p = 89.54%. Furthermore, a sub-linear KS Law index was found in both upper and lower arms.
A case study on the impact of geomagnetic storms events with Dst ≤ 350nT in May 2024
Authors: Shah Raja Adibah Raja Halim , Hamid Nurul Shazana Abdul , Abdullah Mardina , Annuar Adlyka , Sarudin Idahwati , Kamarudin Farahana , Yoshikawa Akimasa
Published: December 2024

This study presented the effect of a geomagnetic storm that was driven by coronal mass ejection (CME) on the ionospheric disturbance dynamo (Ddyn) near the equatorial region. The Ddyn variation was calculated using Earth’s magnetic field’s H component data. On the other hand, the Space Weather Prediction Center (SWPC) provides the data on the CME events utilized in this analysis. The geomagnetic storm is identified using the disturbance storm time (Dst) index. Multiple CME on 8 May 2024 and 9 May 2024 triggered the two-step storm with great storm type where the Dst values are -352 nT (10 May 2024, 22:00 UT) and -412 nT (11 May 2024, 02:00 UT), whose recovery phase lasted approximately ∼11 days. During this geomagnetic storm’s recovery phase, no clear magnetic signature on the Ddyn variation was observed at the Ranau station in Malaysia.
Climate Analysis for Tourist Comfort Level in Belitong Geopark
Authors: Yuliarti Aflah , Setiawan Budhi , Yusup Nur Khakim M.
Published: December 2024

Tourism, a sector with significant potential to be developed into a source of regional income, is one of the focuses of the Ministry of Tourism and Creative Economy/Tourism and Creative Economy Agency (Kemenparekraf/Baparekraf) in their quest for sustainable tourism in Indonesia. Their efforts have resulted in Belitong Geopark being designated as a UNESCO Global Geopark., a new environmentally-based tourism branding. The comfort of the climate and the natural beauty of the tourist attractions play a crucial role in influencing tourists’ decisions to visit a destination. The Tourism Climate Index (TCI) and the Thermal Humidity Index (THI) are employed in this research to analyze the climate comfort level for tourism. (1) The factors that make up the climate comfort index, including precipitation, temperature, sunshine duration, wind speed and cloud coverage, are components of the thermal, physical, and aesthetic dimensions used to assess climate comfort levels. The climate data from 1991 to 2020 were obtained from the H.AS Hanandjoeddin Meteorological Station, cooperation rain-gauge stations from 2014 to 2020, and ECMWF reanalysis data with a data resolution of 0.25° x 0.25° for 1991-2020. According to the THI values in the Belitung Geopark, they are in the comfort category all year round, with the Tajam Mountain and Lumut Hill geosites showing the lowest THI values and having an extremely comfortable THI category, respectively. In comparison, the TCI results indicate that the best time to travel to Geopark Belitung is between December and June, mainly with TCI values in the excellent and perfect categories. In conclusion, climatic conditions in Belitung Geopark support tourism activities all year round.
The True Mother Earth Geotrail, in Kebumen Geopark
Authors: Ansori Chusni , Kusworo Aris , Mareta Nandian , Hastria Defry , Novy Yono Putro Iwan
Published: December 2024

Geopark is the concept of sustainable development based on geological heritage, geodiversity, cultural diversity, and biodiversity for conservation, education, and sustainable economic development. The Global Unesco Network has validated the Kebumen Geopark and its status as an aspiring UNESCO Global Geopark. Geopark management prepares the geotrail at the beginning before validation.

Geotourism is a tourism activity based on A.B.C. components in the form of geological diversity (Abiotic), geological heritage (Abiotic), biological diversity (Biotic), and culture diversity (Culture), which are related to geological diversity. Geotrail is a geotourism route arranged with a specific theme to connect A.B.C. components and become a fun/melodic and educational tourist route. One of the geotrails being prepared is in the Karangsambung area, a trace of the ancient subduction zone with its rich geodiversity. The Karangsambung area is the best evidence of plate tectonic theory in South East Asia with the oldest rocks in Java. The True Mother Earth of Java means that the oldest rocks in Java are exposed and can be used for geotourism about the concept of plate tectonics.

The results of scientific value analysis, potential education value, tourism value, and degradation risk are created to geotrail. It is hoped that by following this trail, tourists can gain an exciting experience in understanding the plate tectonics concept combined with cultural and biological diversity.
Geosite Gunung Benau Karst Area, North Kalimantan, Indonesia
Authors: Heriyanto  , Sabrian P G , Haryono E , Sonaria M , Naomy A , Maslihatul  , Aqila D
Published: December 2024

Mount of Benau is located in the North Borneo, precisely on the border between Bulungan Regency and Berau Regency. Thuis geological sites has rich in geological diversity and natural beauty. As part of a unique karting ecosystem, Mount Benau offers stunning views and high scientific value. This article will discuss various aspects related to Mount Benau, including geological characteristics, biodiversity, and potential for tourism development. Mount Benau is a residence for the Dayak Punan Batu tribe who has for generations occupied the existing caves or burrows. Until now, they still live in a nomadic or mobile home system. The method used is direct observation in the field and classifying existing geosites. Geosite classification on the Gunung Benau can be divided into 3 clusters, which are Lithology Cluster, Cave Cluster and Niche Cluster.
Geotourism Potensial on Geoheritage in Natuna Geopark
Authors: Ryannaldo  , Intan Ratih K
Published: December 2024

Natuna is an archipelago and the name of a regency located in the Riau Islands Province. Bunguran Island, the largest island, has a unique geological diversity, where the rocks are derived from continental and oceanic crusts, including old river deposits. Natuna is rich in biological and cultural diversity of local communities. The diversity of the Earth’s heritage made Natuna designated as a national geopark in 2018. One of geopark’s goals is to foster a local economic value, which is usually approached through geotourism activities. The purpose of this research is to assess the potential of geotourism, especially from geological heritage aspect. The research method used were literature review, field data sampling, including analysis and classification. It was identified that five geoheritage sites are feasible to be developed into geotourism objects and attractions.
Implementation of WISE (Wonderful Indonesia Sustainable Tourism) Trips – A Journey Towards Low Carbon Geotourism Activities in Raja Ampat Geopark
Authors: Septiana A R , Lamatenggo Y N , Musa’ad M , Samodra H
Published: December 2024

Tourism is a sector that significantly impacts the Indonesian economy and contributing 8% of carbon emissions in the atmosphere. Raja Ampat, renowned as one of the best diving destinations in the world, faces a serious threat due to the occurrence of coral bleaching events at several diving sites. As the UNESCO Global Geopark, the Encouraging the Implementation of the Manokwari Declaration program aims to implement national policies, including WISE (Wonderful Indonesia Sustainable Experience) Trips, which focus on low-carbon practices in tourism activities. In collaboration with CarbonEthics, carbon emissions related to geotourism are calculated by considering factors such as transportation, accommodation, food and beverage, and energy and plastic waste from activities. Geotourism activities packaged in the Raja Ampat UGGp geotrail are part of the Authentic Experience of Southwest Papua activity package. The calculation results indicate that the Geotrail Cruising the Sea of The Legend carbon emissions of 0.098 tons of CO2e per person, and tourists are encouraged to plant at least one mangrove trees in areas managed by BUMDES (Village-Owned Enterprises). Through this initiative, local communities not only benefit economically but also become educated and directly involved in climate change mitigation and conservation of their villages, in accordance with the principles of the SDG’s where this program fulfills 10 of the 17 Sustainable Development Goals.
Assessment of Geoconservation Potential in Part of Sukabumi Area Using Swot Analysis Based on Regulation by Ministry of Energy and Mineral Resources no 32 of 2016
Authors: Afifah Nurul , Masitoh Ferryati , Afrida Pungkisari Visky
Published: December 2024

Sukabumi located in West Java, Indonesia. The regional structure of the Sukabumi region is influenced by the convergence plate of the Eurasian and East Indies-Australia plates. The geological dynamic creates uniqueness and threat in the area studied. The uniqueness of the Sukabumi Region with the existence of the Cimandiri fault gives rise to the natural beauty that is considered to have potential as a geotourism area. Geotourism needs to be maintained and preserved as Geological Nature Reserve Areas (GNRA). The background of this research is the lack of public attention to the geotourism potential areas in Sukabumi. The study method uses thematic map analysis with the overlapping and the SWOT (scoring)-methods at 3 study areas: Cikundul, Santa Sea, and Karang Para. The potential of GNRA is given weight considering the regulation of the Minister of Energy and Mineral Resources No. 32 of 2016. The results of this study include development directions and the potential maps of Geological Reserves in the Sukabumi Region, West Java Province. The research output is to provide development directions related to the utilization and protection of Sukabumi geological uniqueness as a Geological Nature Reserve Area.
Geotechnical Aspects of Salo Lawo Waterfall in Salopuru Pattappa, Pujananting District, Barru Regency, South Sulawesi
Authors: Salam Munir Abdul , Anwar Habibie , Hardin Wakila Muhamad
Published: December 2024

The Salo Lawo waterfall represents a significant geotourism destination for the community in Pujananting, Barru district. It is of critical importance to identify the geotechnical aspects of this site in order to ensure the safety of visitors and to prevent potential rock mass movements. This research identifies fundamental geotechnical aspects through measuring and observing joints or discontinuities using the scanline method in the field. This is complemented by a kinematic analysis of stereographic projections, which enables the determination of failure modes potential and the classification of rock masses. The Salo Lawo waterfall is formed by sandstone in the Balang Baru formation, which exhibits a medium rock compressive strength. The kinematic analysis indicated that two types of failure could potentially occur on the rock slope wall: wedge sliding (26.29%) and oblique toppling, which is part of direct toppling (23.67%). The potential for planar sliding and flexural toppling was not identified, as indicated by the absence of critical intersections and the presence of only very small critical intersections obtained from stereographic projections. The kinematic analysis conducted in this research project predicts the potential for failure modes to occur at this location. This is considered to be a basic or initial stage in the assessment of the geotechnical aspects of the area. Consequently, further research is required to employ more detailed methods and laboratory testing to estimate the stability of the rock slopes at Salo Lawo waterfall. This will enable the information on geotechnical aspects to become more complete and valuable.
Contingency Planning for Tourism Development in Volcanic Disaster-Prone Areas in Indonesia
Authors: Kristianto  , Nugraha Kartadinata Mochamad , Kamil Syahbana Devy
Published: December 2024

Indonesia is geologically recognized as a complex region due to its location at the convergence of the Eurasian, Pacific, and Indo-Australian tectonic plates, making it highly susceptible to geological hazards. Among these hazards, volcanic activity poses a significant threat, with 127 volcanoes identified as potential eruption hazards. Volcanic disasters often result in substantial loss of life and property. The natural beauty and allure of volcanic landscapes attract numerous tourists, leading to heavy concentrations of people in potentially dangerous areas. If tourism in these regions is not managed effectively, the risk of disasters may increase. Catastrophic volcanic eruptions, such as those at Lokon (1991), Semeru (2000), Bromo (2004), and Marapi (2023), have resulted in considerable casualties among tourists. This paper aims to provide essential considerations for tourism stakeholders in active volcanic regions to enhance safety and reduce fatalities associated with volcanic eruption hazards. It will explore the challenges and risks posed by tourism in these areas, emphasizing the need for comprehensive contingency planning. To safeguard tourists, future tourism development in areas prone to volcanic disasters must incorporate disaster risk assessments, early integration of volcanic hazard maps into tourist site designs, adherence to technical guidance from volcanological institutions, implementation of early warning systems, and regular dissemination of volcanic hazard mitigation measures.
Exploring Academic Perspectives for Enhancing Geopark Potentials in Cianjur: A Viewpoint Study
Authors: Muslim G O , Herdiansyah A R , Alfiyalin Y Y , Fahira G H , Muslim F N , William G , Muslim D
Published: December 2024

This study investigates how academic institutions can contribute to enhancing the geopark potential of Gunung Padang in Cianjur, Indonesia. As a significant megalithic site in Southeast Asia, Gunung Padang combines geological and cultural heritage, offering valuable opportunities for geotourism and education. However, limited research and awareness hinder the full realization of these assets. This research focuses on perspectives within the Islamic boarding school community, particularly Al Kautsar Islamic Boarding School, to understand local perceptions of the site’s potential as a tourism destination. Using literature reviews and key informant interviews, the study analyzes the role of local educational institutions in promoting environmental stewardship and community involvement. By integrating geopark concepts into educational curricula, these institutions can foster sustainable development, bridging cultural preservation with economic growth through tourism.
Enhancing Electrical Conductivity and pH Sensor Measurements in Precision Hydroponics: Comparative Analysis of Six Data Processing Methods
Authors: Sulaiman Hamdan , Anas Yusof Ahmad , Khairi Mohamed Nor Mohd
Published: December 2024

Precision hydroponics requires precise and accurate Electrical Conductivity (EC) and Potential of Hydrogen (pH) measurements. The analog signals from the EC and pH sensor are converted to voltage and then into either EC or pH readings depending on the type of the sensor used. This paper presents a comparative study of six data processing methods to increase the precision and accuracy of EC and pH sensor measurements. The data processing includes six data processing methods that comprise direct (Methods 1 and 2) and selective methods (Methods 3, 4, 5, and 6). The precision of each data processing method was measured by comparing the standard deviation (SD) and coefficient of variance (CV). The accuracy of the methods was calculated using Mean Absolute Error (MAE) and Root Mean Square Errors (RMSE). Outliers were identified through the interquartile range (IQR). The results show that Method 1 (SD = 4.935 mV; CV = 7.16; MAE = 3.090 mV; RMSE = 5.290 mV) is the unreliable method, whereas Method 5 (SD = 0.777 mV; CV = 1.15; MAE = 0.610 mV; RMSE = 0.866 mV) and Method 6 (SD = 0.669 mV; CV = 0.99; MAE = 0.640 mV; RMSE = 0.883 mV) demonstrate high precision and accurate measurements. This study offers reliable data processing methods in taking EC and pH measurements. Future research and hydroponics practitioners should use our suggested data processing methods.
Prediction of Soluble Solids Content in Tomatoes Due to Mechanical Impact Using NIR Spectroscopy
Authors: Andasuryani Andasuryani , Cherie Dinah , Maulana Raisal
Published: December 2024

Soluble Solids Content (SSC) is an important indicator that reflects tomatoes’ taste quality and sugar content (Lycopersicon esculentum Mill). During post-harvest handling using sorting and grading machines, tomatoes are at risk of mechanical impact that can cause changes in SSC content. This study aims to investigate the NIR spectroscopy method in predicting the SSC content of tomatoes that experience mechanical impact. We simulated mechanical impact at a drop height of 0 cm, 20 cm, 40 cm, and 60 cm and collected NIR spectra of tomatoes from a wavelength of 1000-2500 nm. We developed a calibration model using the partial least squares (PLS) method, preprocessing baseline correction, and Standard Normal Variate (SNV). The results showed that the best calibration model was the one with preprocessing baseline correction, which had Rc2, Rv2 SEC, SEP, and CV values of 0.90, 0.71, 0.14, 0.19, and 0.05, respectively. This study demonstrates the ability of NIR spectroscopy to predict SSC content in tomatoes due to mechanical impact.
Design of Pasaman Orange Grading Machine Based on Color and Size Using ESP32 Based Fuzzy Logic
Authors: fmalinda I , Fauzi F. F. , Azrifirwan
Published: December 2024

Pasaman oranges are one of the flagship agricultural commodities in West Sumatra, Indonesia. In the production process, orange classification is required to group the fruit based on its quality. However, many farmers still classify Pasaman oranges manually, which leads to issues with consistency in classification. This research aims to address this problem by designing an automatic grading machine for Pasaman oranges based on color and size, utilizing color sensor technology (TCS-3200) and ultrasonic sensors (HC-SR04) combined with fuzzy logic based on ESP32. The grading machine is designed to improve efficiency and reduce errors in the classification process. The results of the research show that the grading machine has a classification accuracy rate of 84.44% and an actual working capacity of an average of 1,363.64 fruits per hour. The developed grading machine has proven capable of classifying Pasaman oranges at a high capacity.
Evaluating the Impact of Agrivoltaic Systems on Microclimate and Andrographis paniculata Growth
Authors: Ashraf Zainol Abidin Mohd , Faqihah Jamrus Nur , Iman Azman Nurul , Illani Abdul Razak Nur , Faezah Omar Nur
Published: December 2024

Agrivoltaic systems (AVS) integrate photovoltaic (PV) systems with agricultural production, presenting a dual strategy that optimize both energy and crop yields. This study aims to evaluate the effects of AVS on microclimate and growth performance of Andrographis paniculata, a medicinal herbaceous. The experiment consists of three treatments; Mono-Photovoltaic (MPV), Monocrop (MC), and AVS system (where the crops are grown under solar panels). Parameters like air temperature, humidity, and light intensity of the microclimate, and soil data such as soil temperature, moisture content, and electrical conductivity values are taken using sensors connected to a datalogger. Next, parameters such as plant height, stem diameter, number of leaves and SPAD value are measured and analyzed. The results show that AVS not only provide shade, but also produce a 6% cooler and 8.9% humid microclimate compared to MC, that benefits the growth of Andrographis paniculata and potentially improve the efficiency of PV. Furthermore, growing media under the AVS recorded higher moisture content, suggesting good water retention, which possibly reduce the irrigation water requirement. The study concludes that AVS system can be a practicable method to improve both productions in Malaysia. Thus, suggesting further research on other crops, irrigation management, and large-scale implementation of AVS.
Strategy for Developing the Rice Milling Business in Bunga Raya District Siak Regency: Case Study of Rice Milling X
Authors: Adha R , Pramana A , Juarsa R P , Kurniawan M A , Johan V S
Published: December 2024

Bunga Raya serves as a significant locus for rice production within the Siak Regency of Riau Province. This study endeavored to examine strategic approaches for business expansion and to identify the critical strategic focal points within the X rice milling enterprise located in Bunga Raya District, Siak Regency, by employing the methodologies of SWOT (strengths, weaknesses, opportunities, and threats) analysis and QSPM (quantitative strategic planning matrix). The data analysis encompassed the identification of both internal and external variables influencing the enterprise, the formulation of alternative strategies through the SWOT matrix, and the establishment of strategic priorities utilizing the QSPM matrix. Based on the results of the SWOT matrix analysis and from the results of the QSPM matrix analysis, the strategy for business development at the X rice mill is in the S-T (strength-threat) strategy, the strategy that can be carried out is to enhance the quality of the products manufactured, which holds a TAS value of 5.080.
Environment friendly synthesis of Fe3O4 nanoparticles using moringa oleifera seed/pulp extract and their application for dye wastewater treatment
Authors: Vora Rutvi , Patel Hima , Parekh Kinnari
Published: December 2024

A simple, eco-friendly, green synthesis protocol for producing biocompatible iron oxide nanoparticles using the Moringa oleifera (MO) seed/pulp extracts (MSE/MPE) is reported. The crystallite phase formation of magnetite nanoparticles is confirmed using a powder x-ray diffractometer. The morphology, surface properties, and magnetic properties are investigated using a transmission electron microscope (TEM), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and vibrating sample magnetometer (VSM). The particles with optimized properties from MSE and MPE synthesis are used for investigating their photocatalytic activity on methylene blue dye. Results of dye degradation show that the particles synthesized using MSE showed 53.46% degradation, whereas MPE showed 37.87% degradation of methylene blue dye under UV light. The photodegradation process follows pseudo-second-order kinetic model indicating that the dye is degraded to its intermediate compounds, which are chemically adsorbed on the particle surface, as confirmed through FTIR. The results show promising potential of synthesizing such nanoparticles for treatment of wastewater using a greener approach.
Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers
Authors: Wojtulewski Adam , Sikora Aleksandra , Dineen Sean , Raoof Mustafa , Karolak Aleksandra
Published: December 2024

Objective

The primary objective of this study is to investigate various applications of artificial intelligence (AI) and statistical methodologies for analyzing and managing peritoneal metastases (PM) caused by gastrointestinal cancers.

Methods

Relevant keywords and search criteria were comprehensively researched on PubMed and Google Scholar to identify articles and reviews related to the topic. The AI approaches considered were conventional machine learning (ML) and deep learning (DL) models, and the relevant statistical approaches included biostatistics and logistic models.

Results

The systematic literature review yielded nearly 30 articles meeting the predefined criteria. Analyses of these studies showed that AI methodologies consistently outperformed traditional statistical approaches. In the AI approaches, DL consistently produced the most precise results, while classical ML demonstrated varied performance but maintained high predictive accuracy. The sample size was the recurring factor that increased the accuracy of the predictions for models of the same type.

Conclusions

AI and statistical approaches can detect PM developing among patients with gastrointestinal cancers. Therefore, if clinicians integrated these approaches into diagnostics and prognostics, they could better analyze and manage PM, enhancing clinical decision-making and patients’ outcomes. Collaboration across multiple institutions would also help in standardizing methods for data collection and allowing consistent results.
Predicting CRISPR-Cas9 off-target effects in human primary cells using bidirectional LSTM with BERT embedding
Authors: Sari Orhan , Liu Ziying , Pan Youlian , Shao Xiaojian
Published: December 2024

Motivation

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system is a ground-breaking genome editing tool, which has revolutionized cell and gene therapies. One of the essential components involved in this system that ensures its success is the design of an optimal single-guide RNA (sgRNA) with high on-target cleavage efficiency and low off-target effects. This is challenging as many conditions need to be considered, and empirically testing every design is time-consuming and costly. In silico prediction using machine learning models provides high-performance alternatives.

Results

We present CrisprBERT, a deep learning model incorporating a Bidirectional Encoder Representations from Transformers (BERT) architecture to provide a high-dimensional embedding for paired sgRNA and DNA sequences and Bidirectional Long Short-term Memory networks for learning, to predict the off-target effects of sgRNAs utilizing only the sgRNAs and their paired DNA sequences. We proposed doublet stack encoding to capture the local energy configuration of the Cas9 binding and applied the BERT model to learn the contextual embedding of the doublet pairs. Our results showed that the new model achieved better performance than state-of-the-art deep learning models regarding single split and leave-one-sgRNA-out cross-validations as well as independent testing.

Availability and implementation

The CrisprBERT is available at GitHub: https://github.com/OSsari/CrisprBERT.
SampleExplorer: using language models to discover relevant transcriptome data
Authors: Chin Wee Loong , Lassmann Timo
Published: December 2024

Motivation

Over the last two decades, transcriptomics has become a standard technique in biomedical research. We now have large databases of RNA-seq data, accompanied by valuable metadata detailing scientific objectives and the experimental procedures used. The metadata is crucial in understanding and replicating published studies, but so far has been underutilized in helping researchers to discover existing datasets.

Results

We present SampleExplorer, a tool allowing researchers to search for relevant data using both text and gene set queries. SampleExplorer embeds sample metadata and uses a transformer-based language model to retrieve similar datasets. Extensive benchmarking (see Supplementary Materials and Methods) using the ARCHS4 database demonstrates that SampleExplorer provides an effective approach for retrieving biologically relevant samples from large-scale transcriptomicdata. This tool provides an efficient approach for discovering relevant gene expression datasets in large public repositories. It improves sample and dataset identification across diverse experimental contexts, helping researchers leverage existing transcriptomic data for potential replication or verification studies.

 

Availability and implementation: SampleExplorer is available as a Python package compatible with versions 3.9 to 3.11, available for installation via the Python Package Index (PyPI). The codebase and documentation are accessible at https://github.com/wlchin/SampleExplorer. Supplementary data (Supplementary Materials and Methods) provides detailed methodological information, including an algorithmic description of the retrieval process and data preparation steps.
Development of pH-responsive crosslinked peptides that form stable α-helices under weakly acidic conditions
Authors: Amano Miwo , Chiba Junya , Yasukagawa Tetsuya , Yokoyama Satoru , Zhou Yue , Ohishi Yuki , Inouye Masahiko
Published: December 2024

α-Helical structures in protein surface are frequently related to protein–protein interactions that play important roles in signal transduction. We have developed various crosslinking agents that stabilize the α-helical structure of short peptides. In this article, we report pH-responsive crosslinked peptides that promote helical conformation of the peptides under weakly acidic conditions. We incorporated critical sequence of a synthetic estrogen receptor activity-regulating peptide into our pH-responsive crosslinked peptide. The pH control could provide total structural regulation of the target peptide.
A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy
Authors: Velotta Jonathan P , Iqbal Azwad R , Glenn Emma S , Franckowiak Ryan P , Formenti Giulio , Mountcastle Jacquelyn , Balacco Jennifer , Tracey Alan , Sims Ying , Howe Kerstin , Fedrigo Olivier , Jarvis Erich D , Therkildsen Nina O
Published: December 2024

Transitions across ecological boundaries, such as those separating freshwater from the sea, are major drivers of phenotypic innovation and biodiversity. Despite their importance to evolutionary history, we know little about the mechanisms by which such transitions are accomplished. To help shed light on these mechanisms, we generated the first high-quality, near-complete assembly and annotation of the genome of the American shad (Alosa sapidissima), an ancestrally diadromous (migratory between salinities) fish in the order Clupeiformes of major cultural and historical significance. Among the Clupeiformes, there is a large amount of variation in salinity habitat and many independent instances of salinity boundary crossing, making this taxon well-suited for studies of mechanisms underlying ecological transitions. Our initial analysis of the American shad genome reveals several unique insights for future study including: (i) that genomic repeat content is among the highest of any fish studied to date; (ii) that genome-wide heterozygosity is low and may be associated with range-wide population collapses since the 19th century; and (iii) that natural selection has acted on the branch leading to the diadromous genus Alosa. Our analysis suggests that functional targets of natural selection may include diet, particularly lipid metabolism, as well as cytoskeletal remodeling and sensing of salinity changes. Natural selection on these functions is expected in the transition from a marine to diadromous life history, particularly in the tolerance of nutrient- and ion-devoid freshwater. We anticipate that our assembly of the American shad genome will be used to test future hypotheses on adaptation to novel environments, the origins of diadromy, and adaptive variation in life history strategies, among others.
Times needed to evolve mating cues under allopatry and parapatry
Authors: Sibly Richard M , Curnow Robert N
Published: December 2024

The time needed for the evolution of mating cues that distinguish species, such as species-specific songs or plumage coloration in birds, has received little attention. Aiming to gain some understanding of the timing of the evolutionary process we here present models of how mating cues evolve in populations split into subpopulations between which there may (parapatry) or may not (allopatry) be migration. Mating cues can be either neutral or directly selected. In models in which evolution commences with a substitution at a neutral mating-cue locus, under allopatry there is no selection on the mating cue, but under parapatry, selection may be induced on the mating cue by the selective conditions in the subpopulations, and the migration rates between them. We use simulation to calculate how selection pressures on mating cues then depend on selective conditions in subpopulations and migration rates between them. In the second part of the paper, we demonstrate quantitatively how the resulting selection pressures on new mating cues together with mutation rate affect speciation time. Our results suggest that species-specific songs or plumage colorations that are selectively neutral evolve faster under parapatry than under allopatry, and this may explain the short speciation times that are sometimes reported. Although our modelling assumptions are restrictive so that caution is needed in comparing the results to empirical data, we hope that our main results, showing quantitatively how parapatry can reduce speciation times, will encourage further work relaxing model assumptions or studying different models of mate choice.
Giant periscapular lipoma unmasked by post-bariatric surgery weight loss: a case report
Authors: Mohammad Hussain , Almajed Suaad , Nawaf Norah , AlMulla Nawar , Lari Ali , Jarragh Ali
Published: December 2024

Giant lipomas, rare benign tumours composed of mature adipose tissue, represent only 1% of all lipomas, typically exceeding 10 cm in diameter or weighing over 1000 g. These tumours can cause nerve compression, discomfort, or functional impairment, necessitating surgical excision. We report a 52-year-old male with a giant intramuscular lipoma in the periscapular region, initially identified following significant weight loss after bariatric surgery. Clinical evaluation revealed a 15 × 20 cm mass, confirmed via computed tomography (CT) scan. Surgical excision was performed, followed by histopathological analysis, which confirmed a benign lipoma. Postoperative management was complicated by seroma formation, requiring drainage. This case underscores the importance of early diagnosis, imaging, and appropriate surgical management for large lipomas to prevent complications and recurrence while ensuring optimal cosmetic outcomes.