bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of forest betel leaf extract (Piper aduncum L.) from various altitudes on the mortality of fall armyworm (S. frugiperda J.E. Smith) in the laboratory
Authors: Rustam R , Utami A R 
Published: May 2024

Abstract

S. frugiperda pests can attack corn plants in the vegetative and generative phases, resulting in yield losses ranging from 15% to 73%. Forest betel plant (P. aduncum L.) is one type of plant that can be used effectively as a botanical pesticide to control these pests. The effectiveness of a plant as a source of botanical insecticide is influenced by the ecology, geography, and climate where the plant grows. This study aimed to obtain the best and most effective forest betel leaf extract from various growing heights against S. frugiperda mortality. The research was conducted at the Plant Pest Laboratory, Faculty of Agriculture, Riau University, from April to June 2023, using a completely randomized design (CRD) consisting of three treatments and six replicates. Application of forest betel leaf extract at different altitudes above sea level, namely 200 meters, 500 meters, and 800 meters. The results showed that the difference in altitude significantly affected the mortality of S. frugiperda. Forest betel leaf extract from 200 meters above sea level was the best treatment for controlling armyworm pests, with a total mortality of 96.67%.
Incidence of the tussock moth attack: Issue, crop damages and management strategies to support sustainable oil palm plantation
Authors: Hendarjanti H 
Published: May 2024

Abstract
The problem of insect pests in the palm oil industry has shown a considerable shift during the second decade of the twenty-first century due to ecosystem and technological changes. The interaction between palm oil as a host plant and the behaviour of insect pests undergoes an adaptation process. Defoliating insects of oil palm in Central Kalimantan, at certain times, experience explosions, such as the tussock moth species Dasychira inclusa (Walker, 1856) and Calliteara horsfieldii (Saunders, 1851). Several factors led to the tussock moth explosion, including environmental factors, human resources, and management strategies. The percentage of crop damage caused by the tussock moths from mild, moderate, severe to very severe categories was 43.48%, 15.57%, 21.74% and 10.87%. The tussock moth outbreak is giving rise to restoration efforts to keep the ecosystem balance in the landscape back to normal. Efforts to maintain ecosystem balance through regular and accurate monitoring, introducing and withdrawing beneficial insects, and planting proper plant vegetation. This action is one of the keys to dealing with small pest outbreaks or significant pests. Ultimately, a diversified ecosystem provides more crop protection opportunities.
Geographical distribution, population density, and fruit damage due to pest, Silba adipata McAlpine (Diptera: Lochaeidae) on cayenne pepper in Bali, Indonesia
Authors: Yuliadhi K A , Merta I N M , Suriani N L , Susila I W 
Published: May 2024

Abstract
Cayenne pepper (Capsicum frutescens L). is one of the leading vegetable plants in Bali. The black fruit fly is a new pest species that strips fruit before it is ripe. Initially, the symptoms of fruit dropping were caused by fruit flies of the Bactrocera dorsalis (Tephritidae), however, preliminary survey results showed that the type of pest that attacked was the black fruit fly Silba adipata from the Lonchaidae family. This study aims to determine distribution, population density, and fruit damage caused by Silba sp. in Bali. Field research was carried out in nine districts/city in Bali. Meanwhile, laboratory research was carried out at the Integrated Pest Management Laboratory, Faculty of Agriculture, Udayana University. The results showed that the S. adipata pest has spread evenly throughout all districts/city in Bali. The highest population was found in the Bangli district, with 22.09 individuals per plant, and the lowest population was found in Denpasar city, with 1.92 individuals per plant. Altiduinally, the highest population density was in altitude areas between 500-750 m above sea level. The highest percentage of attack and damage to small chilies due to fly attack was in Bangli at 41.33%, and the lowest was found in Denpasar City.
Effect of abamectin and profenofos insecticide on stingless bee, Tetragonula laeviceps Smith (Hymenoptera: Apidae: Meliponini)
Authors: Mubin N , Nurvaidah R , Kusdiandini N R , Audia B H , Dadang  
Published: May 2024

Abstract
Pollinators such as the bee Tetragonula laeviceps Smith are essential components of ecosystems that provide services to plants. However, the massive use of pesticides in crops can affect the existence of pollinating bees and even cause a decrease in bee populations in the field. This study aimed to determine the effect of abamectin and profenofos insecticides on T. laeviceps. The methods used in the test were bee attractiveness bioassay, toxicity test of dermal application (topical and residual), and oral application with the abamectin and profenofos. The results of the bioassay showed that bees were more attracted to the aroma of the insecticide abamectin 180 ppm than profenofos 1500 ppm. The recommended concentrations of abamectin and profenofos in the field were 180 and 1500 ppm, respectively, so this topical and oral application showed a high level of danger to bees because it can kill >80% of bees. The LD50 values of the insecticides abamectin (0.0064 ppm) and profenofos (0.0345 ppm) were classified as highly toxic based on EPA classification. Therefore, insecticides with active ingredients, particularly abamectin and profenofos, are harmful to T. laeviceps.
Simple circuit and experimental proposal for the detection of gauge-waves
Authors: Minotti F , Modanese G 
Published: May 2024

Abstract
Aharonov-Bohm electrodynamics predicts the existence of traveling waves of pure potentials, with zero electromagnetic fields, denoted as gauge waves, or g-waves for short. In general, these waves cannot be shielded by matter since their lack of electromagnetic fields prevents the material from reacting to them. However, a not-locally-conserved electric current present in the material does interact with the potentials in the wave, giving the possibility of its detection. In [1] the basic theoretical description of a detecting circuit was presented, based on a phenomenological theory of materials that can sustain not-locally-conserved electric currents. In the present work we discuss how that circuit can be built in practice, and used for the effective detection of g-waves.
Femtosecond laser ultrafast photothermal exsolution
Authors: Xu Lurun , Tao Jingchao , Li Zhuguo , He Guo , Zhang Dongshi 
Published: May 2024

Abstract
Exsolution, as an effective approach to constructing particle-decorated interfaces, is still challenging to yield interfacial films rather than isolated particles. Inspired by in vivo near-infrared laser photothermal therapy, using 3 mol% Y2O3 stabilized tetragonal zirconia polycrystals (3Y-TZP) as host oxide matrix and iron-oxide (Fe3O4/γ-Fe2O3/α-Fe2O3) materials as photothermal modulator and exsolution resource, femtosecond laser ultrafast exsolution approach is presented enabling to conquer this challenge. The key is to trigger photothermal annealing behavior via femtosecond laser ablation to initialize phase transition from monoclinic zirconia (m-ZrO2) to tetragonal zirconia (t-ZrO2) and induce t-ZrO2 columnar crystal growth. Fe-ions rapidly segregate along grain boundaries and diffuse towards the outmost surface, and become ‘frozen’, highlighting the potential to use photothermal materials and ultrafast heating/quenching behaviors of femtosecond laser ablation for interfacial exsolution. Triggering interfacial iron-oxide coloring exsolution is composition and concentration dependent. Photothermal materials themselves and corresponding photothermal transition capacity play a crucial role, initializing at 2 wt%, 3 wt%, and 5 wt% for Fe3O4/γ-Fe2O3/α-Fe2O3 doped 3Y-TZP samples. Due to different photothermal effects, exsolution states of ablated 5 wt% Fe3O4/γ-Fe2O3/α-Fe2O3-doped 3Y-TZP samples are totally different, with whole coverage, exhaustion (ablated away) and partial exsolution (rich in the grain boundaries in subsurface), respectively. Femtosecond laser ultrafast photothermal exsolution is uniquely featured by up to now the deepest microscale (10 μm from 5 wt%-Fe3O4-3Y-TZP sample) Fe-elemental deficient layer for exsolution and the whole coverage of exsolved materials rather than the formation of isolated exsolved particles by other methods. It is believed that this novel exsolution method may pave a good way to modulate interfacial properties for extensive applications in the fields of biology, optics/photonics, energy, catalysis, environment, etc.
Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression
Authors: Barra Jasmine , Taverna Federico , Bong Fabian , Ahmed Ibrahim , Karakach Tobias K 
Published: May 2024

AbstractTemporal RNA-sequencing (RNA-seq) studies of bulk samples provide an opportunity for improved understanding of gene regulation during dynamic phenomena such as development, tumor progression or response to an incremental dose of a pharmacotherapeutic. Moreover, single-cell RNA-seq (scRNA-seq) data implicitly exhibit temporal characteristics because gene expression values recapitulate dynamic processes such as cellular transitions. Unfortunately, temporal RNA-seq data continue to be analyzed by methods that ignore this ordinal structure and yield results that are often difficult to interpret. Here, we present Error Modelled Gene Expression Analysis (EMOGEA), a framework for analyzing RNA-seq data that incorporates measurement uncertainty, while introducing a special formulation for those acquired to monitor dynamic phenomena. This method is specifically suited for RNA-seq studies in which low-count transcripts with small-fold changes lead to significant biological effects. Such transcripts include genes involved in signaling and non-coding RNAs that inherently exhibit low levels of expression. Using simulation studies, we show that this framework down-weights samples that exhibit extreme responses such as batch effects allowing them to be modeled with the rest of the samples and maintain the degrees of freedom originally envisioned for a study. Using temporal experimental data, we demonstrate the framework by extracting a cascade of gene expression waves from a well-designed RNA-seq study of zebrafish embryogenesis and an scRNA-seq study of mouse pre-implantation and provide unique biological insights into the regulation of genes in each wave. For non-ordinal measurements, we show that EMOGEA has a much higher rate of true positive calls and a vanishingly small rate of false negative discoveries compared to common approaches. Finally, we provide two packages in Python and R that are self-contained and easy to use, including test data.
A perspective on genetic and polygenic risk scores—advances and limitations and overview of associated tools
Authors: Schwarzerova Jana , Hurta Martin , Barton Vojtech , Lexa Matej , Walther Dirk , Provaznik Valentine , Weckwerth Wolfram 
Published: May 2024

Abstract
Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.
Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design
Authors: Lin Yicheng , Ma Jiakang , Yuan Haozhe , Chen Ziqiang , Xu Xingyu , Jiang Mengping , Zhu Jialiang , Meng Weida , Qiu Wenqing , Liu Yun 
Published: May 2024

Abstract
Recent advances in cancer immunotherapy have highlighted the potential of neoantigen-based vaccines. However, the design of such vaccines is hindered by the possibility of weak binding affinity between the peptides and the patient’s specific human leukocyte antigen (HLA) alleles, which may not elicit a robust adaptive immune response. Triggering cross-immunity by utilizing peptide mutations that have enhanced binding affinity to target HLA molecules, while preserving their homology with the original one, can be a promising avenue for neoantigen vaccine design. In this study, we introduced UltraMutate, a novel algorithm that combines Reinforcement Learning and Monte Carlo Tree Search, which identifies peptide mutations that not only exhibit enhanced binding affinities to target HLA molecules but also retains a high degree of homology with the original neoantigen. UltraMutate outperformed existing state-of-the-art methods in identifying affinity-enhancing mutations in an independent test set consisting of 3660 peptide–HLA pairs. UltraMutate further showed its applicability in the design of peptide vaccines for Human Papillomavirus and Human Cytomegalovirus, demonstrating its potential as a promising tool in the advancement of personalized immunotherapy.
Volumetric and diffusion MRI abnormalities associated with dysarthria in multiple sclerosis
Authors: Kenyon Katherine H , Strik Myrte , Noffs Gustavo , Morgan Angela , Kolbe Scott , Harding Ian H , Vogel Adam P , Boonstra Frederique M C , van der Walt Anneke 
Published: May 2024

Abstract
Up to half of all people with multiple sclerosis experience communication difficulties due to dysarthria, a disorder that impacts the motor aspects of speech production. Dysarthria in multiple sclerosis is linked to cerebellar dysfunction, disease severity and lesion load, but the neuroanatomical substrates of these symptoms remain unclear. In this study, 52 participants with multiple sclerosis and 14 age- and sex-matched healthy controls underwent structural and diffusion MRI, clinical assessment of disease severity and cerebellar dysfunction and a battery of motor speech tasks. Assessments of regional brain volume and white matter integrity, and their relationships with clinical and speech measures, were undertaken. White matter tracts of interest included the interhemispheric sensorimotor tract, cerebello-thalamo-cortical tract and arcuate fasciculus, based on their roles in motor and speech behaviours. Volumetric analyses were targeted to Broca’s area, Wernicke’s area, the corpus callosum, thalamus and cerebellum. Our results indicated that multiple sclerosis participants scored worse on all motor speech tasks. Fixel-based diffusion MRI analyses showed significant evidence of white matter tract atrophy in each tract of interest. Correlational analyses further indicated that higher speech naturalness—a perceptual measure of dysarthria—and lower reading rate were associated with axonal damage in the interhemispheric sensorimotor tract and left arcuate fasciculus in people with multiple sclerosis. Axonal damage in all tracts of interest also correlated with clinical scales sensitive to cerebellar dysfunction. Participants with multiple sclerosis had lower volumes of the thalamus and corpus callosum compared with controls, although no brain volumetrics correlated with measures of dysarthria. These findings indicate that axonal damage, particularly when measured using diffusion metrics, underpin dysarthria in multiple sclerosis.
Single-molecule characterization of salivary protein aggregates from Parkinson’s disease patients: a pilot study
Authors: Furlepa Martin , Zhang Yu P , Lobanova Evgeniia , Kahanawita Lakmini , Vivacqua Giorgio , Williams-Gray Caroline H , Klenerman David 
Published: May 2024

Abstract
Saliva is a convenient and accessible biofluid that has potential as a future diagnostic tool for Parkinson’s disease. Candidate diagnostic tests for Parkinson’s disease to date have predominantly focused on measurements of α-synuclein in CSF, but there is a need for accurate tests utilizing more easily accessible sample types. Prior studies utilizing saliva have used bulk measurements of salivary α-synuclein to provide diagnostic insight. Aggregate structure may influence the contribution of α-synuclein to disease pathology. Single-molecule approaches can characterize the structure of individual aggregates present in the biofluid and may, therefore, provide greater insight than bulk measurements. We have employed an antibody-based single-molecule pulldown assay to quantify salivary α-synuclein and amyloid-β peptide aggregate numbers and subsequently super-resolved captured aggregates using direct Stochastic Optical Reconstruction Microscopy to describe their morphological features. We show that the salivary α-synuclein aggregate/amyloid-β aggregate ratio is increased almost 2-fold in patients with Parkinson’s disease (n = 20) compared with controls (n = 20, P &lt; 0.05). Morphological information also provides insight, with saliva from patients with Parkinson’s disease containing a greater proportion of larger and more fibrillar amyloid-β aggregates than control saliva (P &lt; 0.05). Furthermore, the combination of count and morphology data provides greater diagnostic value than either measure alone, distinguishing between patients with Parkinson’s disease (n = 17) and controls (n = 18) with a high degree of accuracy (area under the curve = 0.87, P &lt; 0.001) and a larger dynamic range. We, therefore, demonstrate for the first time the application of highly sensitive single-molecule imaging techniques to saliva. In addition, we show that aggregates present within saliva retain relevant structural information, further expanding the potential utility of saliva-based diagnostic methods.
Megalin Knockout Reduces SGLT2 Expression and Sensitizes to Western Diet-induced Kidney Injury
Authors: Youm Elynna B , Shipman Katherine E , Albalawy Wafaa N , Vandevender Amber M , Sipula Ian J , Rbaibi Youssef , Marciszyn Allison E , Lashway Jared A , Brown Emma E , Bondi Corry B , Boyd-Shiwarski Cary R , Tan Roderick J , Jurczak Michael J , Weisz Ora A 
Published: May 2024

Abstract
Megalin (Lrp2) is a multiligand receptor that drives endocytic flux in the kidney proximal tubule (PT) and is necessary for the recovery of albumin and other filtered proteins that escape the glomerular filtration barrier. Studies in our lab have shown that knockout (KO) of Lrp2 in opossum PT cells leads to a dramatic reduction in sodium–glucose co-transporter 2 (SGLT2) transcript and protein levels, as well as differential expression of genes involved in mitochondrial and metabolic function. SGLT2 transcript levels are reduced more modestly in Lrp2 KO mice. Here, we investigated the effects of Lrp2 KO on kidney function and health in mice fed regular chow (RC) or a Western-style diet (WD) high in fat and refined sugar. Despite a modest reduction in SGLT2 expression, Lrp2 KO mice on either diet showed increased glucose tolerance compared to control mice. Moreover, Lrp2 KO mice were protected against WD-induced fat gain. Surprisingly, renal function in male Lrp2 KO mice on WD was compromised, and the mice exhibited significant kidney injury compared with control mice on WD. Female Lrp2 KO mice were less susceptible to WD-induced kidney injury than male Lrp2 KO. Together, our findings reveal both positive and negative contributions of megalin expression to metabolic health, and highlight a megalin-mediated sex-dependent response to injury following WD.
Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing
Authors: Elguweidi Abir , Crease Teresa 
Published: May 2024

Abstract
Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.