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Oryzalexin S biosynthesis:a cross-stitched disappearing pathway

aBIOTECH 2023年第1期4卷 1-7页

作者： Le Zhao richard oyagbenro Yiling Feng Meimei Xu Reuben J.Peters Roy J.Carver Department of Biochemistry Biophysics and Molecular BiologyIowa State UniversityAmesIA50011USA

Rice produces many diterpenoid phytoalexins and,reflecting the importance of these natural products in this important cereal crop plant,its genome contains three biosynthetic gene clusters(BGCs)for such metabolism.The chromosome 4 BGC(c4BGC)is largely associated with momilactone production,in part due to the presence of the initiating syn-copalyl diphosphate(CPP)synthase gene(OsCPS4).Oryzalexin S is also derived from syn-CPP.However,the relevant subsequently acting syn-stemarene synthase gene(OsKSL8)is not located in the c4BGC.Production of oryzalexin S further requires hydroxylation at carbons 2 and 19(C2 and C19),presumably catalyzed by cytochrome P450(CYP)monooxygenases.Here it is reported the closely related CYP99A2 and CYP99A3,whose genes are also found in the c4BGC catalyze the necessary C19-hydroxylation,while the closely related CYP71Z21 and CYP71Z22,whose genes are found in the recently reported chromosome 7 BGC(c7BGC),catalyze subsequent hydroxylation at C2α.Thus,oryzalexin S biosynthesis utilizes two distinct BGCs,in a pathway cross-stitched together by OsKSL8.Notably,in contrast to the widely conserved c4BGC,the c7BGC is subspecies(ssp.)specific,being prevalent in ssp.japonica and only rarely found in the other major ssp.indica.Moreover,while the closely related syn-stemodene synthase OsKSL11 was originally considered to be distinct from OsKSL8,it has now been reported to be a ssp.indica derived allele at the same genetic loci.Intriguingly,more detailed analysis indicates that OsKSL8(j)is being replaced by OsKSL11(OsKSL8i),suggesting introgression from ssp.indica to(sub)tropical japonica,with concurrent disappearance of oryzalexin S production.

关键词： Biosynthetic gene clusters Phytoalexins Diterpenoids Rice evolution

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RecBERT:Semantic recommendation engine with large language model enhanced query segmentation for k-nearest neighbors ranking retrieval

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Intelligent and Converged Networks 2024年第1期5卷 42-52页

作者： richard Wu the Dublin Unified School District and the SF Artificial Intelligence Club DublinCA 94568USA

The increasing amount of user traffic on Internet discussion forums has led to a huge amount of unstructured natural language data in the form of user comments.Most modern recommendation systems rely on manual tagging,relying on administrators to label the features of a class,or story,which a user comment corresponds to.Another common approach is to use pre-trained word embeddings to compare class descriptions for textual similarity,then use a distance metric such as cosine similarity or Euclidean distance to find top k neighbors.However,neither approach is able to fully utilize this user-generated unstructured natural language data,reducing the scope of these recommendation systems.This paper studies the application of domain adaptation on a transformer for the set of user comments to be indexed,and the use of simple contrastive learning for the sentence transformer fine-tuning process to generate meaningful semantic embeddings for the various user comments that apply to each class.In order to match a query containing content from multiple user comments belonging to the same class,the construction of a subquery channel for computing class-level similarity is proposed.This channel uses query segmentation of the aggregate query into subqueries,performing k-nearest neighbors(KNN)search on each individual subquery.RecBERT achieves state-of-the-art performance,outperforming other state-of-the-art models in accuracy,precision,recall,and F1 score for classifying comments between four and eight classes,respectively.RecBERT outperforms the most precise state-of-the-art model(distilRoBERTa)in precision by 6.97%for matching comments between eight classes.

关键词： sentence transformer simple contrastive learning large language models query segmentation k-nearest neighbors

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Liver transplantation as an alternative for the treatment of non-resectable liver colorectal cancer: Advancing the therapeutic algorithm

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Hepatobiliary & Pancreatic Diseases International 2024年第2期23卷 154-159页

作者： Badi Rawashdeh richard Bell Abdul Hakeem Raj Prasad Division of Transplant Surgery Department of General SurgeryMedical College of WisconsinMilwaukeeWI53226USA Leeds Teaching Hospital LeedsUK

Colorectal cancer is a leading cause of cancerrelated mortality,with nearly half of the affected patients developing liver metastases.For three decades,liver resection(LR)has been the primary curative strategy,yet its applicability is limited to about 20%of cases.Liver transplantation(LT)for unresectable metastases was attempted unsuccessfully in the 1990s,with high rates of perioperative death and recurrence.There is now more interest in this strategy due to improvements in systemic therapies and surgical techniques.A significant study conducted by the Oslo group showed that patients receiving liver transplants had a 60%chance of survival after five years.Significantly better results have been achieved by using advanced imaging for risk stratification and further refining selection criteria,especially in the Norvegian SECA trials.This review carefully charts the development and history of LT as a treatment option for colorectal cancer liver metastases.The revolutionary path from the early days of exploratory surgery to the current situation of cautious optimism is traced,highlighting the critical clinical developments and improved patient selection standards that have made LT a potentially curative treatment for such challenging very well selected cases.

关键词： Liver transplantation Colorectal cancer liver metastases Non-resectable liver metastases

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Amino acid and mineral digestibility,bone ash,and plasma inositol is increased by including microbial phytase in diets for growing pigs

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Journal of Animal Science and Biotechnology 2024年第2期15卷 699-712页

作者： Liz Vanessa Lagos Mike richard Bedford Hans Henrik Stein Division of Nutritional Sciences University of IllinoisUrbanaIL 61801USA AB Vista Marlborough SN84ANUK

Background The effect of microbial phytase on amino acid and energy digestibility is not consistent in pigs,which may be related to the phytase dosage or the adaptation length to the diet.Therefore,an experiment was conducted to test the hypotheses that increasing dietary phytase after an 18-day adaptation period:1)increases nutrient and energy digestibility;2)increases plasma P,plasma inositol,and bone ash of young pigs;and 3)demonstrates that maximum phytate degradation requires more phytase than maximum P digestibility.Results Data indicated that increasing inclusion of phytase[0,250,500,1,000,2,000,and 4,000 phytase units(FTU)/kg feed]in corn-soybean meal-based diets increased apparent ileal digestibility(AID)of Trp(quadratic;P<0.05),and of Lys and Thr(linear;P<0.05),and tended to increase AID of Met(linear;P<0.10).Increasing dietary phytase also increased AID and apparent total tract digestibility(ATTD)of Ca and P(quadratic;P<0.05)and increased ATTD of K and Na(linear;P<0.05),but phytase did not influence the ATTD of Mg or gross energy.Concentrations of plasma P and bone ash increased(quadratic;P<0.05),and plasma inositol also increased(linear;P<0.05)with increasing inclusion of phytase.Reduced concentrations of inositol phosphate(IP)6 and IP5(quadratic;P<0.05),reduced IP4 and IP3(linear;P<0.05),but increased inositol concentrations(linear;P<0.05)were observed in ileal digesta as dietary phytase increased.The ATTD of P was maximized if at least 1,200 FTU/kg were used,whereas more than 4,000 FTU/kg were needed to maximize inositol release.Conclusions Increasing dietary levels of phytase after an 18-day adaptation period increased phytate and IP ester degradation and inositol release in the small intestine.Consequently,increasing dietary phytase resulted in improved digestibility of Ca,P,K,Na,and the first 4 limiting amino acids,and in increased concentrations of bone ash and plasma P and inositol.In a corn-soybean meal diet,maximum inositol release requires approximately 3,200 FTU/kg more phytase than that re

关键词： Bone ash Inositol Nutrient digestibility Phytase Phytate degradation Pigs

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Genetic pathways in cerebral palsy:a review of the implications for precision diagnosis and understanding disease mechanisms

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Neural Regeneration Research 2024年第7期19卷 1499-1508页

作者： Yiran Xu Yifei Li Seidu A.richard Yanyan Sun Changlian Zhu Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center Institute of Neuroscience and The Third Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina National Health Council(NHC)Key Laboratory of Birth Defects Prevention Henan Key Laboratory of Population Defects PreventionZhengzhouHenan ProvinceChina Department of Human Anatomy School of Basic Medicine and Institute of NeuroscienceZhengzhou UniversityZhengzhouHenan ProvinceChina Center for Brain Repair and Rehabilitation Institute of Neuroscience and PhysiologyUniversity of GothenburgGothenburgSweden

Ce rebral palsy is a diagnostic term utilized to describe a group of permanent disorders affecting movement and posture.Patients with cerebral palsy are often only capable of limited activity,resulting from non-progressive disturbances in the fetal or neonatal brain.These disturbances severely impact the child’s daily life and impose a substantial economic burden on the family.Although cerebral palsy encompasses various brain injuries leading to similar clinical outcomes,the unde rstanding of its etiological pathways remains incomplete owing to its complexity and heterogeneity.This review aims to summarize the current knowledge on the genetic factors influencing cerebral palsy development.It is now widely acknowledged that genetic mutations and alterations play a pivotal role in cerebral palsy development,which can be further influenced by environmental fa ctors.Des pite continuous research endeavors,the underlying fa ctors contributing to cerebral palsy remain are still elusive.However,significant progress has been made in genetic research that has markedly enhanced our comprehension of the genetic factors underlying cerebral palsy development.Moreove r,these genetic factors have been categorized based on the identified gene mutations in patients through clinical genotyping,including thrombosis,angiogenesis,mitochondrial and oxidative phosphorylation function,neuronal migration,and cellular autophagy.Furthermore,exploring targeted genotypes holds potential for precision treatment.In conclusion,advancements in genetic research have substantially improved our understanding of the genetic causes underlying cerebral palsy.These breakthroughs have the potential to pave the way for new treatments and therapies,consequently shaping the future of cerebral palsy research and its clinical management.The investigation of cerebral palsy genetics holds the potential to significantly advance treatments and management strategies.By elucidating the underlying cellular mechanisms,we can develop to rgeted interventions to optimiz

关键词： cerebral palsy environmental factors etiology genetic factors genetic mutation movement disorder spastic diplegia

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New analytical modelling of fractional generalized Kuramoto-Sivashinky equation via Atangana-Baleanu operator and J-transform method

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Journal of Ocean Engineering and Science 2024年第1期9卷 66-88页

作者： Metonou richard Weidong Zhao Shehu Maitama School of Mathematics Shandong UniversityJinanShandongChina

In this paper,we propose a new analytical modelling of the well-known fractional generalized Kuramoto-Sivashinky equation(FGKSE)using fractional operator with non-singular kernel and the homotopy anal-ysis transform method via J-transform method.Also,using fixed-point theorem,we prove the existence and uniqueness of our proposed solution to the fractional Kuramoto-Sivashinky equation.To further val-idate the efficiency of the suggested technique,we proved the convergence analysis of the method and provide the error estimate.The obtained solutions of the FGKSE,describing turbulence processes in the field of ocean engineering are analytically and numerically compared to show the behaviors of many parameters of the present model.

关键词： Homotopy analysis J-transform method J-transform method Fractional generalized Kuramoto-Sivashinky equation Fixed-point theorem Numeric-symbolic computation

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Parameter-Free Shifted Laplacian Reconstruction for Multiple Kernel Clustering

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IEEE/CAA Journal of Automatica Sinica 2024年第4期11卷 1072-1074页

作者： Xi Wu Zhenwen Ren F.richard Yu the School of National Defence Science and Technology Southwest University of Science and TechnologyMianyang 621010China the School of National Defence Science and Technology Southwest University of Science and TechnologyMianyang 621010 the Guangxi Key Laboratory of Machine Vision and Intelligent Control Wuzhou UniversityWuzhou 543002 the Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ) Shenzhen 518060China

Dear Editor,This letter proposes a parameter-free multiple kernel clustering(MKC)method by using shifted Laplacian reconstruction.Traditional MKC can effectively cluster nonlinear data,but it faces two main challenges:1)As an unsupervised method,it is up against parameter problems which makes the parameters intractable to tune and is unfeasible in real-life applications;2)Only considers the clustering information,but ignores the interference of noise within Laplacian.

关键词： parameter letter Parameter

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Using clinical cases to guide healthcare

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World Journal of Clinical Cases 2024年第9期12卷 1555-1559页

作者： Michael Colwill Samantha Baillie richard Pollok Andrew Poullis Department of Gastroenterology St George's University Hospital NHS Foundation TrustLondon SW170QTUnited Kingdom

Evidence-based practice(EBP)has been the gold standard in healthcare for nearly three centuries and aims to assist physicians in providing the safest and most effective healthcare for their patients.The well-established hierarchy of evidence lists systematic reviews and meta-analyses at the top however these methodologies are not always appropriate or possible and in these instances case-control studies,case series and case reports are utilised to support EBP.Case-control studies allow simultaneous study of multiple risk factors and can be performed rapidly and relatively cheaply.A recent example was during the Coronavirus pandemic where case-control studies were used to assess the efficacy of personal protective equipment for healthcare workers.Case series and case reports also play a role in EBP and are particularly useful to study rare diseases such as inflammatory bowel disease in transgender and gender non-conforming individuals.They are also vital in generating and disseminating early signals and encouraging further research.Whilst these methodologies have weaknesses,particularly with regards to bias and loss of patient confidentiality for rare pathologies,they have an important part to play in EBP and when appropriately utilised can significantly impact upon clinical practice.

关键词： Evidence based medicine Hierarchy of evidence Case reports Case series

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Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

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Zoological Research 2024年第1期45卷 160-175页

作者： Yu-Ran Li Zheng-Wei Wang richard T.Corlett Wen-Bin Yu Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants&Center for Integrative Conservation Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China CAS Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China Southeast Asia Biodiversity Research Institute Chinese Academy of SciencesMenglaYunnan 666303China University of Chinese Academy of Sciences Shijingshan DistrictBeijing 100049China

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.

关键词： Social bees Phylogeny Mitogenome structure Gene rearrangement Inverted repeats

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Autolysosomal acidification impairment as a mediator for TNFR1 induced neuronal necroptosis in Alzheimer’s disease

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Neural Regeneration Research 2024年第9期19卷 1869-1870页

作者： Evridiki Asimakidou richard Reynolds Anna M.Barron Chih Hung Lo Department of Clinical Neurosciences University of CambridgeCambridgeUK Department of Brain Sciences Faculty of MedicineImperial College LondonLondonUK Lee Kong Chian School of Medicine Nanyang Technological UniversitySingaporeSingapore

Neuronal necroptosis-an emerging form of regulated cell death associated with neuroinflammatory signaling:Alzheimer’s disease(AD)is characterized by the presence of extracellular amyloid-β(Aβ)plaques and intracellular tau neurofibrillary tangles as well as progressive neuronal loss.Recent evidence has suggested that prolonged neuroinflammation with increased levels of cytokines,arising from neuronal injury,innate immune responses from glial cells,and peripheral inflammation,leads to neuronal death and AD progression.

关键词： Alzheimer death tau Aβ

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