bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes
Authors: Song Yanhong , Peng Yanling , Liu Lifeng , Li Gang , Zhao Xia , Wang Xu , Cao Shuo , Muyle Aline , Zhou Yongfeng , Zhou Houcheng 
Published: November 2023

Abstract
The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.
Nitrogen–potassium balance improves leaf photosynthetic capacity by regulating leaf nitrogen allocation in apple
Authors: Xu Xinxiang , Zhang Xu , Ni Wei , Liu Chunling , Qin Hanhan , Guan Yafei , Liu Jingquan , Feng Ziquan , Xing Yue , Tian Ge , Zhu Zhanling , Ge Shunfeng , Jiang Yuanmao 
Published: November 2023

Abstract
Nitrogen (N) and potassium (K) are two important mineral nutrients in regulating leaf photosynthesis. However, the influence of N and K interaction on photosynthesis is still not fully understood. Using a hydroponics approach, we studied the effects of different N and K conditions on the physiological characteristics, N allocation and photosynthetic capacity of apple rootstock M9T337. The results showed that high N and low K conditions significantly reduced K content in roots and leaves, resulting in N/K imbalance, and allocated more N in leaves to non-photosynthetic N. Low K conditions increased biochemical limitation (BL), mesophyll limitation (MCL), and stomatal limitation (SL). By setting different N supplies, lowering N levels under low K conditions increased the proportion of water-soluble protein N (Nw) and sodium dodecyl sulfate-soluble proteins (Ns) by balancing N/K and increased the proportion of carboxylation N and electron transfer N. This increased the maximum carboxylation rate and mesophyll conductance, which reduced MCL and BL and alleviated the low K limitation of photosynthesis in apple rootstocks. In general, our results provide new insights into the regulation of photosynthetic capacity by N/K balance, which is conducive to the coordinated supply of N and K nutrients.
The Ecosystem Concept, the DMA, and Section 19a GWB
Authors: Hornung Philipp 
Published: November 2023

Abstract
The debate about competition concerns in the digital economy cumulated in the adoption of new legislation, Section 19a GWB in Germany and the Digital Markets Act at the EU level. At around the same time, a new term gained prevalence in the competition law discourse—the ‘ecosystem’. Often, it is not quite clear, what is meant by it or what the economics behind it are. In this article, I look to the strategic management literature, whose scholars have developed a coherent ecosystem concept. I will explain the economic benefits of the ecosystem structure and the essential role governance plays in it. From the economics of the ecosystem, several insights can be won for competition law. These insights will be applied to the new legislation in the second part. It will be analysed to what extent the DMA and Section 19a GWB are based on the ecosystem concept, whether they identify the problematic actors as addressees, and whether they capture the restrictive conduct. Although both legislative responses do not build on the ecosystem concept, they do not completely fail to address the right issues. Their neglect of the concept, though, could lead to serious enforcement failures.
Identification and characterization of motile Aeromonas spp. isolated from farmed Nile tilapia (Oreochromis niloticus) in the Philippines
Authors: Legario Francis S , Choresca Casiano H , Grace Kathryn , Turnbull James F , Crumlish Margaret 
Published: November 2023

Abstract

Aims
Motile Aeromonas septicaemia (MAS) caused by motile Aeromonas species is an important disease in farmed freshwater fish due to intensification of culture and improper farm practices. This study characterized and profiled motile Aeromonas species recovered from clinically sick tilapia farmed in the Philippines, with a view to identifying targeted disease prevention and control measures against MAS in farmed tilapia species.

Methods and results
Sixteen isolates from diseased farmed Nile tilapia were identified as Aeromonas veronii (n = 14), Aeromonas caviae (n = 1), and Aeromonas dhakensis (n = 1). Five biochemical profiles using API 20E were exhibited by the A. veronii strains giving an unreliable identification. A high level of agreement was observed in identifying the Aeromonas strains using 16S rRNA and rpoD gene sequencing, although the latter has a higher discriminatory value. Three or more virulence genes dominated by cytotoxic enterotoxin act and aerolysin aer were detected. Different genotypes based on virulence gene clustering suggested varied mechanisms used by Aeromonas to colonize and infect or to mutualistically co-exist with the fish. Acquired multiple antibiotic resistance was found in a single A. veronii isolate. All were susceptible to enrofloxacin, oxolinic acid, florfenicol, and chloramphenicol. Tetracycline and sulfonamide resistances and class 1 integron were detected in three A. veronii isolates.

Conclusion
Several strains of motile aeromonads, especially A. veronii, which have varied genotypes based on virulence, biochemical profile, and antibiotic resistance, are involved in MAS in natural disease outbreaks in farmed Nile tilapia in the Philippines.
The application of demographic characteristics of Ectropis grisescens (Lepidoptera: Geometridae) in pest risk assessment of IPM
Authors: Shi Fan , Ma Xu , Lin Chang-Jin , Gao Xiao-Han , Wang Xing-Yu , Kuang Yang-Fan , Wang Lin-Lin , Li Shitang , Lin Changlu , Chen Li-Lin 
Published: November 2023

Abstract
Ectropis grisescens Warren is one of the most important pests of tea plants. In this study, data on the development, survival, and fecundity of E. grisescens were collected at 15, 22, and 32 °C and analyzed by using the age-stage, two-sex life table. At 15 °C, the duration of the preadult period of E. grisescens was significantly prolonged (81.06 days), with high mortality (69.0%), and the proportion of emerged female adults was extremely low (7.0%). At 32 °C, the preadult period was significantly shortened (29.12 days), with high preadult mortality (74.0%), and a low proportion of emerged female adults (15.0%). At 22 °C, with low preadult mortality (24.0%), and a high proportion of emerged female adults (26.0%). The overall effects of the shorter preadult duration, higher preadult survival rate, higher proportion of emerged female adults, higher fecundity (F = 350.88 eggs/♀), and higher net reproductive rate (R0 = 91.23 offspring/individual) at 22 °C resulted in the highest values of the intrinsic rate of increase (r = 0.1054 days−1) and finite rate of increase (λ = 1.1112 days−1). Computer simulation showed that E. grisescens populations can increase much faster at 22 °C than at 15 and 32 °C. The weighted population size and cumulative weighted insect-days provided the dynamics necessary for estimating the damage potential of E. grisescens in devising economical pest management programs. Our results demonstrate that populations of E. grisescens were able to develop at a broad range of temperatures and adapt to the high temperatures. These finding can be utilized to improve the management of E. grisescens.
Trunk injection to control Xylosandrus germanus (Coleoptera: Curculionidae) in topworked apple trees
Authors: Wheeler Celeste E , Vandervoort Christine , Wise John C 
Published: November 2023

Abstract
Xylosandrus germanus (Blandford) is an invasive species of ambrosia beetle known to attack apple trees in North America. Xylosandrus germanus are attracted to ethanol produced by stressed and injured trees and can be a serious problem when grafting a new cultivar onto established fruit trees (topworking). The objective of this study was to evaluate the efficacy of 2 insecticides (emamectin benzoate and azadirachtin) and injection timing (fall and spring) on their ability to control X. germanus colonization in apple trees with simulated topworking. Our study shows evidence that both emamectin benzoate and azadirachtin injections can reduce X. germanus infestations; however, our results were inconsistent. The timing of injections influenced X. germanus, with spring injected azadirachtin being more effective than fall injections. Residue analyses of emamectin benzoate and azadirachtin showed the presence of residues in woody tissue comparable to those found in leaves.
Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex
Authors: Johnson Nathan A , Henderson Andrew R , Jones Jess W , Beaver Caitlin E , Ahlstedt Steven A , Dinkins Gerald R , Eckert Nathan L , Endries Mark J , Garner Jeffrey T , Harris John L , Hartfield Paul D , Hubbs Don W , Lane Timothy W , McGregor Monte A , Moles Kendall R , Morrison Cheryl L , Wagner Matthew D , Williams James D , Smith Chase H 
Published: November 2023

Abstract
Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America’s Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia—a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species (Erimystax dissimilis) confirmed to serve as a parasitic larval host for P. sintoxia. Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.
Dynamics of the natural enemy community of Hyphantria cunea (Lepidoptera: Erebidae) in Dandong, China
Authors: Zhang Xinyang , Yang Liyuan , Chen Chen , Shi Junrui , Zhang Yixin , Sun Shouhui 
Published: November 2023

Abstract
This study aims to explore the composition of natural enemy species in the fall webworm, Hyphantria cunea (Drury) population and the dynamics of its natural enemy community in Dandong, Liaoning Province, China, where it was first reported. We collected the natural enemy of eggs, larvae, and pupae of H. cunea on host trees at 12 survey sites from June 2019 to October 2020. The results showed that the community consists of 34 species: 20 predatory species, including 15 spiders and 5 insects, and 14 parasitic species, including 10 parasitic wasps and 4 parasitic flies. The top 3 dominant species based on the importance value index for both parasitic and predatory species were Pediobius pupariae &gt; Chouioia cunea &gt; Cotesia gregalis in the natural enemy community of H. cunea. Analysis of all 3 principal components by principal component analysis showed that Clubionidae sp. 1, Parena cavipennis, or other predators were the main factors affecting the natural enemy community. Analysis of the community structure parameters of the H. cunea natural enemy community in different developmental stages across generations revealed the following: (i) Compared with the degree of complexity of the egg and pupal stages, the larval stage was the highest. (ii) The complexity was determined by means of comprehensive evaluation: first-generation larvae in 2020 &gt; first-generation larvae in 2019 &gt; second-generation larvae in 2020 &gt; second-generation larvae in 2019. These results clarify the dynamics of natural enemy species, coevolution with the host in the invaded habitat of H. cunea and development of biological control technologies.
Carabidae and Tenebrionidae diversity in the Great Basin Province of California
Authors: Tonkel Kirk C , Kirchoff Veronica S , Rector Brian G 
Published: November 2023

Abstract
The high desert regions of eastern California within the Great Basin are vast areas of shrub-dominated habitat heavily impacted by invasive exotic grasses and forbs. Trapping efforts within these areas provided distributional information about various surface-active arthropod taxa. Two groups with high species diversity and abundance encountered at our sites were the coleopteran families Carabidae and Tenebrionidae. Here, we report trapping of 45 species of carabids and 46 species of tenebrionids, along with mitochondrial cytochrome c oxidase subunit 1 (COI) sequence data for 65 of these 92 species. These results build upon existing distributional information regarding these families in California and further refine our knowledge of the biodiversity of the understudied Great Basin provinces.
Molecular identification and functional analysis of chitinase genes reveal their importance in the metamorphosis of Sarcophaga peregrina (Diptera: Sarcophagidae)
Authors: Feng Yakai , Wang Shiwen , Yang Fengqin , Shang Yanjie , Jocelin Ngando Fernand , Huang Jingjing , Guo Yadong 
Published: November 2023

Abstract
Chitinases play a crucial role in insect metamorphosis by facilitating chitin degradation. Sarcophaga peregrina (Robineau-Desvoidy, 1830) (Diptera: Sarcophagidae) is a typical holometabolous insect and an important hygiene pest that causes myiasis in humans and other mammals and acts as a vector for various parasitic agents, including bacteria, viruses, and parasites. Enhancing the understanding of the metamorphosis in this species has significance for vector control. In this study, we identified a total of 12 chitinase genes in S. peregrina using bioinformatic analysis methods. Based on transcriptome data, SpIDGF2 and SpCht10 were selected for further functional investigation. The down-regulation of these genes by RNA interference led to developmental delays, disruptions in molting, and differences in cuticle composition during the pupal stage. These findings underscore the pivotal role of chitinase genes in the metamorphic process and offer valuable insights for effective control strategies.
Latent Profiles of Sleep Disturbance and Impairment in Elementary School-Age Youth: Concurrent and Longitudinal Associations with Emotional, Behavioral, and Academic Functioning
Authors: Mitchell Tarrah B , Cooley John L , Cummings Caroline , Lelakowska Gabriela , Wolfe Laurel D , Ricker Brianna T , Farias Rebecca 
Published: November 2023

Abstract

Objective
The links from youth sleep problems to emotional, behavioral, and academic functioning are well documented. Latent variable mixture modeling (LVMM) has been used to explore these relations; however, additional research is needed in diverse samples and with self-reports of sleep-related difficulties. The objectives of the current study were to identify profiles based on patterns of sleep disturbance and impairment and explore associations among profiles and functioning at baseline and over a subsequent 6-month period.

Methods
Participants were 278 third- through fifth-grade students (M age = 9.27; 51.8% male; 51.1% Hispanic/Latine) and homeroom teachers. Children completed measures of sleep disturbance and impairment, emotion (dys)regulation, and depressive, anxiety, and anger symptoms. Teachers completed measures of youth’s emotional and conduct problems, emotion (dys)regulation, and academic performance. LVMM was conducted.

Results
Three profiles emerged: (1) “Average Sleep Disturbance and Impairment” (n = 148); (2) “Elevated Sleep Disturbance and Average Sleep Impairment” (n = 40); and (3) “Elevated Sleep Disturbance and Impairment” (n = 90). Overall, youth with above average sleep problems had worse functioning at baseline. Further, youth in Profile 3 exhibited increases in self-reported symptoms of depression, anxiety, and anger, as well as worsening teacher-reported academic performance and conduct problems. In contrast, youth in Profile 2 exhibited improvements in self-reported symptoms of depression, anxiety, and anger, as well as teacher-reported emotion regulation, conduct problems, and academic performance.

Conclusions
Results highlight the importance of examining self-reports of sleep problems and the need for intervention among children exhibiting elevated sleep disturbance and impairment.
Prognostic factors of poor surgical outcome after clitoral reconstruction in women with female genital mutilation/cutting
Authors: Gnofam Mayi , Crequit Simon , Renevier Bruno , Abramowicz Sarah 
Published: November 2023

Abstract

Background
Complications of surgical clitoral reconstruction for female genital mutilation/cutting (FGM/C) are a rare occurrence, but there has been reports of patients experiencing chronic pain or clitoral burial.

Aim
This study aims to assess which factors are predictive of the occurrence of surgical complications in women who had surgical reconstruction for FGM/C (type 1, 2, or 3).

Methods
This monocentric retrospective study was conducted among patients who underwent clitoral reconstruction after FGM/C from January 2016 to March 2020. Demographic and clinical data were abstracted from the medical records.

Outcomes
The primary outcome was the occurrence of chronic pain (defined as occurrence or persistence of any clitoral pain &gt;3 months after surgery), and the secondary outcome was the occurrence of clitoral burial.

Results
A total of 87 women were included in the analysis. Univariate analysis indicated significantly higher rates of a history of physical abuse in the group of women who experienced chronic pain after surgery (4 [100%] vs 2 [37.1%], P = .049). Patients with clitoral burial were significantly younger than the rest of the sample in univariate analysis (median [IQR], 29.6 years [24.6-30.2] vs 33.8 [28.2-37.9]; P = .049).

Clinical Implications
Surgical treatment of women who underwent FGM/C should include the entire history of the patient and especially a record of experiencing physical abuse.

Strengths and Limitations
The study stands out for its originality, the extensive sample size gathered over nearly 4 years, the surgical clitoral reconstructions conducted by an experienced surgeon, and the minimal amount of missing data. However, because the occurrence of these complications was rare, the number of patients in the subgroups was extremely low, preventing a valid multivariate analysis to be conducted.

Conclusion
The study suggests that women with a history of physical abuse could be at greater risk for chronic pain after surgery and that younger women tend to experience more clitoral burial.
Void probability function inside cosmic voids: evidence for hierarchical scaling of high-order correlations in real space
Authors: Dávila-Kurbán Federico , Ruiz Andrés N , Paz Dante J , Lambas Diego Garcia 
Published: November 2023

ABSTRACT
We compare the reduced void probability function (VPF) inside and outside of cosmic voids in the TNG300-1 simulation, both in real and simulated redshift space. The VPF is a special case of the Counts-in-Cells approach for extracting information of high-order clustering that is crucial for a full understanding of the distribution of galaxies. Previous studies have validated the hierarchical scaling paradigm of galaxy clustering moments, in good agreement with the ‘negative binomial’ model, in redshift surveys but have also reported that this paradigm is not valid in real space. However, in this work, we find that hierarchical scaling can indeed be found in real space inside cosmic voids. This is well fitted by the negative binomial model. We find this result to be robust against changes in void identification, galaxy mass, random dilutions, and redshift. We also obtain that the VPF in real space at high redshift approaches the negative binomial model, and, therefore, it is similar to the VPF inside voids at the present time. This study points, for the first time, towards evidence of hierarchical scaling of high-order clustering of galaxies in real space inside voids, preserving the pristine structure formation processes of the Universe.
The star formation histories of galaxies in different stages of pre-processing in the Fornax A group
Authors: Loubser S I , Mosia K , Serra P , Kleiner D , Peletier R F , Kraan-Korteweg R C , Iodice E , Loni A , Kamphuis P , Zabel N 
Published: November 2023

ABSTRACT
We study the recent star formation histories of 10 galaxies in the Fornax A galaxy group, on the outskirts of the Fornax cluster. The group galaxies are gas-rich, and their neutral atomic hydrogen (H i) was studied in detail with observations from the MeerKAT telescope. This allowed them to be classified into different stages of pre-processing (early, ongoing, advanced). We use long-slit spectra obtained with the South African Large Telescope (SALT) to analyse stellar population indicators to constrain quenching time-scales and to compare these to the H i gas content of the galaxies. The H α equivalent width, EW(H α), suggest that the pre-processing stage is closely related to the recent (&lt;10 Myr) specific Star Formation Rate (sSFR). The early-stage galaxy (NGC 1326B) is not yet quenched in its outer parts, while the ongoing-stage galaxies mostly have a distributed population of very young stars, though less so in their outer parts. The galaxies in the advanced stage of pre-processing show very low recent sSFR in the outer parts. Our results suggest that NGC 1326B, FCC 35, and FCC 46 underwent significantly different histories from secular evolution during the last Gyr. The fact that most galaxies are on the secular evolution sequence implies that pre-processing has a negligible effect on these galaxies compared to secular evolution. We find EW(H α) to be a useful tool for classifying the stage of pre-processing in group galaxies. The recent sSFR and H i morphology show that galaxies in the Fornax A vicinity are pre-processing from the outside in.