bluuebunny/crossref_metadata_2025 huggingface dataset:
Wave functions consistent with experimental x-ray diffraction data: A hircocervus becomes reality
Authors: Genoni Alessandro
Published: June 2024

Since the early days of quantum physics, the possibility of obtaining wave functions consistent with experimental x-ray diffraction data has been envisioned. The idea is firmly grounded in the postulates of quantum mechanics and finds full support in the Hohenberg and Kohn theorem and Levy–Lieb search formulation of density functional theory. Within this framework, a rich history of research has unfolded over the years, introducing various strategies to obtain plausible one-electron reduced density matrices or wave functions that are compatible with x-ray structure factors. Approximately twenty-five years ago, all of this culminated with the development of the x-ray restrained wave function (XRW) approach. This method aims to determine wave functions that minimize the electronic energy of the examined systems while maximizing the statistical agreement between experimental and calculated x-ray diffraction data. Presently, the XRW technique stands as a well-established strategy, manifesting in various forms, and addressing numerous problems and challenges across chemistry, physics, and materials science. Moreover, there remains large room for improvement and extensions in the coming years. This paper will comprehensively review the current state of the x-ray restrained wave function approach, discussing its underlying foundations, historical background, theoretical details and extensions, practical applications, and forthcoming perspectives.
Maximization of linear independence of basis function products
Authors: Sizov Georgii N. , Lazeran Vincent , Balada Gaggioli Llorenç , Staroverov Viktor N.
Published: June 2024

Basis sets consisting of functions that form linearly independent products (LIPs) have remarkable applications in quantum chemistry but are scarce because of mathematical limitations. We show how to linearly transform a given set of basis functions to maximize the linear independence of their products by maximizing the determinant of the appropriate Gram matrix. The proposed method enhances the utility of the LIP basis set technology and clarifies why canonical molecular orbitals form LIPs more readily than atomic orbitals. The same approach can also be used to orthogonalize basis functions themselves, which means that various orthogonalization techniques may be viewed as special cases of a certain nonlinear optimization problem.
SAMSGL: Series-aligned multi-scale graph learning for spatiotemporal forecasting
Authors: Zou Xiaobei , Xiong Luolin , Tang Yang , Kurths Jürgen
Published: June 2024

Spatiotemporal forecasting in various domains, like traffic prediction and weather forecasting, is a challenging endeavor, primarily due to the difficulties in modeling propagation dynamics and capturing high-dimensional interactions among nodes. Despite the significant strides made by graph-based networks in spatiotemporal forecasting, there remain two pivotal factors closely related to forecasting performance that need further consideration: time delays in propagation dynamics and multi-scale high-dimensional interactions. In this work, we present a Series-Aligned Multi-Scale Graph Learning (SAMSGL) framework, aiming to enhance forecasting performance. In order to handle time delays in spatial interactions, we propose a series-aligned graph convolution layer to facilitate the aggregation of non-delayed graph signals, thereby mitigating the influence of time delays for the improvement in accuracy. To understand global and local spatiotemporal interactions, we develop a spatiotemporal architecture via multi-scale graph learning, which encompasses two essential components: multi-scale graph structure learning and graph-fully connected (Graph-FC) blocks. The multi-scale graph structure learning includes a global graph structure to learn both delayed and non-delayed node embeddings, as well as a local one to learn node variations influenced by neighboring factors. The Graph-FC blocks synergistically fuse spatial and temporal information to boost prediction accuracy. To evaluate the performance of SAMSGL, we conduct experiments on meteorological and traffic forecasting datasets, which demonstrate its effectiveness and superiority.
Intrinsic spin Hall and Rashba effects in metal nitride bromide monolayer for spin-orbitronics
Authors: Nandi Pradip , Sharma Shivam , De Sarkar Abir
Published: June 2024

Investigating the interplay between charge and spin conversion in two-dimensional (2D) materials holds significant promise for futuristic electronic applications. Through density functional theory, our study delves into the charge-spin conversion and spin density dynamics in the non-magnetic SnNBr monolayer under time-reversal invariance. The breaking of out-of-plane mirror symmetry and inversion symmetry, along with the presence of spin–orbit coupling (SOC) lead to a notable momentum-dependent spin band splitting or Rashba effect induced by the inherent out-of-plane electric field. Theoretical calculations reveal not only the presence of profound Rashba spin splitting but also the coexistence of intrinsic spin Hall effects in the SnNBr monolayer. Analysis of k-resolved spin Berry curvature sheds light on the origin of the substantial intrinsic spin Hall conductivity. Furthermore, our research highlights the modulation of charge-to-spin conversion and spin density accumulation through in-plane biaxial strains. Moreover, the variation in the Rashba parameter is correlated with the changes in the built-in out-of-plane electric field and microscopic atomic orbital contributions. These findings underscore the exceptional potential of the non-centrosymmetric SnNBr monolayer for advanced spintronics, spin-orbitronics, and piezo-spintronic applications, and serve as a catalyst for further experimental investigations.
Multimodal dementia identification using lifestyle and brain lesions, a machine learning approach
Authors: Akbarifar Ahmad , Maghsoudpour Adel , Mohammadian Fatemeh , Mohammadzaheri Morteza , Ghaemi Omid
Published: June 2024

Dementia diagnosis often relies on expensive and invasive neuroimaging techniques that limit access to early screening. This study proposes an innovative approach for facilitating early dementia screening by estimating diffusion tensor imaging (DTI) measures using accessible lifestyle and brain imaging factors. Conventional DTI analysis, though effective, is often hindered by high costs and limited accessibility. To address this challenge, fuzzy subtractive clustering identified 14 influential variables from the Lifestyle for Brain Health and Brain Atrophy and Lesion Index frameworks, encompassing demographics, medical conditions, lifestyle factors, and structural brain markers. A multilayer perceptron (MLP) neural network was developed using these selected variables to predict fractional anisotropy (FA), a DTI metric reflecting white matter integrity and cognitive function. The MLP model achieved promising results, with a mean squared error of 0.000 878 on the test set for FA prediction, demonstrating its potential for accurate DTI estimation without costly neuroimaging techniques. The FA values in the dataset ranged from 0 to 1, with higher values indicating greater white matter integrity. Thus, a mean squared error of 0.000 878 suggests that the model’s predictions were highly accurate compared to the observed FA values. This multifactorial approach aligns with the current understanding of dementia’s complex etiology influenced by various biological, environmental, and lifestyle factors. By integrating readily available data into a predictive model, this method enables widespread, cost-effective screening for early dementia risk assessment. The proposed accessible screening tool could facilitate timely interventions, preventive strategies, and efficient resource allocation in public health programs, ultimately improving patient outcomes and caregiver burden.
Exact solutions of the Navier–Stokes equations generated by the eigenfunctions of the Stokes operator
Authors: Baron Alexander
Published: June 2024

We derive a class of exact solutions to the incompressible unsteady Navier–Stokes equations. These solutions are generated by the eigenfunctions of the Stokes operator and can be applied to studying boundary value problems for the Navier–Stokes equations related to pipe and channel flows. We explore the relation between the spectrum of the Stokes operator, generalized Beltrami flows, and exact solutions of the Navier–Stokes equations. Relevant properties of the Stokes eigenfunctions are also discussed in some detail.
Synergistic effects of copper and oxygen vacancies in enhancing the efficacy of partially crystalline CuMnxOy catalyst for ozone decomposition
Authors: Song Yuna , Shin Min Jae , Kwon Byung Chan , So Jungseob , Kim Young Jin , Kang Dohyung , Park No-Kuk , Kim Minkyu
Published: June 2024

To tackle the challenge of ground-level ozone pollution, this study proposed a potential catalytic design approach for ozone decomposition using Cu–Mn bimetallic oxide. This approach is grounded in an understanding of the intrinsic reactivity for catalyst and incorporates a novel potassium-driven low-temperature oxidation process for catalyst synthesis. The research highlights the creation of a highly reactive Cu–Mn oxide phase with extensive defect coverage, leading to significantly increased reaction rates. It also identifies the MnO2(100) facet as a crucial active phase, where oxygen vacancies simultaneously enhance O3 adsorption and decomposition, albeit with a concurrent risk of O2 poisoning due to the stabilization of adsorbed O2. Crucially, the incorporation of Cu offsets the effects of oxygen vacancies, influencing conversion rates and lessening O2 poisoning. The synergistic interplay between Cu and oxygen vacancies elevates the performance of the defect-rich Cu–Mn oxide catalyst. By combining computational and experimental methods, this study not only advances the understanding of the Cu–Mn oxide system for ozone decomposition but also contributes valuable insights into developing more efficient catalysts to mitigate ozone pollution.
Phenylethylammonium iodide induced “in situ healing” behavior for carbon-electrode basing, hole-conductor-free perovskite solar cells
Authors: Lin Siyuan , Xiao Yuhuan , Ma Jiao , Yu Xiaohan , Xie Haipeng , Fang Mei , Zhou Conghua
Published: June 2024

Previous study showed that blending octylammonium iodide (OAI) in a carbon paste induced a kind of in situ healing effect for carbon-electrode basing, hole-conductor-free, planar perovskite solar cells. Here, the strategy is re-examined by considering another kind of ammonium halide molecule or phenethylammonium iodide (PEAI). It is observed that, after moderate PEAI blending, power conversion efficiency of devices rises from 11.56 (±0.82)% to 15.77 (±0.53)% (championed at ∼17.9%), with open-circuit voltage increasing from 969 (±28) to 1033 (±13) mV, and fill factor increasing from 51.17 (±2.68)% to 65.71 (±1.36)%. The improved device efficiency is due to the retarded charge recombination and the improved charge transfer processes. Transient photovoltage/photocurrent decay curve tests show that, after PEAI blending, lifetime of charge carriers in device increases from 3.21 to 5.67 μs, while the charge extraction time decreases from 2.99 to 2.18 μs. Moreover, built-in potential rises according to the Mott–Schottky study. A designated “penetration-reaction” test reveals that PEAI could also induce the in situ healing effect, which accounts for the improved charge transfer/recombination processes. The study could tell the universality of this strategy to certain extent.
Dielectrophoretic motion of a red blood cell in a microfluidic environment: Insights from numerical simulations
Authors: Ranjbaran Azam
Published: June 2024

This research delves into the dielectrophoresis (DEP) behavior of a biological cell within a sinusoidal-shaped microchannel utilizing the Maxwell stress tensor (MST) theory. A red blood cell (RBC), immersed in a viscoelastic fluid, is studied considering the Oldroyd-B model. The study aims to fill a gap in the literature by examining the DEP characteristics of RBC in a realistic geometric configuration and fluid environment, bridging the divide between theoretical modeling and practical application. This work uniquely explores the DEP behavior of an RBC within a sinusoidal microchannel in the presence of a viscoelastic flow regime, which simulates plasma properties, marking a novel contribution to the field. The two-dimensional numerical model incorporates the finite element method to accurately simulate the DEP effect and describe the behavior of the viscoelastic fluid. Validation results confirm the accuracy of the MST model. Crucially, numerical findings highlight the strong dependence of DEP force on electric potential and fluid permittivity. As a consequence of their heightened levels, there is an associated increase in both the DEP force and velocity. While the augmentation of fluid viscosity merely results in a deceleration of DEP velocity. The study provides valuable insights into the interplay between physical parameters and particle behavior, paving the way for advancements in microfluidic particle manipulation techniques.
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.
Factors affecting crop damage by elephants in the buffer zone of Huai Kha Khaeng, a world heritage site
Authors: Sutthiboriban Natsuda , Simcharoen Achara , Gale George A. , Ngoprasert Dusit , Chutipong Wanlop , Tantipisanuh Naruemon
Published: June 2024

Context Human–elephant conflict is a growing global problem. To mitigate such conflict, understanding factors affecting elephant intrusions into human-dominated areas is crucial. These factors are, however, complex because they are site specific and context dependent. Aims This study aimed to identify factors associated with crop damage incidents from elephants in a buffer zone of a protected area in western Thailand. Methods Interviews were conducted with local people to quantify crop damage by elephants between November 2020 to April 2021. We used compositional analysis to determine whether different crop types received different damage from elephants, and logistic regression analysis to examine environmental factors associated with crop damage incidents. Key results Although it was previously thought that elephants focus on dominant palatable crops, we found that small patches of highly preferred crops can influence where elephants choose to feed. Distance from village was also a significant factor in crop foraging. Crop damage was not different between dry and wet seasons, probably because key crops were available year-round. Conclusions Crop damage occurred across multiple crop types but mainly those with higher sugar content. The damage mostly occurred in fields farther from villages, suggesting that presence of humans may alter elephant crop foraging. No specific seasonal period of crop damage was observed. Implications Changing crop types from species preferred by elephants to less preferred species and growing mixed species (multi-crop systems) instead of single species (mono-crops) may reduce elephant incursions. However, this needs field testing, including market-based assessments to evaluate the economic viability for farmers.
Modifications in the T arm of tRNA globally determine tRNA maturation, function, and cellular fitness
Authors: Schultz Sarah K. , Katanski Christopher D. , Halucha Mateusz , Peña Noah , Fahlman Richard P. , Pan Tao , Kothe Ute
Published: June 2024

Almost all elongator tRNAs (Transfer RNAs) harbor 5-methyluridine 54 and pseudouridine 55 in the T arm, generated by the enzymes TrmA and TruB, respectively, in
Escherichia coli.
TrmA and TruB both act as tRNA chaperones, and strains lacking
trmA
or
truB
are outcompeted by wild type. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of
trmA
and
truB
in
E. coli
causes a global decrease in aminoacylation and alters other tRNA modifications such as acp
3
U47. While overall protein synthesis is not affected in
Δ
trmA
and
Δ
truB
strains, the translation of a subset of codons is significantly impaired. As a consequence, we observe translationally reduced expression of many specific proteins, that are either encoded with a high frequency of these codons or that are large proteins. The resulting proteome changes are not related to a specific growth phenotype, but overall cellular fitness is impaired upon deleting
trmA
and
truB
in accordance with a general protein synthesis impact. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing tRNA maturation, tRNA aminoacylation, and translation, thereby improving cellular fitness irrespective of the growth conditions which explains the conservation of
trmA
and
truB
.
Inducing superconductivity in quantum anomalous Hall regime
Authors: Huang Yu , Fu Yu , Zhang Peng , Wang Kang L , He Qing Lin
Published: June 2024

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

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

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

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

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

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

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

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

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

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

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

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

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.
MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet
Authors: Wang Ziqing , Cassidy Michael , Wallace Danielle A , Sofer Tamar
Published: June 2024

Genome-wide DNA methylation (DNAm) profiling is indispensable for unveiling how DNAm regulates biological pathways and individual phenotypes. However, managing and analyzing extensive DNAm data generated from large cohort studies present computational obstacles. Apache Parquet is a data file format that allows for efficient data storage, retrieval, and manipulation, alleviating computational hurdles associated with conventional row-based formats. We here introduce MethParquet, the first R package leveraging the columnar Parquet format for efficient DNAm data analysis. It can be used for data extraction, methylation risk score calculation, epigenome-wide association analyses, and other standard post-quality control tasks. The package flexibly implements diverse regression models. Via a public methylation dataset, we show the efficiency of this package in reducing running time and RAM usage in large-scale EWAS.

Availability and implementation

The MethParquet R package is publicly available on the GitHub repository https://github.com/ZWangTen/MethParquet. It includes a vignette and a toy dataset derived from a public resource.
DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes
Authors: Tiberi Simone , Meili Joël , Cai Peiying , Soneson Charlotte , He Dongze , Sarkar Hirak , Avalos-Pacheco Alejandra , Patro Rob , Robinson Mark D
Published: June 2024

Although transcriptomics data is typically used to analyze mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g. healthy vs. diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, ie reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. Here, we present DifferentialRegulation, a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, vs. state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. DifferentialRegulation is distributed as a Bioconductor R package.
Default mode network electrophysiological dynamics and causal role in creative thinking
Authors: Bartoli Eleonora , Devara Ethan , Dang Huy Q , Rabinovich Rikki , Mathura Raissa K , Anand Adrish , Pascuzzi Bailey R , Adkinson Joshua , Kenett Yoed N , Bijanki Kelly R , Sheth Sameer A , Shofty Ben
Published: June 2024

The default mode network (DMN) is a widely distributed, intrinsic brain network thought to play a crucial role in internally directed cognition. The present study employs stereo-EEG in 13 human patients, obtaining high resolution neural recordings across multiple canonical DMN regions during two processes that have been associated with creative thinking: spontaneous and divergent thought. We probe these two DMN-associated higher cognitive functions through mind wandering and alternate uses tasks, respectively. Our results reveal DMN recruitment during both tasks, as well as a task-specific dissociation in spatiotemporal response dynamics.

When compared to the fronto-parietal network, DMN activity was characterized by a stronger increase in gamma band power (30–70 Hz) coupled with lower theta band power (4–8 Hz). The difference in activity between the two networks was especially strong during the mind wandering task. Within the DMN, we found that the tasks showed different dynamics, with the alternate uses task engaging the DMN more during the initial stage of the task, and mind wandering in the later stage. Gamma power changes were mainly driven by lateral DMN sites, while theta power displayed task-specific effects. During alternate uses task, theta changes did not show spatial differences within the DMN, while mind wandering was associated to an early lateral and late dorsomedial DMN engagement. Furthermore, causal manipulations of DMN regions using direct cortical stimulation preferentially decreased the originality of responses in the alternative uses task, without affecting fluency or mind wandering.

Our results suggest that DMN activity is flexibly modulated as a function of specific cognitive processes and supports its causal role in divergent thinking. These findings shed light on the neural constructs supporting different forms of cognition and provide causal evidence for the role of DMN in the generation of original connections among concepts.
Neurovascular coupling dysfunction associated with cognitive impairment in presbycusis
Authors: Xing Chunhua , Feng Jianhua , Yao Jun , Xu Xiao-Min , Wu Yuanqing , Yin Xindao , Salvi Richard , Chen Yu-Chen , Fang Xiangming
Published: June 2024

The neuropathological mechanism underlying presbycusis remains unclear. This study aimed to illustrate the mechanism of neurovascular coupling associated with cognitive impairment in patients with presbycusis. We assessed the coupling of cerebral blood perfusion with spontaneous neuronal activity by calculating the correlation coefficients between cerebral blood flow and blood oxygen level-dependent-derived quantitative maps (amplitude of low-frequency fluctuation, fractional amplitude of low-frequency fluctuation, regional homogeneity, degree centrality). Four neurovascular coupling metrics (cerebral blood flow-amplitude of low-frequency fluctuation, cerebral blood flow-fractional amplitude of low-frequency fluctuation, cerebral blood flow-regional homogeneity and cerebral blood flow-degree centrality) were compared at the global and regional levels between the presbycusis group and the healthy control group, and the intrinsic association between the altered neurovascular coupling metrics and the neuropsychological scale was further analysed in the presbycusis group. At the global level, neurovascular coupling was significantly lower in the presbycusis group than in the control group and partially related to cognitive level. At the regional level, neurovascular biomarkers were significantly elevated in three brain regions and significantly decreased in one brain region, all of which involved the Papez circuit. Regional neurovascular coupling provides more information than global neurovascular coupling, and neurovascular coupling dysfunction within the Papez circuit has been shown to reveal the causes of poor cognitive and emotional responses in age-related hearing loss patients.
Uncovering the power of neurofeedback: a meta-analysis of its effectiveness in treating major depressive disorders
Authors: Xia Zheng , Yang Peng-Yuan , Chen Si-Lu , Zhou Han-Yu , Yan Chao
Published: June 2024

Neurofeedback, a non-invasive intervention, has been increasingly used as a potential treatment for major depressive disorders. However, the effectiveness of neurofeedback in alleviating depressive symptoms remains uncertain. To address this gap, we conducted a comprehensive meta-analysis to evaluate the efficacy of neurofeedback as a treatment for major depressive disorders. We conducted a comprehensive meta-analysis of 22 studies investigating the effects of neurofeedback interventions on depression symptoms, neurophysiological outcomes, and neuropsychological function. Our analysis included the calculation of Hedges’ g effect sizes and explored various moderators like intervention settings, study designs, and demographics. Our findings revealed that neurofeedback intervention had a significant impact on depression symptoms (Hedges’ g = −0.600) and neurophysiological outcomes (Hedges’ g = −0.726). We also observed a moderate effect size for neurofeedback intervention on neuropsychological function (Hedges’ g = −0.418). As expected, we observed that longer intervention length was associated with better outcomes for depressive symptoms (β = −4.36, P < 0.001) and neuropsychological function (β = −2.89, P = 0.003). Surprisingly, we found that shorter neurofeedback sessions were associated with improvements in neurophysiological outcomes (β = 3.34, P < 0.001). Our meta-analysis provides compelling evidence that neurofeedback holds promising potential as a non-pharmacological intervention option for effectively improving depressive symptoms, neurophysiological outcomes, and neuropsychological function in individuals with major depressive disorders.