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Problematic use of sustainability claims in recent scientific literature on crop gene technologies: toward improving practices and communication
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-04-12 DOI: 10.1111/tpj.70137
Chris Wenzl, Emily A. Buddle, Rachel A. Ankeny

There is growing interest in the role of agricultural genomics, including biotechnology, in enhancing the “sustainability” of food production systems. However, as “sustainability” becomes more frequently linked to the goals of agricultural genomics, a critical question arises: what claims are made about “sustainability” and how is the concept of “sustainability” defined in the scholarly literature on agricultural genomics? Using a structured analysis of the recent scientific literature, this article investigates increasingly frequent claims about “sustainability,” including how this term is defined and measured in the field of agricultural genomics. It argues that more transparent definitions and clearer metrics, tied to appropriate scholarly literature, are crucial for improving the coherence, impact, and credibility of research in agricultural genomics.

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引用次数: 0
Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-04-12 DOI: 10.1111/tpj.70118
Davide Annese, Facundo Romani, Carolina Grandellis, Lesley Ives, Eftychios Frangedakis, Felipe X. Buson, Jennifer C. Molloy, Jim Haseloff

High-throughput experiments in plants are hindered by long generation times and high costs. To address these challenges, we present an optimized pipeline for Agrobacterium tumefaciens transformation and a simplified a protocol to obtain stable transgenic lines of the model liverwort Marchantia polymorpha, paving the way for efficient high-throughput experiments for plant synthetic biology and other applications. Our protocol involves a freeze–thaw Agrobacterium transformation method in six-well plates that can be adapted to robotic automation. Using the Opentrons open-source platform, we implemented a semi-automated protocol showing similar efficiency compared to manual manipulation. Additionally, we have streamlined and simplified the process of stable transformation and selection of M. polymorpha, reducing cost, time, and manual labor without compromising transformation efficiency. The addition of sucrose in the selection media significantly enhances the production of gemmae, accelerating the generation of isogenic plants. We believe these protocols have the potential to facilitate high-throughput screenings in diverse plant species and represent a significant step towards the full automation of plant transformation pipelines. This approach allows testing ~100 constructs per month, using conventional plant tissue culture facilities. We recently demonstrated the successful implementation of this protocol for screening hundreds of fluorescent reporters in Marchantia gemmae.

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引用次数: 0
Characteristics and clinical outcomes of patients with myeloid malignancies and cohesin mutations
IF 6.1 2区 医学 Q1 ONCOLOGY Pub Date : 2025-04-12 DOI: 10.1002/cncr.35846
Maria R. Khouri MD, Bofei Wang PhD, Laurie K. Pearson MD, Andrew J. Gillis-Smith MD, Sakiko Suzuki MD, Lloyd M. Hutchinson PhD, Poorva Bindal MD, Muthalagu Ramanathan MD, Jonathan M. Gerber MD, Jan Cerny MD, PhD, Shyam A. Patel MD, PhD

Background

The prognostic impact of cohesin mutations in patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) is controversial.

Methods

In patients with AML and MDS who underwent next-generation sequencing at the authors' center during 2017–2023, the authors assessed the landscape of cohesin mutations and the impact of co-occurring mutations on overall survival (OS) and compared outcomes between patients with cohesin mutations and those with wild-type (WT) cohesin genes.

Results

The study included 83 patients, 36 with cohesin mutations (STAG2, n = 28; SMC1A, n = 7; SMC3, n = 3; co-expression of cohesin mutations, n = 2) and 47 with WT cohesin genes. Of the 36 patients with cohesin mutations, 17 (47%) had AML (six de novo and 11 secondary), and 19 (53%) had MDS. Patients who had STAG2 mutations had better median OS than patients who had only SMC1A and SMC3 mutations (26 vs. 10 months; p = .043). SRSF2 mutation was the most frequent co-occurring mutation (n = 12; 33%) and was associated with worse median OS than WT SRSF2 (13 vs. 43 months; p = .016). Seven patients (19%) with cohesin mutations underwent hematopoietic transplantation; their median OS was 70 months. Compared with the WT cohesin group, patients who had cohesin mutations were more likely to have adverse-risk AML (82% vs. 53%). The median OS was similar among patients with adverse-risk AML in the cohesin-mutation and WT cohesin groups (10 vs. 14 months, respectively; p = .9).

Conclusions

The current study provides insight into the prognostic impact of cohesin mutations and co-occurring mutations in patients with myeloid malignancies.

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引用次数: 0
A Third Biodiversity Metric in the Third Pole
IF 10.8 1区 环境科学与生态学 Q1 BIODIVERSITY CONSERVATION Pub Date : 2025-04-12 DOI: 10.1111/gcb.70192
Kenneth Oberlander
<p>The readers of this journal need no introduction to the threat posed to biodiversity by anthropogenic factors such as habitat degradation and climate change. The (sometimes considerable) efforts by many national governments to increase biodiversity protection over the last few decades, via the establishment of protected areas for conservation, have nevertheless met with criticism, particularly with regard to the evidence base used for the establishment and expansion of such protected areas (Maxwell et al. <span>2020</span>). This is particularly acute for regional planning efforts involving multiple governments, where the effects of national borders on biodiversity conservation may have profound consequences in the near future (Li et al. <span>2025</span>). Ideally, such decisions should be made taking into account evidence from multiple different levels of biological organisation, but this is seldom achieved in reality.</p><p>Much of the diversity information utilised for conservation planning is at the species level, that is, simple metrics of species diversity or endemism. Alternatively, metrics above the species level are used, such as phylogenetic diversity (representing the amount of independent evolutionary history represented in a region) or functional or ecosystem diversity (maximising trait or ecosystem-level diversity; Cadotte and Tucker <span>2018</span>). In either case, the basic building blocks of what is conserved by such methods are species—treated as atomic, indivisible units. While undeniably valuable, these approaches can overlook the extraordinary wealth of readily available data, suggesting that members of a species are not all the same.</p><p>In the paper by Wambulwa et al. (<span>2025</span>), the authors set out to assess this third, somewhat overlooked biodiversity metric—genetic diversity, that is, diversity <i>below</i> the species level—as a potentially useful factor to include in evidence-based conservation planning. While assessment of genetic structure and diversity underpins multiple fields of science, it is surprising how seldom it has been used—particularly in aggregate across large numbers of species—to help plan and expand protected areas. The implications of treating species as non-atomic units—with interpopulational variability that is worth conserving and which may impact conservation success under scenarios of global change—have often been neglected in favour of other biodiversity metrics when it comes to protected area planning, particularly at the regional level. There is increased recognition that genetic diversity should play a greater role in future decision-making around protected areas in general (Hoban et al. <span>2020</span>).</p><p>Wambulwa et al. (<span>2025</span>) used genetic diversity patterns for this purpose in the Third Pole, a region corresponding to the Tibetan Plateau and associated high-altitude mountain ranges of central Asia (Liu et al. <span>2022</span>). The name is apt—outsid
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引用次数: 0
Guest Editorial: Towards large-scale commercialisation of space-division multiplexing fibres
IF 2.3 4区 计算机科学 Q2 ENGINEERING, ELECTRICAL & ELECTRONIC Pub Date : 2025-04-12 DOI: 10.1049/ote2.70001
Toshio Morioka, David Braganza, Werner Klaus

We are delighted to present this special issue of IET Optoelectronics on ‘Towards large-scale commercialisation of Space-division multiplexing (SDM) fibres’. This issue features contributions from five speakers at the ECOC 2023 workshop ‘What Will Eventually Trigger Large-Scale Commercialisation of SDM Fibres?’, held in Glasgow on 1 October 2023.

SDM is a promising technology to effectively deal with the unabated growth of data traffic in optical fibre networks. Over the past decade, extensive research on SDM optical fibres has resulted in the development of high-quality, multicore and few-mode fibres as well as other network elements that leverage the SDM concept. Whereas large-scale commercialisation of SDM fibres is essential to meet the ever-increasing demand for higher data rates, achieving practical deployment requires more than innovative fibre designs. It also necessitates system optimisation to reduce cost per bit and standardisation to ensure interoperability. The successful commercialisation of SDM fibres also hinges on the advancement of other network elements such as optical amplifiers, multiplexers, connectors and splices. This special issue explores the challenges and opportunities associated with SDM fibre commercialisation. It aims to identify potential triggers that could accelerate the adoption of SDM technology across various applications such as submarine optical cable systems, terrestrial fibre networks and data centre interconnects.

We hope this special issue provides readers with a comprehensive overview of the latest advancements in SDM technologies and valuable insights into their large-scale deployment, paving the way for significant upgrades in optical fibre communication systems in the years ahead.

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引用次数: 0
Research Progress and Development Trends of Building Energy Conservation Based on Bibliometric Analysis
IF 2.6 4区 工程技术 Q3 ENERGY & FUELS Pub Date : 2025-04-12 DOI: 10.1049/rpg2.70035
Youzhuo Zheng, Xiaobing Xiao, Yongxiang Cai, Zhenghao Gao, Yuanhong Ye, Hongwei Li, Zhufeng Wang

In order to mitigate the negative impact of increasing energy demand for buildings, a series of measures are taken to improve the energy efficiency in the built environment. Previous studies have found that household appliances, hot water supply and space heating in buildings account for a large proportion of energy consumption, where heating, ventilation, and air conditioning (HVAC) contribute about 40% of the energy consumption as well as a large amount of greenhouse gas emissions. Energy saving while maintaining occupant comfort, therefore attract tremendous interest in the field where HVAC energy reduction or efficiency improvement are the key issues. By employing data mining and visualization technologies, this paper has reviewed highly crucial work in building energy systems with an attempt to explore the key researches as well as the future development trend. On the platform of CiteSpace with Web of Science (WOS) database, the key findings in line with building energy conservation technologies are collected. An innovative bibliometric method is used to map the knowledge in a visualizing way where research directions and cutting-edge technologies are discovered. This article also discusses the relationship between energy system development and national energy conservation policies with a specific focus on China's photovoltaic policies.

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引用次数: 0
A Systematic Literature Review on Graphical User Interface Testing Through Software Patterns
IF 1.5 4区 计算机科学 Q3 COMPUTER SCIENCE, SOFTWARE ENGINEERING Pub Date : 2025-04-12 DOI: 10.1049/sfw2/9140693
Ambreen Kousar, Saif Ur Rehman Khan, Atif Mashkoor, Javed Iqbal

Context: Graphical user interface (GUI) testing of mobile applications (apps) is significant from a user perspective to ensure that the apps are visually appealing and user-friendly. Pattern-based GUI testing (PBGT) is an innovative model-based testing (MBT) approach designed to enhance user satisfaction and reusability while minimizing the effort required to model and test UIs of mobile apps. In the literature, several primary studies have been conducted in the domain of PBGT.

Problem: The current state-of-the-art lacks comprehensive secondary studies within the PBGT domain. To our knowledge, this area has insufficient focus on in-depth research. Consequently, numerous challenges and limitations persist in the existing literature.

Objective: This study aims to fill the gaps mentioned above in the existing body of knowledge. We highlight popular research topics and analyze their relationships. We explore current state-of-the-art approaches and techniques, a taxonomy of tools and modeling languages, a list of reported UI test patterns (UITPs), and a taxonomy of writing UITPs. We also highlight practical challenges, limitations, and gaps in the targeted research area. Furthermore, the current study intends to highlight future research directions in this domain.

Method: We conducted a systematic literature review (SLR) on PBGT in the context of Android and web apps. A hybrid methodology that combines the Kitchenham and PRISMA guidelines is adopted to achieve the targeted research objectives (ROs). We perform a keyword-based search on well-known databases and select 30 (out of 557) studies.

Results: The current study identifies 11 tools used in PBGT and devises a taxonomy to categorize these tools. A taxonomy for writing UITPs has also been developed. In addition, we outline the limitations of the targeted research domain and future directions.

Conclusion: This study benefits the community and readers by better understanding the targeted research area. A comprehensive knowledge of existing tools, techniques, and methodologies is helpful for practitioners. Moreover, the identified limitations, gaps, emerging trends, and future research directions will benefit researchers who intend to work further in future research.

{"title":"A Systematic Literature Review on Graphical User Interface Testing Through Software Patterns","authors":"Ambreen Kousar,&nbsp;Saif Ur Rehman Khan,&nbsp;Atif Mashkoor,&nbsp;Javed Iqbal","doi":"10.1049/sfw2/9140693","DOIUrl":"https://doi.org/10.1049/sfw2/9140693","url":null,"abstract":"<div>\u0000 <p><b>Context:</b> Graphical user interface (GUI) testing of mobile applications (apps) is significant from a user perspective to ensure that the apps are visually appealing and user-friendly. Pattern-based GUI testing (PBGT) is an innovative model-based testing (MBT) approach designed to enhance user satisfaction and reusability while minimizing the effort required to model and test UIs of mobile apps. In the literature, several primary studies have been conducted in the domain of PBGT.</p>\u0000 <p><b>Problem:</b> The current state-of-the-art lacks comprehensive secondary studies within the PBGT domain. To our knowledge, this area has insufficient focus on in-depth research. Consequently, numerous challenges and limitations persist in the existing literature.</p>\u0000 <p><b>Objective:</b> This study aims to fill the gaps mentioned above in the existing body of knowledge. We highlight popular research topics and analyze their relationships. We explore current state-of-the-art approaches and techniques, a taxonomy of tools and modeling languages, a list of reported UI test patterns (UITPs), and a taxonomy of writing UITPs. We also highlight practical challenges, limitations, and gaps in the targeted research area. Furthermore, the current study intends to highlight future research directions in this domain.</p>\u0000 <p><b>Method:</b> We conducted a systematic literature review (SLR) on PBGT in the context of Android and web apps. A hybrid methodology that combines the Kitchenham and PRISMA guidelines is adopted to achieve the targeted research objectives (ROs). We perform a keyword-based search on well-known databases and select 30 (out of 557) studies.</p>\u0000 <p><b>Results:</b> The current study identifies 11 tools used in PBGT and devises a taxonomy to categorize these tools. A taxonomy for writing UITPs has also been developed. In addition, we outline the limitations of the targeted research domain and future directions.</p>\u0000 <p><b>Conclusion:</b> This study benefits the community and readers by better understanding the targeted research area. A comprehensive knowledge of existing tools, techniques, and methodologies is helpful for practitioners. Moreover, the identified limitations, gaps, emerging trends, and future research directions will benefit researchers who intend to work further in future research.</p>\u0000 </div>","PeriodicalId":50378,"journal":{"name":"IET Software","volume":"2025 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/sfw2/9140693","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Berberine bridge enzyme-like oxidases orchestrate homeostasis and signaling of oligogalacturonides in defense and upon mechanical damage
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-04-12 DOI: 10.1111/tpj.70150
Ascenzo Salvati, Alessandra Diomaiuti, Federica Locci, Matteo Gravino, Giovanna Gramegna, Muhammad Ilyas, Manuel Benedetti, Sara Costantini, Monica De Caroli, Baptiste Castel, Jonathan D. G. Jones, Felice Cervone, Daniela Pontiggia, Giulia De Lorenzo

Plant immunity is triggered by endogenous elicitors known as damage-associated molecular patterns (DAMPs). Oligogalacturonides (OGs) are DAMPs released from the cell wall (CW) demethylated homogalacturonan during microbial colonization, mechanical or pest-provoked mechanical damage, and physiological CW remodeling. Berberine bridge enzyme-like (BBE-l) proteins named OG oxidases (OGOXs) oxidize and inactivate OGs to avoid deleterious growth-affecting hyper-immunity and possible cell death. Using OGOX1 over-expressing lines and ogox1/2 double mutants, we show that these enzymes determine the levels of active OGs vs. inactive oxidized products (ox-OGs). The ogox1/2-deficient plants have elevated levels of OGs, while plants overexpressing OGOX1 accumulate ox-OGs. The balance between OGs and ox-OGs affects disease resistance against Pseudomonas syringae pv. tomato, Pectobacterium carotovorum, and Botrytis cinerea depending on the microbial capacity to respond to OGs and metabolize ox-OGs. Gene expression upon plant infiltration with OGs reveals that OGOXs orchestrate OG signaling in defense as well as upon mechanical damage, pointing to these enzymes as apoplastic players in immunity and tissue repair.

{"title":"Berberine bridge enzyme-like oxidases orchestrate homeostasis and signaling of oligogalacturonides in defense and upon mechanical damage","authors":"Ascenzo Salvati,&nbsp;Alessandra Diomaiuti,&nbsp;Federica Locci,&nbsp;Matteo Gravino,&nbsp;Giovanna Gramegna,&nbsp;Muhammad Ilyas,&nbsp;Manuel Benedetti,&nbsp;Sara Costantini,&nbsp;Monica De Caroli,&nbsp;Baptiste Castel,&nbsp;Jonathan D. G. Jones,&nbsp;Felice Cervone,&nbsp;Daniela Pontiggia,&nbsp;Giulia De Lorenzo","doi":"10.1111/tpj.70150","DOIUrl":"https://doi.org/10.1111/tpj.70150","url":null,"abstract":"<p>Plant immunity is triggered by endogenous elicitors known as damage-associated molecular patterns (DAMPs). Oligogalacturonides (OGs) are DAMPs released from the cell wall (CW) demethylated homogalacturonan during microbial colonization, mechanical or pest-provoked mechanical damage, and physiological CW remodeling. Berberine bridge enzyme-like (BBE-l) proteins named OG oxidases (OGOXs) oxidize and inactivate OGs to avoid deleterious growth-affecting hyper-immunity and possible cell death. Using OGOX1 over-expressing lines and <i>ogox1/2</i> double mutants, we show that these enzymes determine the levels of active OGs vs. inactive oxidized products (ox-OGs). The <i>ogox1/2</i>-deficient plants have elevated levels of OGs, while plants overexpressing OGOX1 accumulate ox-OGs. The balance between OGs and ox-OGs affects disease resistance against <i>Pseudomonas syringae</i> pv. <i>tomato</i>, <i>Pectobacterium carotovorum</i>, and <i>Botrytis cinerea</i> depending on the microbial capacity to respond to OGs and metabolize ox-OGs. Gene expression upon plant infiltration with OGs reveals that OGOXs orchestrate OG signaling in defense as well as upon mechanical damage, pointing to these enzymes as apoplastic players in immunity and tissue repair.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Natural trajectory subclasses of cognitive impairment in breast cancer patients experiencing insomnia
IF 6.1 2区 医学 Q1 ONCOLOGY Pub Date : 2025-04-12 DOI: 10.1002/cncr.35816
Oxana Palesh PhD, MPH, Sarah E. Braun PhD, LCP, Tina Truong BS, MS, Susan Hong MD, Masato Mitsuhashi MD, PhD, Ruth Nyagaka BA, Susanne Lee MPH, Adithi Gandhi BA, Alexa De La Torre Schutz BS, Shelli R. Kesler PhD

Background

Cancer-related cognitive impairment (CRCI) has traditionally been assessed in a dichotomous manner. Identifying subclasses of CRCI and novel biomarkers can improve the accuracy of identifying patients most at risk for CRCI.

Methods

A total of 139 breast cancer patients undergoing chemotherapy completed neurocognitive batteries over 12 months. Growth mixture modeling (GMM) was used to determine latent subgroups based on different trajectories of cognitive test performance across the four time points. Additionally, the authors collected peripheral blood to measure neuron-derived exosomes (NDE).

Results

Mean cognitive performance improved significantly over time (p < .001). However, GMM identified three distinct latent subgroups: patients with stable, high performance (class 1, N = 45), patients with variable low performance (class 2, N = 15), and patients with average performance who improved over time (class 3, N = 79). Cognitive subclass 2 was characterized by significantly lower education levels than the other two classes (p = .001). Cognitive subclass 1 had fewer racial/ethnic minority patients than the other two classes (p = .015). Cognitive subclasses did not differ significantly in any other demographic or clinical characteristic. There were no significant differences observed by NDE.

Conclusions

There are multiple distinct longitudinal trajectories of CRCI and these may be influenced by social determinants of health such as education and race/ethnicity. Future research can focus on ways to administer interventions earlier to those at most risk for CRCI and continue to explore novel biomarkers of CRCI.

{"title":"Natural trajectory subclasses of cognitive impairment in breast cancer patients experiencing insomnia","authors":"Oxana Palesh PhD, MPH,&nbsp;Sarah E. Braun PhD, LCP,&nbsp;Tina Truong BS, MS,&nbsp;Susan Hong MD,&nbsp;Masato Mitsuhashi MD, PhD,&nbsp;Ruth Nyagaka BA,&nbsp;Susanne Lee MPH,&nbsp;Adithi Gandhi BA,&nbsp;Alexa De La Torre Schutz BS,&nbsp;Shelli R. Kesler PhD","doi":"10.1002/cncr.35816","DOIUrl":"https://doi.org/10.1002/cncr.35816","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Cancer-related cognitive impairment (CRCI) has traditionally been assessed in a dichotomous manner. Identifying subclasses of CRCI and novel biomarkers can improve the accuracy of identifying patients most at risk for CRCI.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>A total of 139 breast cancer patients undergoing chemotherapy completed neurocognitive batteries over 12 months. Growth mixture modeling (GMM) was used to determine latent subgroups based on different trajectories of cognitive test performance across the four time points. Additionally, the authors collected peripheral blood to measure neuron-derived exosomes (NDE).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Mean cognitive performance improved significantly over time (<i>p</i> &lt; .001). However, GMM identified three distinct latent subgroups: patients with stable, high performance (class 1, <i>N</i> = 45), patients with variable low performance (class 2, <i>N</i> = 15), and patients with average performance who improved over time (class 3, <i>N</i> = 79). Cognitive subclass 2 was characterized by significantly lower education levels than the other two classes (<i>p</i> = .001). Cognitive subclass 1 had fewer racial/ethnic minority patients than the other two classes (<i>p</i> = .015). Cognitive subclasses did not differ significantly in any other demographic or clinical characteristic. There were no significant differences observed by NDE.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>There are multiple distinct longitudinal trajectories of CRCI and these may be influenced by social determinants of health such as education and race/ethnicity. Future research can focus on ways to administer interventions earlier to those at most risk for CRCI and continue to explore novel biomarkers of CRCI.</p>\u0000 </section>\u0000 </div>","PeriodicalId":138,"journal":{"name":"Cancer","volume":"131 8","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cncr.35816","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PlantPan: A comprehensive multi-species plant pan-genome database
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2025-04-12 DOI: 10.1111/tpj.70144
Meiye Jiang, Qiheng Qian, Mingming Lu, Meili Chen, Zhuojing Fan, Yunfei Shang, Congfan Bu, ZhengLin Du, Shuhui Song, Jingyao Zeng, Jingfa Xiao

The pan-genome represents the complete genomic diversity of specific species, serving as a valuable resource for studying species evolution, crop domestication, and guiding crop breeding and improvement. While there are several single-species-specific plant pan-genome databases, the availability of multi-species pan-genome databases is limited. Additionally, variations in methods and data types used for plant pan-genome analysis across different databases hinder the comparison and integration of pan-genome information from various projects at multi-species or single-species levels. To tackle this challenge, we introduce PlantPan, a comprehensive database housing the results of pan-genome analysis for 195 genomes from 11 plant species. PlantPan aims to provide extensive information, including gene-centric and sequence-centric pan-genome information, graph-based pan-genome, pan-genome openness profiles, gene functions and its variation characteristics, homologous genes, and gene clusters across different species. Statistically, PlantPan incorporates 9 163 011 genes, 694 191 gene clusters, 526 973 370 genome variations, and 1 616 089 non-redundant genome variation groups at the species level, 33 455,098 genome synteny, and 177 827 non-redundant genome synteny groups at the species level. Regarding functional genes, PlantPan contains 5 222 720 genes related to transcription factors, 395 247 literature-reported resistance genes, 455 748 predicted microbial/disease resistance genes, and 1 612 112 genes related to molecular pathways. In summary, PlantPan is a vital platform for advancing the application of pan-genomes in molecular breeding for crops and evolutionary research for plants.

{"title":"PlantPan: A comprehensive multi-species plant pan-genome database","authors":"Meiye Jiang,&nbsp;Qiheng Qian,&nbsp;Mingming Lu,&nbsp;Meili Chen,&nbsp;Zhuojing Fan,&nbsp;Yunfei Shang,&nbsp;Congfan Bu,&nbsp;ZhengLin Du,&nbsp;Shuhui Song,&nbsp;Jingyao Zeng,&nbsp;Jingfa Xiao","doi":"10.1111/tpj.70144","DOIUrl":"https://doi.org/10.1111/tpj.70144","url":null,"abstract":"<div>\u0000 \u0000 <p>The pan-genome represents the complete genomic diversity of specific species, serving as a valuable resource for studying species evolution, crop domestication, and guiding crop breeding and improvement. While there are several single-species-specific plant pan-genome databases, the availability of multi-species pan-genome databases is limited. Additionally, variations in methods and data types used for plant pan-genome analysis across different databases hinder the comparison and integration of pan-genome information from various projects at multi-species or single-species levels. To tackle this challenge, we introduce PlantPan, a comprehensive database housing the results of pan-genome analysis for 195 genomes from 11 plant species. PlantPan aims to provide extensive information, including gene-centric and sequence-centric pan-genome information, graph-based pan-genome, pan-genome openness profiles, gene functions and its variation characteristics, homologous genes, and gene clusters across different species. Statistically, PlantPan incorporates 9 163 011 genes, 694 191 gene clusters, 526 973 370 genome variations, and 1 616 089 non-redundant genome variation groups at the species level, 33 455,098 genome synteny, and 177 827 non-redundant genome synteny groups at the species level. Regarding functional genes, PlantPan contains 5 222 720 genes related to transcription factors, 395 247 literature-reported resistance genes, 455 748 predicted microbial/disease resistance genes, and 1 612 112 genes related to molecular pathways. In summary, PlantPan is a vital platform for advancing the application of pan-genomes in molecular breeding for crops and evolutionary research for plants.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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