bluuebunny/crossref_metadata_2025_split huggingface dataset:
GWAS and Transcriptomic Analysis Identify OsRING315 as a New Candidate Gene Controlling Amylose Content and Gel Consistency in Rice
Authors: Nie Shuai , Chen Luo , Zheng Minhua , Dong Jingfang , Ma Yamei , Zhou Lian , Wang Jian , Chen Jiansong , Hu Haifei , Yang Tifeng , Zhao Junliang , Zhang Shaohong , Yang Wu 
Published: June 2024

AbstractCooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice.
Diagnosis and multidisciplinary management of a large primary retroperitoneal hydatid cyst: report of a sporadic case
Authors: Nedjim Saleh Abdelkerim , Bencherki Youssef , Daghdagh Yassine , Nachid Abdellah , Tmiri Anas , El Badr Mouad , Moataz Amine , Dakir Mohamed , Adil Debbagh , Aboutaieb Rachid 
Published: June 2024

Abstract
Background
Hydatid cysts, a parasite caused by infestation with Echinococcosis granulose, are rarely found in isolation in the retroperitoneum. Diagnosis is based on clinical and paraclinical criteria, and the symptoms are often aspecific. In large, symptomatic forms, surgical excision is the mainstay of treatment. However, a multidisciplinary approach, including infectious diseases specialists, can improve results and reduce the risk of recurrence.

Case presentation
We report the case of a 38-year-old woman presenting with a large primary retroperitoneal hydatid cyst. After 13 years of asymptomatic evolution, she developed lumbar pain and a sensation of heaviness. The diagnosis was confirmed by a battery of biological and radiological tests. Due to the size of the cyst, open surgery was performed. Follow-up revealed no clinical complaints or recurrences.

Conclusion
Considered a rare condition, hydatid cyst requires special attention when evaluating lumbar masses or cystic masses, particularly in endemic areas. In addition to surgery, it is essential to take into account the risk of contamination of other sites during surgery. Collaboration with specialists in infectious diseases is therefore essential.
Regulating “forever chemicals”: social data are necessary for the successful implementation of the essential use concept
Authors: Suffill Ellise , White Mathew P. , Hale Sarah , Pahl Sabine 
Published: June 2024

AbstractPer- and polyfluoroalkyl substances (PFAS) are a large class of synthetic compounds, many of which are persistent, mobile and toxic (PMT). The sheer number of PFAS makes a substance-by-substance based approach to regulating this group unfeasible. Given the known risks of many PFAS, a precautionary approach (i.e., the Essential Use Concept; EUC) has been called for, whereby any substance is assumed to be harmful and should be phased out, unless it is shown that: (a) the use of this substance is necessary for health and safety, or is critical for the functioning of society and (b) there are no available technically and economically feasible alternatives. While experts, including chemists and toxicologists, are well-placed to assess the second criteria, determining what is necessary for the “functioning of society” requires a wider consideration of societal beliefs and preferences and greater involvement of various interested and affected parties, especially those whose voices are less heard but may be most vulnerable. The aim of the current paper is to provide a preliminary framework and research agenda outlining why and at what points in the essential use decision-making process broader societal perspectives are required, and how such ‘social data’ can be collected. The ultimate goal is to improve chemicals management by supporting citizens in becoming more informed and engaged participants in relevant debates and policies, including in how to operationalise the EUC.
The impact of global value chains on wages, employment, and productivity: a survey of theoretical approaches
Authors: Szymczak Sabina 
Published: June 2024

AbstractThis study presents a systematic literature review to provide a collection of theories explaining the impact of global value chains (GVCs) on labour market outcomes. Due to the complex nature of GVCs and the interconnectedness of wages, employment, and productivity, many direct and indirect effects are at play. To ensure a transparent and systematic flow of the review process, I follow the PRISMA guide. Eventually, 36 records out of 1221 results from Scopus database were selected. This review may be useful for theorists, empirical economists, and policy makers as an overview of theoretical developments and convenient map of potential outcomes expected from involvement in GVCs. It identifies and systematizes a number of effects existing in the literature under various names. The results show that the predictions from the theory are ambiguous. The positive effects which may emerge regardless the characteristics of the GVC are the productivity-enhancing effect and the cross-effect, especially important considering growing servicification of manufacturing. Here lies the critical role of the state and policies to assure that the losses will not exceed the gains in the aggregate terms. One of the main factors shaping the outcome is the power distribution among the GVC’s firms. Additionally, this paper shows the shortcomings of the existing theories. Less aggregated levels of analysis could be a great input to the discussion, as well as addressing different GVCs’ dimensions and types of organisation. The understanding of relation between GVC position and labour market is especially worth exploration as the existing evidence adopt different and even contradicting perspectives on the definition of upgrading the GVC position.
Integrating transformers and many-objective optimization for drug design
Authors: Aksamit Nicholas , Hou Jinqiang , Li Yifeng , Ombuki-Berman Beatrice 
Published: June 2024

Abstract
Background
Drug design is a challenging and important task that requires the generation of novel and effective molecules that can bind to specific protein targets. Artificial intelligence algorithms have recently showed promising potential to expedite the drug design process. However, existing methods adopt multi-objective approaches which limits the number of objectives.

Results
In this paper, we expand this thread of research from the many-objective perspective, by proposing a novel framework that integrates a latent Transformer-based model for molecular generation, with a drug design system that incorporates absorption, distribution, metabolism, excretion, and toxicity prediction, molecular docking, and many-objective metaheuristics. We compared the performance of two latent Transformer models (ReLSO and FragNet) on a molecular generation task and show that ReLSO outperforms FragNet in terms of reconstruction and latent space organization. We then explored six different many-objective metaheuristics based on evolutionary algorithms and particle swarm optimization on a drug design task involving potential drug candidates to human lysophosphatidic acid receptor 1, a cancer-related protein target.

Conclusion
We show that multi-objective evolutionary algorithm based on dominance and decomposition performs the best in terms of finding molecules that satisfy many objectives, such as high binding affinity and low toxicity, and high drug-likeness. Our framework demonstrates the potential of combining Transformers and many-objective computational intelligence for drug design.
De novo transcriptome assembly of the oak processionary moth Thaumetopoea processionea
Authors: Zicola Johan , Dasari Prasad , Hahn Katharina Klara , Ziese-Kubon Katharina , Meurer Armin , Buhl Timo , Scholten Stefan 
Published: June 2024

Abstract
Objectives
The oak processionary moth (OPM) (Thaumetopoea processionea) is a species of moth (order: Lepidoptera) native to parts of central Europe. However, in recent years, it has become an invasive species in various countries, particularly in the United Kingdom and the Netherlands. The larvae of the OPM are covered with urticating barbed hairs (setae) causing irritating and allergic reactions at the three last larval stages (L3-L5). The aim of our study was to generate a de novo transcriptomic assembly for OPM larvae by including one non-allergenic stage (L2) and two allergenic stages (L4 and L5). A transcriptomic assembly will help identify potential allergenic peptides produced by OPM larvae, providing valuable information for developing novel therapeutic strategies and allergic immunodiagnostic assays.

Data
Transcriptomes of three larval stages of the OPM were de novo assembled and annotated using Trinity and Trinotate, respectively. A total of 145,251 transcripts from 99,868 genes were identified. Bench-marking universal single-copy orthologues analysis indicated high completeness of the assembly. About 19,600 genes are differentially expressed between the non-allergenic and allergenic larval stages. The data provided here contribute to the characterization of OPM, which is both an invasive species and a health hazard.
Molecular prevalence and phylogenetic analysis of hemotropic Mycoplasma species in cats in different regions of Iran
Authors: Hoseinpoor Elham , Goudarztalejerdi Ali , Sazmand Alireza 
Published: June 2024

Abstract
Background
Hemotropic Mycoplasma species (hemoplasmas) cause hemolytic anemia in cats worldwide and are recognized as emerging zoonotic pathogens. There is no comprehensive study on the prevalence and species diversity of hemoplasmas in domestic cat populations in different regions in Iran. Thus, the aims of the present study were to provide data on the prevalence and molecular characterization of hemotropic Mycoplasma species in apparently healthy cats from six Iranian provinces with different climates. In addition, potential risk factors associated with hemoplasmosis in cats were assessed.

Results
Mycoplasma spp. DNA was detected in the blood of 56 / 361 cats (15.5%) using genus-specific PCR. Further examinations with species-specific PCR and Sanger sequencing showed that 38 cats (10.5%) tested positive for Candidatus Mycoplasma haemominutum (CMhm), 8 cats (2.2%) tested positive for Mycoplasma haemofelis (Mhf), and 2 cats (0.6%) tested positive for Candidatus Mycoplasma turicensis (CMt). Co-infection with CMhm, and Mhf was observed in 7 cats (1.9%). One cat (0.3%) showed mixed infection with CMhm, Mhf, and CMt. There were statistically significant relationships between Mycoplasma positivity and being female, living in shelter (cattery), and being over 3 years old (P < 0.05). No significant association was observed for the cat breed and sampling localities.

Conclusions
Current study findings revealed that hemoplasma infections are common among Iran cat populations. Considering the impact of such emerging zoonotic pathogens on the One Health, routine screenings, increasing public awareness, effective control, and prophylactic strategies for minimizing infection in cats and subsequently in human are strongly recommended.
CRISPR/Cas9-induced knockout of an amino acid permease gene (AAP6) reduced Arabidopsis thaliana susceptibility to Meloidogyne incognita
Authors: Dutta Tushar K. , Rupinikrishna Katakam , Akhil Voodikala S. , Vashisth Neeraj , Phani Victor , Pankaj  , Sirohi Anil , Chinnusamy Viswanathan 
Published: June 2024

Abstract
Background
Plant-parasitic root-knot nematode (Meloidogyne incognita) causes global yield loss in agri- and horticultural crops. Nematode management options rely on chemical method. However, only a handful of nematicides are commercially available. Resistance breeding efforts are not sustainable because R gene sources are limited and nematodes have developed resistance-breaking populations against the commercially available Mi-1.2 gene-expressing tomatoes. RNAi crops that manage nematode infection are yet to be commercialized because of the regulatory hurdles associated with transgenic crops. The deployment of the CRISPR/Cas9 system to improve nematode tolerance (by knocking out the susceptibility factors) in plants has emerged as a feasible alternative lately.

Results
In the present study, a M. incognita-responsive susceptibility (S) gene, amino acid permease (AAP6), was characterized from the model plant Arabidodpsis thaliana by generating the AtAAP6 overexpression line, followed by performing the GUS reporter assay by fusing the promoter of AtAAP6 with the β-glucuronidase (GUS) gene. Upon challenge inoculation with M. incognita, overexpression lines supported greater nematode multiplication, and AtAAP6 expression was inducible to the early stage of nematode infection. Next, using CRISPR/Cas9, AtAAP6 was selectively knocked out without incurring any growth penalty in the host plant. The ‘Cas9-free’ homozygous T3 line was challenge inoculated with M. incognita, and CRISPR-edited A. thaliana plants exhibited considerably reduced susceptibility to nematode infection compared to the non-edited plants. Additionally, host defense response genes were unaltered between edited and non-edited plants, implicating the direct role of AtAAP6 towards nematode susceptibility.

Conclusion
The present findings enrich the existing literature on CRISPR/Cas9 research in plant-nematode interactions, which is quite limited currently while compared with the other plant-pathogen interaction systems.
Population differentiation and dynamics of five pioneer species of Gaultheria from the secondary forests in subtropical China
Authors: Li Yi-Rong , Fritsch Peter W. , Zhao Gui-Gang , Cheng Xiao-Juan , Ding Zhao-Li , Lu Lu 
Published: June 2024

Abstract
Background
The influence of native secondary succession associated with anthropogenic disturbance on the biodiversity of the forests in subtropical China remains uncertain. In particular, the evolutionary response of small understory shrubs, particularly pioneer species inhabiting continuously disturbed habitats, to topographic heterogeneity and climate change is poorly understood. This study aimed to address this knowledge gap by focusing on the Gaultheria crenulata group, a clade of small pioneer shrubs in subtropical China.

Results
We examined the genetic structure and demographic history of all five species of the G. crenulata group with two maternally inherited chloroplast DNA (cpDNA) fragments and two biparentally inherited low-copy nuclear genes (LCG) over 89 natural populations. We found that the genetic differentiation of this group was influenced by the geomorphological boundary between different regions of China in association with Quaternary climatic events. Despite low overall genetic diversity, we observed an isolation-by-distance (IBD) pattern at a regional scale, rather than isolation-by-environment (IBE), which was attributed to ongoing human disturbance in the region.

Conclusion
Our findings suggest that the genetic structure of the G. crenulata group reflects the interplay of geological topography, historical climates, and anthropogenic disturbance during the Pliocene–Pleistocene-Holocene periods in subtropical China. The observed IBD pattern, particularly prominent in western China, highlights the role of limited dispersal and gene flow, possibly influenced by physical barriers or decreased connectivity over geographic distance. Furthermore, the east-to-west trend of gene flow, potentially facilitated by the East Asian monsoon system, underscores the complex interplay of biotic and abiotic factors shaping the genetic dynamics of pioneer species in subtropical China’s secondary forests. These findings can be used to assess the impact of environmental changes on the adaptation and persistence of biodiversity in subtropical forest ecosystems.
Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus
Authors: Sun Weiqi , Li Mengdi , Wang Jianbo 
Published: June 2024

AbstractPlant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution and enhanced adaptability. However, few studies have been conducted on the relationship between gene expression and epigenetic modification in different plant tissues after allopolyploidization. In this study, we studied gene expression and DNA methylation modification patterns in four tissues (stems, leaves, flowers and siliques) of Brassica napusand its diploid progenitors. On this basis, the alternative splicing patterns and cis-trans regulation patterns of four tissues in B. napus and its diploid progenitors were also analyzed. It can be seen that the number of alternative splicing occurs in the B. napus is higher than that in the diploid progenitors, and the IR type increases the most during allopolyploidy. In addition, we studied the fate changes of duplicated genes after allopolyploidization in B. napus. We found that the fate of most duplicated genes is conserved, but the number of neofunctionalization and specialization is also large. The genetic fate of B. napus was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study also analyzed generational transmission analysis of expression and DNA methylation patterns. Our study provides a reference for the fate differentiation of duplicated genes during allopolyploidization.
Non-targeted GC–MS metabolomics-based differences in Indica rice seeds of different varieties
Authors: Zhou Dahu , Jing Hao , Yuan Jun , Zhou Mingming , Liu Lin , Fu Junru , Ouyang Linjuan , Xu Jie , Bian Jianmin , Fu Haihui , He Haohua 
Published: June 2024

AbstractRice seeds of different varieties exhibited distinct metabolic profiles in our study. We analyzed the metabolites in seeds of six rice varieties (CH, HM, NX, YX, HY, and MX) using non-targeted GC–MS. Our findings revealed that amino acids, sugars, and organic acids were predominant in all varieties, with significant differences observed in CH compared to the others. Specifically phenylalanine and glycine content differed notably in NX and YX, respectively. Additionally, 1,5-anhydroglucitol content in NX, and glutamate, aspartate, and lactulose in NX, YX, HM, HY, and MX were up-regulated. Due to the biological functions of these amino acids and sugars, these indicated that compared to CH, rice of NX were more conducive to metabolism of carbohydrate and fat, and healthy growth maintenance in the human body, but mightThese variations suggest that NX rice may be more beneficial for carbohydrate and fat metabolism and overall health maintenance compared to CH. However, it may not be suitable for diabetic patients. YX rice may not be an ideal glycine supplement, rice ofwhile HM, HY, and MX rice could serve as potential lactulose sources. Furthermore, NX and YX rice exhibited higher levels of main storage proteins compared to CH. This study offers valuable insights into the metabolic differences among various rice varieties.
Remimazolam anaphylaxis in a patient not allergic to brotizolam: a case report and literature review
Authors: Nakai Toshihiro , Kako Eisuke , Ota Haruko , So MinHye , Sobue Kazuya 
Published: June 2024

Abstract
Background
Remimazolam is a recently developed, ultrashort-acting benzodiazepine that is used as a general anesthetic. Some cases of remimazolam anaphylaxis have been reported, but its characteristics are not fully understood. We present an interesting case report and review of the literature to better understand remimazolam anaphylaxis.

Case presentation
A 75-year-old man scheduled for robot-assisted gastrectomy was administered remimazolam for the induction of general anesthesia. After intubation, low end-expiratory CO2, high airway pressure and concurrent circulatory collapse were observed. Bronchoscopy revealed marked tracheal and bronchial edema, which we diagnosed as anaphylaxis. The patient suffered cardiac arrest after bronchoscopy but recovered immediately with intravenous adrenaline administration and chest compressions. We performed skin prick tests for the drugs used during induction except for remimazolam, considering the high risk of systemic adverse reactions to remimazolam. We diagnosed remimazolam anaphylaxis because the skin prick test results for the other drugs used during anesthesia were negative, and these drugs could have been used without allergic reactions during the subsequent surgery. Furthermore, this patient had experienced severe anaphylactic-like reactions when he underwent cardiac surgery a year earlier, in which midazolam had been used, but it was not thought to be the allergen at that time. Based on these findings, cross-reactivity to remimazolam and midazolam was suspected. However, the patient had previously received another benzodiazepine, brotizolam, to which he was not allergic, suggesting that cross-reactivity of remimazolam may vary among benzodiazepines. In this article, we reviewed the 11 cases of remimazolam anaphylaxis that have been described in the literature.

Conclusions
Remimazolam is an ultrashort-acting sedative; however, it can cause life-threatening anaphylaxis. In addition, its cross-reactivity with other benzodiazepines is not fully understood. To increase the safety of this drug, further research and more experience in its use are needed.