The number of systematic reviews is gradually increas-ing over time. Also, the methods to perform a systematic review are being improved. However, little attention has been paid for the issue regarding how to fnd dupl...The number of systematic reviews is gradually increas-ing over time. Also, the methods to perform a systematic review are being improved. However, little attention has been paid for the issue regarding how to fnd duplicates in systematic reviews. On the basis of the survey and systematic reviews by our team and others, we review the prevalence, significance and classification of duplicates and the method to fnd duplicates in a systematic review. Notably, although a preliminary method to fnd duplicates is established, its usefulness and convenience need to be further confrmed.展开更多
The reliability evaluation of a multistate network is primarily based on d-minimal paths/cuts(d-MPs/d-MCs).However,being a nondeterminism polynomial hard(NP-hard)problem,searching for all d-MPs is a rather challenging...The reliability evaluation of a multistate network is primarily based on d-minimal paths/cuts(d-MPs/d-MCs).However,being a nondeterminism polynomial hard(NP-hard)problem,searching for all d-MPs is a rather challenging task.In existing implicit enumeration algorithms based on minimal paths(MPs),duplicate d-MP candidates may be generated.An extra step is needed to locate and remove these duplicate d-MP candidates,which costs significant computational effort.This paper proposes an efficient method to prevent the generation of duplicate d-MP candidates for implicit enumeration algorithms for d-MPs.First,the mechanism of generating duplicate d-MP candidates in the implicit enumeration algorithms is discussed.Second,a direct and efficient avoiding-duplicates method is proposed.Third,an improved algorithm is developed,followed by complexity analysis and illustrative examples.Based on the computational experiments comparing with two existing algorithms,it is found that the proposed method can significantly improve the efficiency of generating d-MPs for a particular demand level d.展开更多
BACKGROUND Gastrointestinal duplication is a rare congenital anomaly of the digestive tract,with colonic manifestations being particularly uncommon.Malignant transformation of colonic duplication cysts is rare,with ad...BACKGROUND Gastrointestinal duplication is a rare congenital anomaly of the digestive tract,with colonic manifestations being particularly uncommon.Malignant transformation of colonic duplication cysts is rare,with adenocarcinoma being the most frequently reported type.Herein,we report a rare case of adenocarcinoma originating from a colonic duplication cyst.CASE SUMMARY A 49-year-old woman was found to have an elevated cancer antigen 19-9 level during a routine checkup.Imaging revealed a well-defined abdominal cavity cystic mass,which was initially suspected to be an ovarian teratoma.Laparoscopic surgery revealed a duplication cyst,and pathological examination confirmed adenocarcinoma arising from the cyst.The mass within the transverse mesocolon was successfully excised by a colorectal surgeon.Immunohistochemical analysis confirmed adenocarcinoma with invasion into the muscularis propria.Postoperative endoscopy and positron emission computed tomography scan showed no signs of malignancy,except for an elevated cancer antigen 19-9 level.A multidisciplinary team recommended no further chemotherapy,advising routine follow-up for monitoring.CONCLUSION Colonic duplications,though rare,remain a differential diagnosis of unexplained abdominal masses,with complete resection being their primary treatment approach.展开更多
Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformat...Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.展开更多
The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysac...The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.展开更多
Heteranthery,the occurrence of functionally and structurally distinct stamens within a flower,represents a striking example of convergent evolution among diverse animal-pollinated lineages.Although the ecological basi...Heteranthery,the occurrence of functionally and structurally distinct stamens within a flower,represents a striking example of convergent evolution among diverse animal-pollinated lineages.Although the ecological basis of this somatic polymorphism is understood,the developmental and molecular mechanisms are largely unknown.To address this knowledge gap,we selected Monochoria elata(Pontederiaceae)as our study system due to its typical heterantherous floral structure.We constructed a chromosome-level genome assembly of M.elata,conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery.We focused on three key stamen characteristics—colour,spatial patterning,and filament elongation—selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species.Our analyses suggest that gene networks involving MelLEAFY3,MADS-box,and TCP genes regulate stamen identity,with anthocyanin influencing colour,and lignin contributing to filament elongation.Additionally,variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence.Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.展开更多
The flowering time is a key trait that determines adaptation,yield and quality of crops.Adlay,a traditional cereal crop,has developed a distinctive agricultural industry in Southwest China and Southeast Asian countrie...The flowering time is a key trait that determines adaptation,yield and quality of crops.Adlay,a traditional cereal crop,has developed a distinctive agricultural industry in Southwest China and Southeast Asian countries.However,the currently planted varieties are all semi-domesticated landraces with delayed flowering and excessive height.These defects limit yield improvement per unit area and mechanized harvesting.In this study,a major QTL associated with flowering time and plant height in adlay has been mapped and identified as Cl CCT,a gene having a conserved function and regulatory pathway for inhibiting flowering time and increasing plant height in gramineous crops.Among the six identified haplotypes of Cl CCT,the haplotype with 38-bp insertion in promoter region of Cl CCT has earlier flowering time and wider geographical distribution than other haplotypes.The insertion variation,which arises from the segmental duplication of Cl CCT,can inhibit the expression level of reporter gene and has been used in breeding for early maturity and dwarfing.These research results not only reinforce our understanding of the importance of CCT domain protein in the tropical crops adapting to high-latitude environment,but also provide a validated breeding target for the early maturity and dwarfing of adlay.展开更多
BACKGROUND Duplicated gallbladder with two completely independent cystic ducts is an exceptionally rare congenital anomaly.This case report documents an example of successful laparoscopic management,adding to the limi...BACKGROUND Duplicated gallbladder with two completely independent cystic ducts is an exceptionally rare congenital anomaly.This case report documents an example of successful laparoscopic management,adding to the limited literature by highlighting the importance of accurate preoperative imaging and surgical planning.CASE SUMMARY We present the case of a 46-year-old Uyghur woman who was admitted with intermittent right upper abdominal pain accompanied by nausea and vomiting that had persisted for 1 week.Her basic blood test results,including liver function test,were normal.Preoperative ultrasound revealed an abnormal echo in the gallbladder region,suggesting a double gallbladder malformation with one chamber containing multiple stones.Computed tomography and magnetic resonance cholangiopancreatography confirmed a double gallbladder anomaly.The patient subsequently underwent successful laparoscopic cholecystectomy.During the procedure,two gallbladder chambers were identified,with each cystic duct being independently inserted into the common bile duct.Surgery was completed without complications,and postoperative pathology confirmed the presence of gallstones and chronic cholecystitis.Because of the effective preoperative assessment,the patient recovered smoothly and was discharged 3 days after surgery,reporting no discomfort during follow-up.CONCLUSION This case highlights the need for thorough evaluation of rare gallbladder anomalies;literature recommends removing both to prevent disease recurrence.We present this case to raise clinical awareness,support appropriate diagnosis,and reinforce the recommendation to remove both gallbladders to prevent recurrence of gallbladder disease.展开更多
Pigment accumulation is an important trait related to wheat domestication,but there remains a limited understanding of its molecular mechanism.The genetic control of the red glume trait by a dominant allele,Rg-B1,on 1...Pigment accumulation is an important trait related to wheat domestication,but there remains a limited understanding of its molecular mechanism.The genetic control of the red glume trait by a dominant allele,Rg-B1,on 1BS was reported in the last century,but the underlying gene and its molecular basis remained elusive.Here,we identified TraesTSP1B01G005700(G57)encoding an R2R3-MYB transcription factor(TF)as the candidate Rg-B1 gene controlling red glume color by a combination of genome-wide association study(GWAS),bulked segregant RNA-sequencing(BSR-Seq),map-based cloning,and RNAseq.The Rg-B1 locus had zero to five duplicate copies only one of which had high transcriptional activity.Genetic evidence suggested that promoter sequence variation in G57 in the glume leads to high expression of G57,resulting in the red glume phenotype.G57 could bind to the promoters of anthocyanin synthesis genes TaCHS,TaF3'H,and TaUFGT,activating their expression and contributing to anthocyanin accumulation in wheat glume.G57 also played a pivotal role in up-regulating expression of genes TaDREB1C and TaFLO2 associated with increased grain weight,thereby causing increased grain weight.Our research offers a better understanding of the molecular basis of red glume in bread wheat.展开更多
BACKGROUND Gastric duplication cysts(GDCs)are rare congenital anomalies,and consensus guidelines for their diagnosis and management are currently lacking.We report a rare case of a GDC in a female child presenting as ...BACKGROUND Gastric duplication cysts(GDCs)are rare congenital anomalies,and consensus guidelines for their diagnosis and management are currently lacking.We report a rare case of a GDC in a female child presenting as a submucosal tumor in the gastric antrum.Subtotal resection was achieved using endoscopic submucosal dissection(ESD),resulting in complete symptom relief and pathological confirmation.This case demonstrates the therapeutic potential of ESD for intraluminal GDCs and underscores the importance of complete resection for definitive diagnosis.CASE SUMMARY A 12-year-old girl presented with abdominal distension and pain for>1 year.Gastroscopy revealed a protruding lesion approximately 30 mm in diameter in the gastric antrum.Superficial biopsies revealed moderate chronic inflammation and intestinal metaplasia.Contrast-enhanced computed tomography showed a mass protruding into the gastric lumen with homogeneous cyst wall enhancement.Endoscopic ultrasonography identified a hypoechoic mass originating from the muscularis mucosa.The patient underwent ESD for diagnosis and symptom relief.Intraoperatively,due to firm adhesion between the cyst base and the muscularis propria,selective preservation of the adherent cyst base was performed to mitigate perforation and stenosis risks.Histopathology confirmed a GDC,with cyst lumen lined by gastric-type columnar epithelium and an outer smooth muscle layer.Focal ectopic pancreatic tissues were identified.The patient recovered without complications and remained asymptomatic during 6-month follow-up.Repeat gastroscopy showed the residual cyst wall conforming to antral mucosa,with no recurrence.CONCLUSION Subtotal resection of GDCs using ESD demonstrates a favorable prognosis.展开更多
Duplicate bug reporting is a critical problem in the software repositories’mining area.Duplicate bug reports can lead to redundant efforts,wasted resources,and delayed software releases.Thus,their accurate identifica...Duplicate bug reporting is a critical problem in the software repositories’mining area.Duplicate bug reports can lead to redundant efforts,wasted resources,and delayed software releases.Thus,their accurate identification is essential for streamlining the bug triage process mining area.Several researchers have explored classical information retrieval,natural language processing,text and data mining,and machine learning approaches.The emergence of large language models(LLMs)(ChatGPT and Huggingface)has presented a new line of models for semantic textual similarity(STS).Although LLMs have shown remarkable advancements,there remains a need for longitudinal studies to determine whether performance improvements are due to the scale of the models or the unique embeddings they produce compared to classical encoding models.This study systematically investigates this issue by comparing classical word embedding techniques against LLM-based embeddings for duplicate bug detection.In this study,we have proposed an amalgamation of models to detect duplicate bug reports using textual and non-textual information about bug reports.The empirical evaluation has been performed on the open-source datasets and evaluated based on established metrics using the mean reciprocal rank(MRR),mean average precision(MAP),and recall rate.The experimental results have shown that combined LLMs can outperform(recall-rate@k 68%–74%)other individual=models for duplicate bug detection.These findings highlight the effectiveness of amalgamating multiple techniques in improving the duplicate bug report detection accuracy.展开更多
Detecting duplicates in data streams is an important problem that has a wide range of applications. In general, precisely detecting duplicates in an unbounded data stream is not feasible in most streaming scenarios, a...Detecting duplicates in data streams is an important problem that has a wide range of applications. In general, precisely detecting duplicates in an unbounded data stream is not feasible in most streaming scenarios, and, on the other hand, the elements in data streams are always time sensitive. These make it particular significant approximately detecting duplicates among newly arrived elements of a data stream within a fixed time frame. In this paper, we present a novel data structure, Decaying Bloom Filter （DBF）, as an extension of the Counting Bloom Filter, that effectively removes stale elements as new elements continuously arrive over sliding windows. On the DBF basis we present an efficient algorithm to approximately detect duplicates over sliding windows. Our algorithm may produce false positive errors, but not false negative errors as in many previous results. We analyze the time complexity and detection accuracy, and give a tight upper bound of false positive rate. For a given space G bits and sliding window size W, our algorithm has an amortized time complexity of O（√G/W）. Both analytical and experimental results on synthetic data demonstrate that our algorithm is superior in both execution time and detection accuracy to the previous results.展开更多
Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as...Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.展开更多
The Fagaceae,a plant family with a wide distribution and diverse adaptability,has garnered significant interest as a subject of study in plant speciation and adaptation.Meanwhile,certain Fagaceae species are regarded ...The Fagaceae,a plant family with a wide distribution and diverse adaptability,has garnered significant interest as a subject of study in plant speciation and adaptation.Meanwhile,certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood.In this study,we present two high-quality,chromosome-scale genome sequences for Quercus sichourensis(848.75 Mb)and Quercus rex(883.46 Mb).Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio(Ka/Ks)of protein-coding genes among Fagaceae species are related to different environmental adaptations.Interestingly,most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome,as compared to the outgroup species,Fagus sylvatica.Furthermore,resequencing and population analysis of Q.sichourensis and Q.rex reveal that Q.sichourensis has lower genetic diversity and higher deleterious mutations compared to Q.rex.The high-quality,chromosome-level genomes and the population genomic analysis of the critically endangered Q.sichourensis and Q.rex will provide an invaluable resource as well as insights for future study in these two species,even the genus Quercus,to facilitate their conservation.展开更多
In tea plants,the abundant flavonoid compounds are responsible for the health benefits for the human body and define the astringent flavor profile.While the downstream mechanisms of flavonoid biosynthesis have been ex...In tea plants,the abundant flavonoid compounds are responsible for the health benefits for the human body and define the astringent flavor profile.While the downstream mechanisms of flavonoid biosynthesis have been extensively studied,the role of chalcone synthase(CHS)in this secondary metabolic process in tea plants remains less clear.In this study,we compared the evolutionary profile of the flavonoid metabolism pathway and discovered that gene duplication of CHS occurred in tea plants.We identified three CsCHS genes,along with a CsCHS-like gene,as potential candidates for further functional investigation.Unlike the CsCHS-like gene,the CsCHS genes effectively restored flavonoid production in Arabidopsis chs-mutants.Additionally,CsCHS transgenic tobacco plants exhibited higher flavonoid compound accumulation compared to their wild-type counterparts.Most notably,our examination of promoter and gene expression levels for the selected CHS genes revealed distinct responses to UV-B stress in tea plants.Our findings suggest that environmental factors such as UV-B exposure could have been the key drivers behind the gene duplication events in CHS.展开更多
BACKGROUND Congenital enteric duplication cysts are tubular or cystic structures that normally lie alongside the gastrointestinal(GI)tract.Enteric duplication cysts are typically solitary lesions that occur anywhere n...BACKGROUND Congenital enteric duplication cysts are tubular or cystic structures that normally lie alongside the gastrointestinal(GI)tract.Enteric duplication cysts are typically solitary lesions that occur anywhere near the GI tract from the neck to the rectum,but having multiple duplication cysts is rare,and presentation within the pancreas is extremely rare.CASE SUMMARY We herein demonstrate a case of esophageal,gastric,and gastric-type duplication cyst of the pancreas in a seventeen-month-old girl who presented with failure to thrive,abdominal pain,vomiting,hematemesis,and melena since the age of three months.The cysts were excised by thoracoscopy and laparoscopy in the same setting.To our knowledge,no such case has been published.CONCLUSION Enteric duplications can occur throughout the entire alimentary tract.When they occur in the pancreas,they present a formidable challenge in both diagnosis and treatment.Due to the risk of complications and malignant transformation,surgical removal is the recommended treatment of all duplication cysts.展开更多
文摘The number of systematic reviews is gradually increas-ing over time. Also, the methods to perform a systematic review are being improved. However, little attention has been paid for the issue regarding how to fnd duplicates in systematic reviews. On the basis of the survey and systematic reviews by our team and others, we review the prevalence, significance and classification of duplicates and the method to fnd duplicates in a systematic review. Notably, although a preliminary method to fnd duplicates is established, its usefulness and convenience need to be further confrmed.
基金supported by the National Natural Science Foundation of China(71701207)the Science and Technology on Reliability&Environmental Engineering Laboratory(6142004004-2)the Science and Technology Commission of the CMC(2019-JCJQ-JJ-180)。
文摘The reliability evaluation of a multistate network is primarily based on d-minimal paths/cuts(d-MPs/d-MCs).However,being a nondeterminism polynomial hard(NP-hard)problem,searching for all d-MPs is a rather challenging task.In existing implicit enumeration algorithms based on minimal paths(MPs),duplicate d-MP candidates may be generated.An extra step is needed to locate and remove these duplicate d-MP candidates,which costs significant computational effort.This paper proposes an efficient method to prevent the generation of duplicate d-MP candidates for implicit enumeration algorithms for d-MPs.First,the mechanism of generating duplicate d-MP candidates in the implicit enumeration algorithms is discussed.Second,a direct and efficient avoiding-duplicates method is proposed.Third,an improved algorithm is developed,followed by complexity analysis and illustrative examples.Based on the computational experiments comparing with two existing algorithms,it is found that the proposed method can significantly improve the efficiency of generating d-MPs for a particular demand level d.
基金Supported by a research fund from Dankook University in 2024this research was supported by the Bio&Medical Technology Development Program of the National Research Foundation(NRF)funded by the Korean government(MSIT)(RS-2023-00220408).
文摘BACKGROUND Gastrointestinal duplication is a rare congenital anomaly of the digestive tract,with colonic manifestations being particularly uncommon.Malignant transformation of colonic duplication cysts is rare,with adenocarcinoma being the most frequently reported type.Herein,we report a rare case of adenocarcinoma originating from a colonic duplication cyst.CASE SUMMARY A 49-year-old woman was found to have an elevated cancer antigen 19-9 level during a routine checkup.Imaging revealed a well-defined abdominal cavity cystic mass,which was initially suspected to be an ovarian teratoma.Laparoscopic surgery revealed a duplication cyst,and pathological examination confirmed adenocarcinoma arising from the cyst.The mass within the transverse mesocolon was successfully excised by a colorectal surgeon.Immunohistochemical analysis confirmed adenocarcinoma with invasion into the muscularis propria.Postoperative endoscopy and positron emission computed tomography scan showed no signs of malignancy,except for an elevated cancer antigen 19-9 level.A multidisciplinary team recommended no further chemotherapy,advising routine follow-up for monitoring.CONCLUSION Colonic duplications,though rare,remain a differential diagnosis of unexplained abdominal masses,with complete resection being their primary treatment approach.
基金supported by the National Natural Science Foundation of China Project(Grant No.32260097)the National Guidance Foundation for Local Science and Technology Development of China(Grant No.[2023]009)the Natural Science Foundation for Distinguished Young Scholars of Hebei(Grant No.C2022209010)。
文摘Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.
基金supported by the National Natural Science Foundation of China(32360058)the Central Government Guides Local Science and Technology Development Projects,China(2023ZYZX1224)Xinjiang University Excellent Doctoral Student Innovation Project(XJU2022BS051)。
文摘The black wolfberry(Lycium ruthenicum;2n=2x=24)is an important medicinal plant with ecological and economic value.Its fruits have numerous beneficial pharmacological activities,especially those of anthocyanins,polysaccharides,and alkaloids,and have high nutritional value.However,the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms.In this study,we developed the telomere-to-telomere(T2T)nearly gapless genome of L.ruthenicum(2.26 Gb)by integrating PacBio HiFi,Nanopore Ultra-Long,and Hi-C technologies.The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated.Approximately 80%of the repetitive sequences were identified,of which long terminal repeats(LTRs)were the most abundant,accounting for 73.01%.The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species.The species-specific genes of L.ruthenicum were related to defense mechanisms,salt tolerance,drought resistance,and oxidative stress,further demonstrating their superior adaptability to arid environments.Based on the assembled genome and fruit transcriptome data,we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L.ruthenicum,most of which were highly expressed at a later stage in fruit development.Furthermore,154 potential disease resistance-related nucleotidebinding genes have been identified in the L.ruthenicum genome.The whole-genome and proximal,dispersed,and tandem duplication genes in the L.ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways.These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.
基金supported by grants from the National Natural Science Foundation of China(32100186)the Selfdetermined Project of the State Key Laboratory of Plant Diversity and Specialty Crops,Chinese Academy of Sciences,China(PDSC2023-5)+1 种基金the Special Research Assistant Project,Chinese Academy of Sciences(E2291M01)a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada.
文摘Heteranthery,the occurrence of functionally and structurally distinct stamens within a flower,represents a striking example of convergent evolution among diverse animal-pollinated lineages.Although the ecological basis of this somatic polymorphism is understood,the developmental and molecular mechanisms are largely unknown.To address this knowledge gap,we selected Monochoria elata(Pontederiaceae)as our study system due to its typical heterantherous floral structure.We constructed a chromosome-level genome assembly of M.elata,conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery.We focused on three key stamen characteristics—colour,spatial patterning,and filament elongation—selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species.Our analyses suggest that gene networks involving MelLEAFY3,MADS-box,and TCP genes regulate stamen identity,with anthocyanin influencing colour,and lignin contributing to filament elongation.Additionally,variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence.Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.
基金supported by the National Natural Science Foundation of China(32241044)Key project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(2060302)+2 种基金China Academy of Chinese Medical Sciences Innovation Fund(CI2023E002)Sichuan Province Natural Science Foundation of China(2022NSFSC1688)Guizhou Province Science and Technology Support Program of China(Qiankehezhongyindi[2024]006-1 and Qiankehezhicheng[2022]Yiban 105)。
文摘The flowering time is a key trait that determines adaptation,yield and quality of crops.Adlay,a traditional cereal crop,has developed a distinctive agricultural industry in Southwest China and Southeast Asian countries.However,the currently planted varieties are all semi-domesticated landraces with delayed flowering and excessive height.These defects limit yield improvement per unit area and mechanized harvesting.In this study,a major QTL associated with flowering time and plant height in adlay has been mapped and identified as Cl CCT,a gene having a conserved function and regulatory pathway for inhibiting flowering time and increasing plant height in gramineous crops.Among the six identified haplotypes of Cl CCT,the haplotype with 38-bp insertion in promoter region of Cl CCT has earlier flowering time and wider geographical distribution than other haplotypes.The insertion variation,which arises from the segmental duplication of Cl CCT,can inhibit the expression level of reporter gene and has been used in breeding for early maturity and dwarfing.These research results not only reinforce our understanding of the importance of CCT domain protein in the tropical crops adapting to high-latitude environment,but also provide a validated breeding target for the early maturity and dwarfing of adlay.
文摘BACKGROUND Duplicated gallbladder with two completely independent cystic ducts is an exceptionally rare congenital anomaly.This case report documents an example of successful laparoscopic management,adding to the limited literature by highlighting the importance of accurate preoperative imaging and surgical planning.CASE SUMMARY We present the case of a 46-year-old Uyghur woman who was admitted with intermittent right upper abdominal pain accompanied by nausea and vomiting that had persisted for 1 week.Her basic blood test results,including liver function test,were normal.Preoperative ultrasound revealed an abnormal echo in the gallbladder region,suggesting a double gallbladder malformation with one chamber containing multiple stones.Computed tomography and magnetic resonance cholangiopancreatography confirmed a double gallbladder anomaly.The patient subsequently underwent successful laparoscopic cholecystectomy.During the procedure,two gallbladder chambers were identified,with each cystic duct being independently inserted into the common bile duct.Surgery was completed without complications,and postoperative pathology confirmed the presence of gallstones and chronic cholecystitis.Because of the effective preoperative assessment,the patient recovered smoothly and was discharged 3 days after surgery,reporting no discomfort during follow-up.CONCLUSION This case highlights the need for thorough evaluation of rare gallbladder anomalies;literature recommends removing both to prevent disease recurrence.We present this case to raise clinical awareness,support appropriate diagnosis,and reinforce the recommendation to remove both gallbladders to prevent recurrence of gallbladder disease.
基金supported by the National Natural Science Foundation of China(31991210)the National Key Research and Development Program of China(2021YFD1200104)。
文摘Pigment accumulation is an important trait related to wheat domestication,but there remains a limited understanding of its molecular mechanism.The genetic control of the red glume trait by a dominant allele,Rg-B1,on 1BS was reported in the last century,but the underlying gene and its molecular basis remained elusive.Here,we identified TraesTSP1B01G005700(G57)encoding an R2R3-MYB transcription factor(TF)as the candidate Rg-B1 gene controlling red glume color by a combination of genome-wide association study(GWAS),bulked segregant RNA-sequencing(BSR-Seq),map-based cloning,and RNAseq.The Rg-B1 locus had zero to five duplicate copies only one of which had high transcriptional activity.Genetic evidence suggested that promoter sequence variation in G57 in the glume leads to high expression of G57,resulting in the red glume phenotype.G57 could bind to the promoters of anthocyanin synthesis genes TaCHS,TaF3'H,and TaUFGT,activating their expression and contributing to anthocyanin accumulation in wheat glume.G57 also played a pivotal role in up-regulating expression of genes TaDREB1C and TaFLO2 associated with increased grain weight,thereby causing increased grain weight.Our research offers a better understanding of the molecular basis of red glume in bread wheat.
文摘BACKGROUND Gastric duplication cysts(GDCs)are rare congenital anomalies,and consensus guidelines for their diagnosis and management are currently lacking.We report a rare case of a GDC in a female child presenting as a submucosal tumor in the gastric antrum.Subtotal resection was achieved using endoscopic submucosal dissection(ESD),resulting in complete symptom relief and pathological confirmation.This case demonstrates the therapeutic potential of ESD for intraluminal GDCs and underscores the importance of complete resection for definitive diagnosis.CASE SUMMARY A 12-year-old girl presented with abdominal distension and pain for>1 year.Gastroscopy revealed a protruding lesion approximately 30 mm in diameter in the gastric antrum.Superficial biopsies revealed moderate chronic inflammation and intestinal metaplasia.Contrast-enhanced computed tomography showed a mass protruding into the gastric lumen with homogeneous cyst wall enhancement.Endoscopic ultrasonography identified a hypoechoic mass originating from the muscularis mucosa.The patient underwent ESD for diagnosis and symptom relief.Intraoperatively,due to firm adhesion between the cyst base and the muscularis propria,selective preservation of the adherent cyst base was performed to mitigate perforation and stenosis risks.Histopathology confirmed a GDC,with cyst lumen lined by gastric-type columnar epithelium and an outer smooth muscle layer.Focal ectopic pancreatic tissues were identified.The patient recovered without complications and remained asymptomatic during 6-month follow-up.Repeat gastroscopy showed the residual cyst wall conforming to antral mucosa,with no recurrence.CONCLUSION Subtotal resection of GDCs using ESD demonstrates a favorable prognosis.
文摘Duplicate bug reporting is a critical problem in the software repositories’mining area.Duplicate bug reports can lead to redundant efforts,wasted resources,and delayed software releases.Thus,their accurate identification is essential for streamlining the bug triage process mining area.Several researchers have explored classical information retrieval,natural language processing,text and data mining,and machine learning approaches.The emergence of large language models(LLMs)(ChatGPT and Huggingface)has presented a new line of models for semantic textual similarity(STS).Although LLMs have shown remarkable advancements,there remains a need for longitudinal studies to determine whether performance improvements are due to the scale of the models or the unique embeddings they produce compared to classical encoding models.This study systematically investigates this issue by comparing classical word embedding techniques against LLM-based embeddings for duplicate bug detection.In this study,we have proposed an amalgamation of models to detect duplicate bug reports using textual and non-textual information about bug reports.The empirical evaluation has been performed on the open-source datasets and evaluated based on established metrics using the mean reciprocal rank(MRR),mean average precision(MAP),and recall rate.The experimental results have shown that combined LLMs can outperform(recall-rate@k 68%–74%)other individual=models for duplicate bug detection.These findings highlight the effectiveness of amalgamating multiple techniques in improving the duplicate bug report detection accuracy.
基金supported by the "Hundred Talents Program" of CAS and the National Natural Science Foundation of China under Grant No. 60772034.
文摘Detecting duplicates in data streams is an important problem that has a wide range of applications. In general, precisely detecting duplicates in an unbounded data stream is not feasible in most streaming scenarios, and, on the other hand, the elements in data streams are always time sensitive. These make it particular significant approximately detecting duplicates among newly arrived elements of a data stream within a fixed time frame. In this paper, we present a novel data structure, Decaying Bloom Filter （DBF）, as an extension of the Counting Bloom Filter, that effectively removes stale elements as new elements continuously arrive over sliding windows. On the DBF basis we present an efficient algorithm to approximately detect duplicates over sliding windows. Our algorithm may produce false positive errors, but not false negative errors as in many previous results. We analyze the time complexity and detection accuracy, and give a tight upper bound of false positive rate. For a given space G bits and sliding window size W, our algorithm has an amortized time complexity of O（√G/W）. Both analytical and experimental results on synthetic data demonstrate that our algorithm is superior in both execution time and detection accuracy to the previous results.
基金supported by the National Natural Science Foundation of China (82021001 and 31825018 to Q.S., 32370658 to Y.M.,82001372 to X.Y.)National Key Research and Development Program of China (2022YFF0710901)+2 种基金National Science and Technology Innovation2030 Major Program (2021ZD0200900) to Q.S.Shanghai Pujiang Program (22PJ1407300)Shanghai Jiao Tong University 2030 Initiative (WH510363001-7) to Y.M。
文摘Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.
基金“the Thousand Talents Plan”(5113190037 to J.C.)Fundamental Research Funds for the Central Universities(3102019JC007)+1 种基金Science and Technology Basic Resources Investigation Program of China(2017FY100100)NSFC(National Natural Science Foundation of China)-Yunnan Joint Fund(U1302262).
文摘The Fagaceae,a plant family with a wide distribution and diverse adaptability,has garnered significant interest as a subject of study in plant speciation and adaptation.Meanwhile,certain Fagaceae species are regarded as highly valuable wood resources due to the exceptional quality of their wood.In this study,we present two high-quality,chromosome-scale genome sequences for Quercus sichourensis(848.75 Mb)and Quercus rex(883.46 Mb).Comparative genomics analysis reveals that the difference in the number of plant disease resistance genes and the nonsynonymous and synonymous substitution ratio(Ka/Ks)of protein-coding genes among Fagaceae species are related to different environmental adaptations.Interestingly,most genes related to starch synthesis in the investigated Quercoideae species are located on a single chromosome,as compared to the outgroup species,Fagus sylvatica.Furthermore,resequencing and population analysis of Q.sichourensis and Q.rex reveal that Q.sichourensis has lower genetic diversity and higher deleterious mutations compared to Q.rex.The high-quality,chromosome-level genomes and the population genomic analysis of the critically endangered Q.sichourensis and Q.rex will provide an invaluable resource as well as insights for future study in these two species,even the genus Quercus,to facilitate their conservation.
基金supported by the National Natural Science Foundation of China(U21A20232,32372756,and 32202551).
文摘In tea plants,the abundant flavonoid compounds are responsible for the health benefits for the human body and define the astringent flavor profile.While the downstream mechanisms of flavonoid biosynthesis have been extensively studied,the role of chalcone synthase(CHS)in this secondary metabolic process in tea plants remains less clear.In this study,we compared the evolutionary profile of the flavonoid metabolism pathway and discovered that gene duplication of CHS occurred in tea plants.We identified three CsCHS genes,along with a CsCHS-like gene,as potential candidates for further functional investigation.Unlike the CsCHS-like gene,the CsCHS genes effectively restored flavonoid production in Arabidopsis chs-mutants.Additionally,CsCHS transgenic tobacco plants exhibited higher flavonoid compound accumulation compared to their wild-type counterparts.Most notably,our examination of promoter and gene expression levels for the selected CHS genes revealed distinct responses to UV-B stress in tea plants.Our findings suggest that environmental factors such as UV-B exposure could have been the key drivers behind the gene duplication events in CHS.
文摘BACKGROUND Congenital enteric duplication cysts are tubular or cystic structures that normally lie alongside the gastrointestinal(GI)tract.Enteric duplication cysts are typically solitary lesions that occur anywhere near the GI tract from the neck to the rectum,but having multiple duplication cysts is rare,and presentation within the pancreas is extremely rare.CASE SUMMARY We herein demonstrate a case of esophageal,gastric,and gastric-type duplication cyst of the pancreas in a seventeen-month-old girl who presented with failure to thrive,abdominal pain,vomiting,hematemesis,and melena since the age of three months.The cysts were excised by thoracoscopy and laparoscopy in the same setting.To our knowledge,no such case has been published.CONCLUSION Enteric duplications can occur throughout the entire alimentary tract.When they occur in the pancreas,they present a formidable challenge in both diagnosis and treatment.Due to the risk of complications and malignant transformation,surgical removal is the recommended treatment of all duplication cysts.
