bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extended curvature birdcage coil design for localized magnetic field in 9.4 T MRI for multiple mouse imaging
Authors: Hernandez Daniel , Nam Taewoo , Lee Eunwoo , Lee Jae Jun , Kim Kyoung-Nam 
Published: June 2024

Magnetic resonance imaging (MRI) for preclinical analysis is useful for testing medical procedures, therapies, and drug development. Preclinical MRI uses small animals, such as mice, for multiple studies. Preclinical studies are often needed to control target mouse models with different parameters; thus, performing simultaneous MRIs is desired to reduce study time and provide a fair comparison. In this study, we propose a variation of a birdcage coil that is capable of providing the same field intensity for each mouse compared to a traditional birdcage coil configuration. The arrangement of the proposed birdcage coil produces a uniform and strongly localized magnetic |B1|-field in each of the four target mice. The design involves rotating the legs of the birdcage coil so that the current distribution produces a uniform field inside each mouse. Electromagnetic simulations were performed to validate the proposed design. The proposed design exhibited a better field intensity than the reference linear, circularly polarized mode birdcage coils and an eight-channel loop array coil. The proposed customized birdcage coil arrangement promises a better field intensity and uniformity across multiple mouse imaging using 9.4 T preclinical MRI scanners.
A novel Leifsonia xyli subsp. xyli quantitative LAMP-based diagnostic correlated with sugarcane ratoon stunting disease rating
Authors: Chakraborty Moutoshi , Bhuiyan Shamsul A. , Strachan Simon , Saha Sithi , Mahmudunnabi Rabbee G. , Nguyen Nam-Trung , Shiddiky Muhammad J. A. , Ford Rebecca 
Published: June 2024

Context Ratoon stunting disease (RSD), caused by Leifsonia xyli subsp. xyli (Lxx), poses a significant economic threat to sugarcane (Saccharum hybrid) worldwide. RSD is hard to manage due to its elusive visible symptomology and disease rating of cultivars is subjective. Aims We aimed to develop a sensitive, rapid, and quantitative Lxx diagnostic method able to correlate Lxx titre and disease resistance rating of sugarcane cultivars. Methods A Lxx diagnostic method was developed using heat lysis-based reagent-free DNA isolation from xylem sap followed by loop-mediated isothermal amplification (LAMP)-based colorimetric and fluorescence quantification within a single microcentrifuge tube. Bacterial titre was then statistically correlated with industry-agreed disease resistance ratings for key sugarcane cultivars. Key results The diagnostic was highly sensitive (1 cell/μL) and reproducible (%s.d. = <5%, for n = 3), and showed excellent linear dynamic range (i.e. 10 pM−1 aM or 107−100 copies/μL, r = 0.99) for quantitative Lxx detection. LAMP quantifications were completely concordant with quantitative polymerase chain reaction quantification from the same samples. Additionally, a strong correlation was determined between the detected quantitative bacterial titres and known cultivar disease resistance ratings (r = 0.82, n = 10, P < 0.001). Conclusion The novel LAMP-based Lxx diagnostic was validated as a fast, simple, and relatively cost-effective means of RSD resistance rating, making it a reliable contribution towards RSD management. Implications The development of this diagnostic tool provides a practical solution for accurately measuring Lxx titre and assessing disease resistance in sugarcane plants, aiding in effective risk management of RSD spread, and mitigating its economic impact on sugarcane crops worldwide.
Inducing superconductivity in quantum anomalous Hall regime
Authors: Huang Yu , Fu Yu , Zhang Peng , Wang Kang L , He Qing Lin 
Published: June 2024

Abstract
Interfacing the quantum anomalous Hall insulator with a conventional superconductor is known to be a promising manner for realizing a topological superconductor, which has been continuously pursued for years. Such a proximity route depends to a great extent on the control of the delicate interfacial coupling of the two constituents. However, a recent experiment reported the failure to reproduce such a topological superconductor, which is ascribed to the negligence of the electrical short by the superconductor in the theoretical proposal. Here, we reproduce this topological superconductor with attention to the interface control. The resulted conductance matrix under a wide magnetic field range agrees with the fingerprint of this topological superconductor. This allows us to develop a phase diagram that unveils three regions parameterized by various coupling limits, which not only supports the feasibility to fabricate the topological superconductor by proximity but also fully explains the origin of the previous debate. The present work provides a comprehensible guide on fabricating the topological superconductor.
The Biochar-Enhanced Phytoextraction of Heavy-Metal-Polluted Tropical Soils by Thorny Amaranth (Amaranthus spinosus)
Authors: Afni Afriyani Nur , Durotussyifa Nabiilah , Nisa Ulfatun , Novpriansyah Hery , Niswati Ainin , Sarno  , Kadir Salam Abdul 
Published: June 2024

Abstract
It was suggested that some tropical plants were able to lower toxic metal concentrations in soils. The phytoextraction potential of thorny amaranth (Amaranthus spinosus) in tropical soils treated with biochar was investigated. Soil samples high in heavy metals were taken from a 22-years old experimental field treated with industrial waste at 0-60 Mg ha-1. Soil samples were evaluated with thorny amaranth for 4 weeks. Planting was also conducted in 0-10 Mg ha-1-biochar-treated soil samples. The soil heavy metals increased with the industrial waste levels but were decreased by plant and/or biochar treatments. The plant growth as well as root and shoot dry-weights were lowered by the high soil Cu and Zn but attenuated in the presence of biochar. The accumulation of Cu and Zn in plant roots and shoots and their translocation factors were also lowered by soil Cu and Zn but were increased by biochar. The accumulation of Cu and Zn were higher in plant shoots than those in roots in good correlations with their concentrations in soils. The thorny amaranth was a good Cu and Zn phytoextractor in heavy-metal-polluted tropical soils and performed better in the presence of biochar.
Selection of Local Maize Resistance to Fall Armyworm (Spodoptera frugiperda J. E. SMITH)
Authors: Sudihardjo D , Samanhudi  , Sholahuddin  , Pujiasmanto B , Rahayu M , Setyawati A 
Published: June 2024

Abstract
One of the obstacles in increasing corn production is the attack of Spodoptera frugiperda. The resistance of each maize variety to this pest attack varies greatly. This research aims to obtain local types of maize that are resistant to attacks by corn armyworms. The research was conducted in Kediri, East Java. The research used a Complete Randomized Block Design with treatment of various maize varieties local and with rivers. The varieties tried consisted of Kebo Bima, Lameran-Latim, Madura Kuning, Madura Putih, Manik Liu, Seraye-Bali and Sumbawa. The results showed that there was no difference in plant height between all the local corn varieties tested, while the highest number of leaves was produced in the Madura-kuning and Madura-putih varieties. The Manik-Liu variety produces the smallest leaf length and leaf angle compared to other varieties, while the widest leaves are produced by the Sumbawa variety. The flowering period and harvest time were the longest for the Manik-Liu variety, while the fastest for the Kebo Bima variety. The highest shoot root ratio was produced in the Seraye-Bali variety. Based on the maize of grains yield per hectare obtained, the Sumbawa and Seraye-Bali varieties are the most resistant varieties compared to the others and able to provide the highest maize seed yield per hectare.
Comparative growth response of three rubber (Hevea brasiliensis Muell. Arg) clones in somatic embryo propagation
Authors: Royani J I , Khairiyah H , Mira F R , Utami Rr N , Rudiyana Y. , Elvini  , Watanabe Norie 
Published: June 2024

Abstract
Plants have the ability to grow with different responses depending on the clones and varieties of plants. In rubber plants, each clone has specific characteristics or traits that distinguish it from other clones, whether in terms of growth, latex production, or resistance to pests and diseases. The objective of this experiment was to assess the response of three rubber (Hevea brasiliensis Muell. Arg) clones to the same media conditions for the growth and development of somatic embryos (SE). Integuments from three rubber clones, namely PB 260, PB 330, and PB 340, were used as explants to induce embryonic callus on MH media. After four weeks post-induction, the callus was sub-cultured to expressed SE then SE was transferred to the RITA® bio-reactor for plantlets development in liquid MD media. Parameters for each steps, such as the percentage of contamination, percentage of callus response, color of callus, percentage of SE induction, number of stage of SE, and number of shoots were recorded. The results revealed that the highest percentage of viable callus was observed in the PB 260 clone at 23.20%. On SE expression, the highest being in clone PB 340 at 2.04%. On SE development the highest shoot growth was observed in the PB 260 clone, with a total of 5 shoots.
Diversity and genome classification of Banana (Musa spp.) at Kuantan Singingi District - Riau Province, Indonesia
Authors: Zulfahmi  , Hermawati P , Suryani P , Rosmaina  
Published: June 2024

Abstract
The objective of this research was to determine the genome group, and to observe the genetic relationship between banana cultivars in the Kuantan Singingi District, Riau Province. Twenty-five local banana cultivars were observed and characterized morphologically by following of IPGRI standard, genome classification was determined according to the Simmond and Shepherd method, and UPGMA clustering were conducted. Twenty-five banana cultivars observed is classified into two genome group, namely AA/AAA genomes, and AAB genome. The coefficient similarity value of twenty-five banana cultivars based on morphological markers ranged from 0.23 to 1.00. Several banana cultivars showed the coefficient similarity value of 1.00, indicating that they are similar morphologically but different in naming in the community. UPGMA dendrogram clustered twenty-five banana cultivars into three groups, The first cluster consists of Kepok, Batu, Tanduk, Nangka, Godang, Ambon, Kapas, and Kolek Siam banana. The second cluster included banana cultivars of Abu, Talun, Godok, Pinang, Kapal, Raja, Sawak, and Serai banana. The third cluster consisted of Lidi, Tunjuk, Rotan, 40Hari, Lomak Manih, Somanih, Emas, Ome, and Bantan banana. This study concluded that a minimum of eighteen banana cultivars should be collected for the conservation program, and hybridization can be performed among banana cultivars having low similarity coefficient values.
Induction of genetic diversity in gepak kuning soybean cultivar and M.1.1.3 line using ethyl methane sulfonate in M1 generation
Authors: Nilahayati  , Selvy Handayani Rd , Nazimah  , Sani Alfikri Harahap Muhammad , Irawan Gusti , Anggraini Ayu , Karisda Siregar Nadya 
Published: June 2024

Abstract
Genetic diversity is the main determining factor in plant breeding activities. Various breeding methods can be used to induce plant variability, including mutation breeding. The chemical mutagen commonly used for mutagenesis is Ethyl Methane Sulfonate (EMS). This study explores the effects of EMS mutagen on the morphological and agronomic diversity of gepak kuning cultivar and M.1.1.3 soybean line. The research was conducted in Tambon Tunong Village, North Aceh District, Indonesia, using a single-factor Randomized Block Completely Design (RCBD). Concentrations of 0%, 0.05%, 0.075%, and 0.1% EMS were tested on the gepak kuning cultivar and M.1.1.3 line. Treating gepak kuning soybeans with EMS significantly impacted various variables, including harvesting age, pod number, seed weight, leaf appearance, and production. Additionally, the treatment resulted in changes in the morphology of the plant, particularly in the shape of its branches. The EMS treatment on M.1.1.3 line also significantly affected various variables like plant height, flowering age, harvesting age, and yield components. However, it led to sterile plants in the line.
Efficiacy test of insectiside with pirimiphos-methyl and alpha-cypermethrin on Musa domestica using surface spraying method
Authors: Subekti N , Salsabila S , Fadhila A 
Published: June 2024

Abstract
The bacteria are in human food through insects that act as disease vectors, such as flies. The housefly (Musa domestica) is one of the insects around human habitation that can affect human health. Therefore, controlling the M. domestica population must be done to prevent disease transmission, such as using insecticide. This research used the pirimiphos-methyl and alpha-cypermethrin active ingredients with different doses applied using the surface spraying method of the paper. Then, it was smeared with honey as an attractant. Methods used in this research include test insect preparation, active ingredient application, and data analysis. The data were analyzed statistically using the one-way ANOVA test. Innovation of the research that comperation about active ingredients of the pirimiphos-methyl and alpha-cypermethrin. Result of the research, insecticides with the pirimiphos-methyl proved effective to controlling M. domestica with doses of MP2 and MP3 to 100% mortality in less than 8 hours. In comparison, for the alpha-cypermethrin active ingredient, the mortality of M. domestica is less than 90%. These results indicate that M. domestica in that area is resistant to the alpha-cypermethrin. This research can be used for pest control to control pests effectively and efficiently.
The rate of net assimilation and the rate of relative growth of amaranth (Amaranthus tricolor L.) varieties on urea fertilizer application
Authors: Wulansari FC , Purwanto E , Rahayu M , Sakya AT 
Published: June 2024

Abstract
Nutrient availability affects plant growth and productivity measures, including net assimilation and relative growth rate. Nitrogen, such as amaranth, is vital for enhancing plant growth. Amaranth cultivation requires more nitrogen during its growth, which is met through fertilization. The most commonly used nitrogen fertilizer is urea. The goal of this research activity was to learn whether urea fertilizer had an impact on the relative growth rate and net assimilation rate of amaranth. This research was conducted in Sukosari village, Jumantono, Karanganyar, from July to August 2023. The experimental design employed a completely randomized approach, using two factors: the dose of urea fertilizer (0, 50, 100, 150, 200, 250, and 300 kg.ha-1) and the varieties of amaranth (green and red). At a significance level of 5%, the data analyzed variance (ANOVA) and the Duncan Multiple Range Test (DMRT). According to the conclusions, there was no interaction between the urea dose and the type of amaranth. At 300 kg.ha-1 of urea, the plant’s height, leaf area, and leaf count all reached their highest points. At a urea dose of 250 kg ha-1, the rates of dry weight gain, net assimilation, and relative growth were greatest. The net assimilation rate is positively correlated to the relative growth rate but not to other growth parameters.
Incidence of viral disease mosaic symptom and vector insects’ presence in several soybean varieties in pine agroforestry system
Authors: Supyani  , Septariani D N , Cahya M A 
Published: June 2024

Abstract
Pine dan soybean agroforestry represents an initiative to enhance land productivity and yield. Nevertheless, various viruses could infect soybeans in agroforestry. Mosaic disease is a predominant viral disease affecting soybeans. This research was conducted at KHDTK (Kawasan Hutan dengan Tujuan Khusus) Forestry Alas Bromo in Karanganyar Regency, Central Java, Indonesia. The study aimed to observe the disease incidence and vector presence in some soybean varieties in the pine agroforestry system. A Randomized Block Design was used for the experiment, encompassing seven treatments of varieties. The varieties were Anjasmoro, Argomulyo, Dena-1, Dena-2, Denasa-1, Denasa-2, and Devon-1. Planted at 2.4 x 3.6 m and replicated three times. The incidence of mosaic disease is observed based on symptoms, especially on the leaves’ surface in the form of chlorosis with mosaic pattern. Results indicated that mosaic symptoms were found in the field and the disease incidence was varied for each variety. Viral vectors visited the soybean varieties: Aphis glycine, Phenacoccus sp., thrips, and Bemisia tabaci.
The effect of shade and drought on the growth and proline content of Medinilla speciosa and Medinilla verrucosa plants
Authors: Dullah I C , Sulandjari  , Purwanto E 
Published: June 2024

Abstract

Medinilla is a cultivated wild plant because it has medicinal properties. This research aims to determine the level of resistance and growth of Medinilla speciosa and Medinilla verrucosa plants in drought and shade conditions. The research was carried out in April 2022 – April 2023 in Pakem District Sleman Regency. Analysis of proline and chlorophyll content was carried out at the Gadjah Mada University Laboratory. This study used a nested complete factorial randomized block design, with the types of Medinilla speciosa, Medinilla verrucosa and the volume of water given, 1750 ml, 1500 ml, 1250 ml per polybag nested in 25%, 50% and 75% shade. Each treatment was repeated three times, resulting in a total sample of 54 plants. The results of the study showed that the volume of water provided in the shade suppressed growth, that is number of leaves, leaf area, root volume, fresh weight of stover, chlorophyll except plant height, dry weight of stover and proline content. Water is one of the essential factors needed by plants to grow and develop well. Appropriate light intensity impacts plant growth and production. Light intensity stress and water supply volume stress are part of abiotic stress that can affect growth morphology productivity.
Lyotropic Liquid Crystals
Authors: Dierking Ingo , Martins Figueiredo Neto Antônio 
Published: June 2024

Abstract
This book on Lyotropic Liquid Crystals covers the current state of the art of materials forming liquid crystals as a function of concentration in an isotropic solvent. After a short introduction to liquid crystals in general, we discuss the basic aspects of phase transitions, Onsager’s theory, and the Landau–de Gennes approach. Phase diagrams are introduced, together with a range of experimental techniques to determine the latter, such as polarizing microscopy, calorimetry, X-ray diffraction, and neutron scattering. Computer simulation approaches are discussed to demonstrate current possibilities as well as limitations in the prediction of lyotropic phases, transitions, and properties. Lyotropic phases have been described for an ever-growing range of materials, of which we first discuss the standard amphiphilic and surfactant molecules, chromonics, and also chiral materials. Much of the book is dedicated to colloidal lyotropics, starting with mineral liquid crystals and clays, followed by biological and living lyotropics, then nanorod, nanotube, nanowire, and nanosheet systems. We terminate our excursion into the world of lyotropic liquid crystals by discussing some of their (potential) applications in the food and cosmetics industries, in sensors, medical applications, and, as fibres, as chemical nanoreactors and in future applications of nanotechnology.
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution
Authors: Chacko Jonathan , Ozadam Hakan , Cenik Can 
Published: June 2024

Abstract

Motivation
Ribosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses.

Results
In this study, we introduce RiboGraph, a dedicated visualization tool designed to work with .ribo files, a specialized and efficient format for ribosome occupancy data. Unlike existing solutions that rely on large alignment files and time-consuming preprocessing steps, RiboGraph operates on a purpose designed compact file type. This efficiency allows for interactive, real-time visualization at ribosome-protected fragment length resolution. By providing an integrated toolset, RiboGraph empowers researchers to conduct comprehensive visual analysis of ribosome occupancy data.

Availability and implementation
Source code, step-by-step installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling/ribograph. On the same page, we provide test files and a step-by-step tutorial highlighting the key features of RiboGraph.
scCross: efficient search for rare subpopulations across multiple single-cell samples
Authors: Gerniers Alexander , Nijssen Siegfried , Dupont Pierre 
Published: June 2024

Abstract

Motivation
Identifying rare cell types is an important task to capture the heterogeneity of single-cell data, such as scRNA-seq. The widespread availability of such data enables to aggregate multiple samples, corresponding for example to different donors, into the same study. Yet, such aggregated data is often subject to batch effects between samples. Clustering it therefore generally requires the use of data integration methods, which can lead to overcorrection, making the identification of rare cells difficult. We present scCross, a biclustering method identifying rare subpopulations of cells present across multiple single-cell samples. It jointly identifies a group of cells with specific marker genes by relying on a global sum criterion, computed over entire subpopulation of cells, rather than pairwise comparisons between individual cells. This proves robust with respect to the high variability of scRNA-seq data, in particular batch effects.

Results
We show through several case studies that scCross is able to identify rare subpopulations across multiple samples without performing prior data integration. Namely, it identifies a cilium subpopulation with potential new ciliary genes from lung cancer cells, which is not detected by typical alternatives. It also highlights rare subpopulations in human pancreas samples sequenced with different protocols, despite visible shifts in expression levels between batches. We further show that scCross outperforms typical alternatives at identifying a target rare cell type in a controlled experiment with artificially created batch effects. This shows the ability of scCross to efficiently identify rare cell subpopulations characterized by specific genes despite the presence of batch effects.

Availability and implementation
The R and Scala implementation of scCross is freely available on GitHub, at https://github.com/agerniers/scCross/. A snapshot of the code and the data underlying this article are available on Zenodo, at https://zenodo.org/doi/10.5281/zenodo.10471063.