bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detailed analysis of agro-industrial byproducts/wastes to enable efficient sorting for various agro-industrial applications
Authors: Priyanka Govindegowda , Singiri Jeevan R. , Adler-Agmon Zachor , Sannidhi Sasank , Daida Spurthi , Novoplansky Nurit , Grafi Gideon 
Published: May 2024

AbstractAgriculture-based industries generate huge amounts of byproducts/wastes every year, which are not exploited or disposed efficiently posing an environmental problem with implications to human and animal health. Finding strategies to increase the recycling of agro-industrial byproducts/wastes (AIBWs) is a primary objective of the current study. A thorough examination of AIBWs in conjunction with experimental research is proposed to facilitate sorting for various agro-industrial applications and consequently increasing byproduct/waste utilization. Accordingly, two sustainable, locally available sources of AIBWs, namely, wheat bran (WB) and garlic straw and peels (GSP) were studied in detail including content and composition of proteins, phytohormones and nutritional elements, as well as the effect of AIBW extracts on plant and microbial growth. Hundreds of proteins were recovered from AIBW mainly from WBs, including chaperons, metabolite and protein modifying enzymes, and antimicrobial proteins. In-gel assays showed that WB and GSP possess high protease and nuclease activities. Conspicuously, phytohormone analysis of AIBWs revealed the presence of high levels of strigolactones, stimulants of seed germination of root parasitic weeds, as well as indole acetic acid (IAA) and abscisic acid (ABA). Garlic straw extract strongly inhibited germination of the weed Amaranthus palmeri but not of Abutilon theophrasti and all examined AIBWs significantly affected post-germination growth. Bacterial growth was strongly inhibited by garlic straw, but enhanced by WBs, which can be used at least partly as a bacterial growth medium. Thus, an in-depth examination of AIBW characteristics will enable appropriate sorting for diverse agro-industrial applications, which will increase their utilization and consequently their economic value.
General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex
Authors: Oyarzún-Cisterna Andrea , Gidi Cristián , Raiqueo Fernanda , Amigo Roberto , Rivas Camila , Torrejón Marcela , Gutiérrez José L. 
Published: May 2024

Abstract
Background
Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regulatory factors (GRFs). These factors contribute to establishment and maintenance of nucleosome-depleted regions (NDRs). These regions are populated by nucleosomes through histone deposition and nucleosome sliding, the latter catalyzed by a number of ATP-dependent chromatin remodeling complexes, including ISW1a. It has been observed that GRFs can act as barriers against nucleosome sliding towards NDRs. However, the relative ability of the different GRFs to hinder sliding activity is currently unknown.

Results
Considering this, we performed a comparative analysis for the main GRFs, with focus in their ability to modulate nucleosome sliding mediated by ISW1a. Among the GRFs tested in nucleosome remodeling assays, Rap1 was the only factor displaying the ability to hinder the activity of ISW1a. This effect requires location of the Rap1 cognate sequence on linker that becomes entry DNA in the nucleosome remodeling process. In addition, Rap1 was able to hinder nucleosome assembly in octamer transfer assays. Concurrently, Rap1 displayed the highest affinity for and longest dwell time from its target sequence, compared to the other GRFs tested. Consistently, through bioinformatics analyses of publicly available genome-wide data, we found that nucleosome occupancy and histone deposition in vivo are inversely correlated with the affinity of Rap1 for its target sequences in the genome.

Conclusions
Our findings point to DNA binding affinity, residence time and location at particular translational positions relative to the nucleosome core as the key features of GRFs underlying their roles played in nucleosome sliding and assembly.
Radiation nanomedicines for cancer treatment: a scientific journey and view of the landscape
Authors: Reilly Raymond M. , Georgiou Constantine J. , Brown Madeline K. , Cai Zhongli 
Published: May 2024

Abstract
Background
Radiation nanomedicines are nanoparticles labeled with radionuclides that emit α- or β-particles or Auger electrons for cancer treatment. We describe here our 15 years scientific journey studying locally-administered radiation nanomedicines for cancer treatment. We further present a view of the radiation nanomedicine landscape by reviewing research reported by other groups.

Main body
Gold nanoparticles were studied initially for radiosensitization of breast cancer to X-radiation therapy. These nanoparticles were labeled with 111In to assess their biodistribution after intratumoural vs. intravenous injection. Intravenous injection was limited by high liver and spleen uptake and low tumour uptake, while intratumoural injection provided high tumour uptake but low normal tissue uptake. Further, [111In]In-labeled gold nanoparticles modified with trastuzumab and injected iintratumourally exhibited strong tumour growth inhibition in mice with subcutaneous HER2-positive human breast cancer xenografts. In subsequent studies, strong tumour growth inhibition in mice was achieved without normal tissue toxicity in mice with human breast cancer xenografts injected intratumourally with gold nanoparticles labeled with β-particle emitting 177Lu and modified with panitumumab or trastuzumab to specifically bind EGFR or HER2, respectively. A nanoparticle depot (nanodepot) was designed to incorporate and deliver radiolabeled gold nanoparticles to tumours using brachytherapy needle insertion techniques. Treatment of mice with s.c. 4T1 murine mammary carcinoma tumours with a nanodepot incorporating [90Y]Y-labeled gold nanoparticles inserted into one tumour arrested tumour growth and caused an abscopal growth-inhibitory effect on a distant second tumour. Convection-enhanced delivery of [177Lu]Lu-AuNPs to orthotopic human glioblastoma multiforme (GBM) tumours in mice arrested tumour growth without normal tissue toxicity. Other groups have explored radiation nanomedicines for cancer treatment in preclinical animal tumour xenograft models using gold nanoparticles, liposomes, block copolymer micelles, dendrimers, carbon nanotubes, cellulose nanocrystals or iron oxide nanoparticles. These nanoparticles were labeled with radionuclides emitting Auger electrons (111In, 99mTc, 125I, 103Pd, 193mPt, 195mPt), β-particles (177Lu, 186Re, 188Re, 90Y, 198Au, 131I) or α-particles (225Ac, 213Bi, 212Pb, 211At, 223Ra). These studies employed intravenous or intratumoural injection or convection enhanced delivery. Local administration of these radiation nanomedicines was most effective and minimized normal tissue toxicity.

Conclusions
Radiation nanomedicines have shown great promise for treating cancer in preclinical studies. Local intratumoural administration avoids sequestration by the liver and spleen and is most effective for treating tumours, while minimizing normal tissue toxicity.
Polar code-based secure transmission with higher message rate combining channel entropy and computational entropy
Authors: An Chen , Huang Mengjie , Lu Xianhui , Bi Lei , Li Weijie 
Published: May 2024

AbstractThe existing physical layer security schemes, which are based on the key generation model and the wire-tap channel model, achieve security by utilizing channel reciprocity entropy and noise entropy, respectively. In contrast, we propose a novel secure transmission framework that combines noise entropy with reciprocity entropy, achieved by inserting reciprocity entropy into the frozen bits of polar codes. Note that in real-world scenarios, when eavesdroppers employ polynomial-time attacks, the bit error rate (BER) increases due to the introduction of computational entropy. To achieve indistinguishability security, we convert the practical physical layer security metric, BER, into the average min-entropy, a widely accepted concept in cryptography. The simulation results demonstrate that the eavesdropper’s BER can be significantly increased without compromising the communication performance of the legitimate receiver. Under concrete parameters we selected, when compared to the joint scheme of physical layer key generation and one time pad, the modular semantically-secure scheme based on the wire-tap channel model, and the simple channel entropy combination scheme, our scheme achieves a message rate approximately 1.2 times, 3.8 times, and 1.4 times better, respectively. Experimental testing validates the feasibility of our scheme.
Accuracy of machine learning to predict the outcomes of shoulder arthroplasty: a systematic review
Authors: Karimi Amir H. , Langberg Joshua , Malige Ajith , Rahman Omar , Abboud Joseph A. , Stone Michael A. 
Published: May 2024

Abstract
Background
Artificial intelligence (AI) uses computer systems to simulate cognitive capacities to accomplish goals like problem-solving and decision-making. Machine learning (ML), a branch of AI, makes algorithms find connections between preset variables, thereby producing prediction models. ML can aid shoulder surgeons in determining which patients may be susceptible to worse outcomes and complications following shoulder arthroplasty (SA) and align patient expectations following SA. However, limited literature is available on ML utilization in total shoulder arthroplasty (TSA) and reverse TSA.

Methods
A systematic literature review in accordance with PRISMA guidelines was performed to identify primary research articles evaluating ML’s ability to predict SA outcomes. With duplicates removed, the initial query yielded 327 articles, and after applying inclusion and exclusion criteria, 12 articles that had at least 1 month follow-up time were included.

Results
ML can predict 30-day postoperative complications with a 90% accuracy, postoperative range of motion with a higher-than-85% accuracy, and clinical improvement in patient-reported outcome measures above minimal clinically important differences with a 93%–99% accuracy. ML can predict length of stay, operative time, discharge disposition, and hospitalization costs.

Conclusion
ML can accurately predict outcomes and complications following SA and healthcare utilization. Outcomes are highly dependent on the type of algorithms used, data input, and features selected for the model.

Level of Evidence
III
Plastic behavior and shakedown limit of defected pressurized pipe under cyclic bending moment
Authors: Youssef Mark Nassef Naguib , Megahed Mohammad Mohammad , Saleh Chahinaz Abdel Rahman , Mohammed Sahour Nabil Sayed 
Published: May 2024

AbstractPipelines subjected to thermal or mechanical loads may fail due to plastic strain accumulation which leads to ratcheting. In this research, cyclic plastic behavior and shakedown limit are investigated experimentally and numerically for a defected pressurized pipe under cyclic bending moment. In the numerical model, the combined isotropic/kinematic hardening model based on the Chaboche model is adopted to represent the cyclic plastic flow of the material. The hardening parameters are determined experimentally and used in the finite element (FE) model. A four-point bending test rig is manufactured to test a pressurized API 5L steel pipe under cyclic bending. An elliptical defect is created by machining to depict corrosion pits in pipes. The plastic strains are measured experimentally and the results are used to tune the parameters of the FE model. The shakedown limit of the defected pipe is determined numerically by tracking the critical points behavior and the results are verified experimentally. Furthermore, the plastic work dissipated energy (PWD) is estimated within the defective structure to study the behavior of the pipe. By running this compatible model, it is found that the yield and the shakedown limits are lowered by mean values of 55% and 25% respectively due to the presence of metal loss defect occupying almost half of the pipe thickness.
Exploration of Oryza sativa drought-responsive element binding protein 2A (OsDREB2A) gene in several local Indonesian rice varieties
Authors: YULIZA YULIZA , SALAMAH ANDI , PUSPITANINGRUM HARDINI 
Published: May 2024

Abstract. Yuliza, Salamah A, Puspitaningrum H. 2024. Exploration of Oryza sativa drought-responsive element binding protein 2A (OsDREB2A) gene in several local Indonesian rice varieties. Biodiversitas 25: 574-582. Drought is one of the abiotic stress factors that reduces rice productivity in Indonesia. OsDREB2A is a member of the DREBP subfamily of AP2/ERF transcription factors and participates in drought stress by directly binding to DRE elements to regulate downstream gene expression. However, further research is still needed to observe each OsDREB2A gene in local Indonesian rice varieties. This research aims to explore the OsDREB2A gene in several local Indonesian rice varieties, namely from Java (Ciherang, Situbagendid, Way Apo, Inpara 32 and Inpari 42), Kalimantan (Black Rice), Aceh (Sigupai) and West Sumba (Pare Lambem and Pare Bakato Kaka). DNA was isolated from the leaves of each variety, amplified using PCR, and then electrophoresed and sequenced. Sequencing data were analyzed using DNA Baser, BioEdit and then visualized using the SWISS-MODEL server, Rice Genome Annotation Project Database, and chromosome map tools. The results showed that nine samples had 100% query cover with the Pokkali OsDREB2A (KU159743.1) cultivar sequence, 99.86% similar percent identity compared to cultivar R180 and WAB540-1-B-P-6-1-1, 99.75% similar percent identity compared to cultivar FL-478 and 99.62% similar percent identity compared to cultivar Nona Bokra. The amino acid structure of each cultivar refers to chromosome 1 at the LOC_Os01g07120 locus.
First report of Pyricularia oryzae the cause of blast disease in upland rice, in Lombok, West Nusa Tenggara
Authors: SANURIZA IRNA IL , SUPRAPTA DEWA NGURAH , KAWURI RETNO , SURIANI NI LUH , SUDANTHA I MADE , JAYADI IRFAN , IHWAN KHAERUL 
Published: May 2024

Rice (Oryza sativa L.) is a maincrop cultivated by farmers in Indonesia. The demand for rice has increased, but rice production has decreased due to attacks by plant pests, including pathogen blast disease. This research aims to (i) determine the symptoms of blast disease in upland rice in Lombok, (ii) determine the incidence of blast disease in upland rice in Lombok, (iii) and identify the pathogen that causes blast disease in upland rice in Lombok. The research was conducted in Lombok, West Nusa Tenggara. A sampling of rice crop tissue infected by blast disease was taken from 50 dryland locations in Lombok West Nusa Tenggara. From each point, three samples of rice crops with blast symptoms were taken to obtain 150 samples. Samples are then isolated and identified at the macroscopic, microscopic, and molecular levels. The study results showed that the macroscopic characteristics of rice leaves were rhombus-shaped and brown, and the pathogen produced white mycelium with a fine structure. In contrast, microscopic characteristics showed that the shape of the hyphae was septate, the structure of conidiophore with autophagic cell death, long pyriform microconidia, and long pyriform macroconidia. Based on 18S rRNA gene analysis, the Blast Lombok isolate had a DNA fragment of ±550bp. Based on these results, it can be concluded that the cause of blast disease in upland rice in Lombok, West Nusa Tenggara, is P. oryzae.
Conserving dipterocarps biodiversity in remnant forests of small islands in Batam Island, Indonesia
Authors: SUSILOWATI ARIDA , WIJAYA KESUMA , MAWAZIN MAWAZIN , RACHMAT HENTI HENDALASTUTI , LISMAYATI YUNITA , KURNIAWAN HERI , GINTING IDA MALLIA 
Published: May 2024

Abstract. Susilowati A, Wijaya K, Mawazin, Rachmat HH, Lismayati Y, Kurniawan H, Ginting IM. 2024. Conserving dipterocarps biodiversity in remnant forests of small islands in Batam Island, Indonesia. Biodiversitas 25: 726-733. The protected forest of Sei Harapan is a remnant forest in Batam Island, the Riau Islands Province, Indonesia and one of the keruing (Dipterocarpus spp.) habitats on Sumatra Island. Illegal logging for its wood and land degradation have significantly reduced the keruing population. The objective of this research was to assess the diversity of keruing species and floristic composition in the Sei Harapan Protected Forest. This study employed a vegetation analysis method using purposive sampling with plotted lines and the transect placement based on the keruing position. The research revealed more than 70 species, three of which were Dipterocarpaceae species, including Vatica pauciflora, Shorea curtisii, and Dipterocarpus rigidus. D. rigidus had the highest IVI at the sapling (52.80%) and pole (67.22%). However, D. rigidus ranked 13th in the seedling stage, with an IVI of 5.79%. The diversity index was high at the seedling stage (3.73), moderate at sapling (2.25), pole (2.76), and tree stage (2.89). The evenness index was high at all growth stages, with values of 0.94 (seedling), 0.98 (sapling), 0.91 (pole), and 0.81 (tree). The richness index at the seedling, pole, and tree stage were categorized as high, with values of 10.40, 5.39, and 7.09, respectively, whereas the richness index at the sapling stage was moderate at 3.51. The study finding pointed out that the existence of Sei Harapan remnant forest requires to be preserved considering its essential function for preserving high economic value tree species, especially Dipterocarp. The comprehensive conservation effort for dipterocarps species, is crucial considering the research findings revealed a problem of continuity of species regeneration and the emergence of new pioneer species as the consequence of anthropogenic disturbance.
Interaction between Eichornia crassipes with Microbacterium sp. SpR3 and Micrococcus luteus RT-9 in Cr6+ reduction in liquid media
Authors: WULANDARI ANDRIYANI DEA , MEITINIARTI V. IRENE , KASMIYATI SRI 
Published: May 2024

Abstract. Wulandari AD, Meitiniarti VI, Kasmiyati S. 2024. Interaction between Eichornia crassipes with Microbacterium sp. SpR3 and Micrococcus luteus RT-9 in Cr6+ reduction in liquid media. Biodiversitas 25: 957-963. Water Pollution caused by Cr6+ contamination is difficult to remove from the environment. One of the efforts to reduce Cr6+ contamination in water is by bioremediation. Bioremediation using the interaction of rhizosphere bacteria with aquatic plants can be employed to decrease the content of Cr6+ in water environment. This study aimed to determine the effect of adding Microbacterium sp. SpR3, Micrococcus luteus RT-9, and a mixture of both bacteria on the ability of Eichornia crassipes to reduce the concentration of Cr6+ in the growth media and the plant's growth potential. This study was conducted in the Microbiology Laboratory of the Faculty of Biology at Satya Wacana Christian University. Eichornia crassipes plans of similar size were grown in 450 mL of Hoaglands solution with Cr6+ 5 mg.L-1 in a container. The treatment in this study involves the addition of 50 mL (10% of the working volume) of Microbacterium sp SpR3 culture, Micrococcus luteus RT- 9, and a combination of both Cr6+-reducing bacteria. The reduction rate of Cr6+ concentration in the mixture of both types of bacteria reached 88.06%, which was higher compared to the control without the addition of the inoculum (87.08%). The inoculation of both Cr6+ reducing bacteria did not hibit the growth rate of the plants. The ability of Microbacterium sp. SpR3 and Micrococcus luteus RT-9 to reduce Cr6+ in liquid media can be employed in the bioremediation of Cr6+ contaminated wastewater.
Effectiveness of Foeniculum vulgare leaf essential oil nanoemulsion as a natural insecticide against Aedes aegypti larvae and mosquitoes
Authors: WARDANI ARUM TRIYAS , KUSUMANINGSIH TRIANA , AINUROFIQ AHMAD 
Published: May 2024

Abstract. Wardani AT, Kusumaningsih T, Ainurofiq A. 2024. Effectiveness of Foeniculum vulgare leaf essential oil nanoemulsion as a natural insecticide against Aedes aegypti larvae and mosquitoes. Biodiversitas 25: 990-997. The control of dengue hemorrhagic fever (DHF) was by breaking the chain of transmission by controlling Aedes aegypti larvae and mosquitoes. One alternative to controlling mosquito larvae is to use natural materials because they are more environmentally friendly and do not cause harmful residual effects. This study used a Foeniculum vulgare Mill. (fennel) leaf as a natural insecticide to kill Ae. aegypti larvae and mosquitoes. Steam distillation was done to extract essential oils from the Foeniculum vulgare Mill. leaves. F. vulgare leaf essential oil was made as nanoemulsion with tween 80, PEG 400, essential oil, and aqua demineralized. GC-MS results showed that the main ingredients in F. vulgare. leaf essential oil were anethole, estragole, bicyclo[3.1.0]hex-2-ene, 4-methyl-1-(1-methyl ethyl)-,?-pinene, cyclohexene, 1-methyl-5-(1-methyl ethenyl)-, (R)-.The current study aimed to determine the effectiveness of an F. vulgare essential oil nanoemulsion as a larvicidal, adulticidal Ae.aegypti mosquito. The study results obtained LC50 values for each formula I, II, and III were 0.098, 0.317, 0.157 µL/mL, and LC90 values for each formula I, II, and III were 0.158, 0.416, 0.245 µL/mL. Fennel leaf essential oil nanoemulsion was tested on adult Ae. aegypti mosquitoes aged 3-5 days. The results of the study obtained LC50 values for each formula I, II, III were 7.768, 10.575, 5.069 g/m3, and LC90 values for each formula I, II, III were 15.191, 27.565, 8.892 g/m3. The difference in the effectiveness of each formula may be due to the large number of essential oils in the formula. F. vulgare leaf essential oil could be an environmentally friendly natural insecticide with less residual effect.
Morphological, anatomical and genetic diversity of Nanhaia speciosa (Champ. ex Benth.) J.Compton & Schrire from Northern Vietnam
Authors: ONG PHONG XUAN , CAO CUONG BA , KHANG DO TAN , HUY TRAN GIA , CAO PHI BANG , CHU HA DUC , NGUYEN DINH VAN , LA HONG VIET 
Published: May 2024

Abstract. Ong PX, Cao CB, Khang DT, Huy TG, Cao PB, Chu HD, Nguyen DV, La HV. 2024. Morphological, anatomical and genetic diversity of Nanhaia speciosa (Champ. ex Benth.) J.Compton & Schrire from Northern Vietnam. Biodiversitas 25: 1174-1184. Nanhaia speciosa (Champ. ex Benth.) J.Compton & Schrire has been considered a captivating plant species known for its remarkable attributes and contributions to ecological systems and human use. This medicinal plant originated from tropical Southeast Asia regions. However, the investigation of this species in Vietnam has been still lacking. This study comprehensively analyzed N. speciosa samples obtained in Vietnam; the morphological and anatomical characteristics of N. speciosa leaflets and flower samples collected from different regions were analyzed. As a result, the structural components of the flower were slightly similar between these samples, whereas the leaflet shape exhibited variations in the leaflet base, petiole, and leaflet apex. According to the ISSR and RAPD analysis, we demonstrated that N. speciosa found in ND genotypes (Tan Yen, Bac Giang) exhibited clearly different genetic backgrounds from CSS (Loc Binh, Lang Son) and CSD (Son Dong, Bac Giang) genotypes. Based on the clustering diagram of ISSR markers, 15 plant genotypes were classified into 2 large clusters, A and B, with genetic similarity ranging from 0.62 to 0.90. The RAPD dendrogram illustrated two main clusters, C and D, with genetic similarity ranging from 0.57 to 0.92. Therefore, this study could provide a solid foundation for identifying and characterizing N. speciosa species in Vietnam and a direction for advanced research on conservation, sustainable breeding, and exploiting pharmaceutical values.