Duplicates in systematic reviews: A critical, but often neglected issue

The number of systematic reviews is gradually increasing 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 find 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 find duplicates in a systematic review. Notably, although a preliminary method to find duplicates is established, its usefulness and convenience need to be further confirmed.

Search for d-MPs without duplicates in two-terminal multistate networks based on MPs

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.

Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

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.

Duplicated chalcone synthase(CHS)genes modulate flavonoid production in tea plants in response to light stress

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.

Multiple thoracic and abdominal foregut duplication cysts:A case report

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.

Comparative analysis of SIMILAR to RCD ONE(SRO)family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development

Background SRO(Similar to RCD1)genes family is largely recognized for their importance in the growth,develop-ment,and in responding to environmental stresses.However,genome-wide identification and functional characteri-zation of SRO genes from cotton species have not been reported so far.Results A total of 36 SRO genes were identified from four cotton species.Phylogenetic analysis divided these genes into three groups with distinct structure.Syntenic and chromosomal distribution analysis indicated uneven distribu-tion of GaSRO,GrSRO,GhSRO,and GbSRO genes on A2,D5 genomes,Gh-At,Gh-Dt,Gb-At,and Gb-Dt subgenomes,respectively.Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes.In promoter analysis,several elements responsive to the growth,development and hormones were found in GhSRO genes,implying gene induction during cotton growth and development.Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes.Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues.In addition,specific expression pattern of some GhSRO genes dur-ing ovule development depicted their involvement in these developmental processes.Conclusion The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.

Duplication of the Urethra in Boys: A Case Report

Supernumerary urethra in boys is a very rare anatomical entity. Sagittal urethral duplications are classified into four groups: epispadias, hypospadias, fusiform and Y-shaped urethra. The most widely used classification is that of Effmann and Lebowitz, which describes 6 types, one of the rarest being the ‘Y’ subtype IIA2, which corresponds to a duplicated urethral path from the vesical neck to an ectopic perineal or anal outlet. We report here the case of a 4-year-old child presenting with subtype IIA2 with a perineal orifice and no other urinary disorders.

Improved Approximate Detection of Duplicates for Data Streams Over Sliding Windows

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.

The updated weeping forsythia genome reveals the genomic basis for the evolution and the forsythin and forsythoside A biosynthesis

Weeping forsythia (Forsythia suspensa,Oleaceae) is a deciduous broad-leaved tree species distributed in the warm temperate zone of China.However,the species still lacks a chromosome-level genome.In this study,the former draft genome (Accession No.WIPI00000000) of weeping forsythia was assembled into 14 chromosomes with a 712.9 Mb genome size.Weeping forsythia underwent a and b whole-genome duplication events.After the divergence between weeping forsythia and Olea europaea,1 453 gene families had a significant expansion,and 1 146 gene families had a significant contraction.The enrichment pathways and ontologies of expanded genes suggested that the tillering,photosynthesis and growth capacity of weeping forsythia were enhanced after the divergence of weeping forsythia and O.europaea.The contracted genes suggested that the resistance of weeping forsythia to cold and drought was weakened.The last glacial period led to a significant decline in the effective population size of weeping forsythia.Forty-six candidate genes were identified for the synthesis of the forsythin and forsythoside A by genomic and transcriptomic data.In this study,we improved the previous draft genome of weeping forsythia.Our genome will provide genomic resources for the subsequent evolution and breeding research of weeping forsythia.

Detection of Copy-Move Forgery in Digital Images Using Singular Value Decomposition

This paper presents an improved approach for detecting copy-move forgery based on singular value decomposition(SVD).It is a block-based method where the image is scanned from left to right and top to down by a sliding window with a determined size.At each step,the SVD is determined.First,the diagonal matrix’s maximum value(norm)is selected(representing the scaling factor for SVD and a fixed value for each set of matrix elements even when rotating thematrix or scaled).Then,the similar norms are grouped,and each leading group is separated into many subgroups(elements of each subgroup are neighbors)according to 8-adjacency(the subgroups for each leading group must be far from others by a specific distance).After that,a weight is assigned for each subgroup to classify the image as forgery or not.Finally,the F1 score of the proposed system is measured,reaching 99.1%.This approach is robust against rotation,scaling,noisy images,and illumination variation.It is compared with other similarmethods and presents very promised results.

Comparative DNA-methylome and transcriptome analysis reveals heterosis-and polyploidy-associated epigenetic changes in rice

Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice lines.The hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid donors.The alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.

Comparative mitochondrial genome analysis of Cynoglossidae(Teleost:Pleuronectiformes)and phylogenetic implications

Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene arrangement.It is interesting,however,that four different types of gene arrangement have been found in the mitochondrial genome(mitogenome)of Cynoglossidae species.So far,the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of controversy.Here,a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes(Pleuronectiformes:Cynoglossidae)were compared.The length ranges from 16417 bp to 18369 bp,which is mainly caused by the length heteroplasmy of control region(CR).Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length heterogeneity.Like most gene rearrangements of Cynoglossinae mitogenomes,tRNA-Gln gene encoded by the L-strand has translocated to the H-strand(Q inversion),accompanied by the translocation of CR in C.puncticpes mitogenome.The typical IQM order(tRNA-Ile-Gln-Met)changed to QIM order.Tandem duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in C.puncticpes mitogenome.Phylogenetic trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny,which provides a fresh idea for phylogenetic studies in future.

Text duplication of papers in four medical related fields

Purpose:To reveal the typical features of text duplication in papers from four medical fields:basic medicine,health management,pharmacology and pharmacy,and public health and preventive medicine.To analyze the reasons for duplication and provide suggestions for the management of medical academic misconduct.Design/methodology/approach:In total,2,469 representative Chinese journal papers were included in our research,which were submitted by researchers in 2020 and 2021.A plagiarism check was carried out using the Academic Misconduct Literature Check System(AMLC).We generated a corrected similarity index based on the AMLC general similarity index for further analysis.We compared the similarity indices of papers in four medical fields and revealed their trends over time;differences in similarity index between review and research articles were also analyzed according to the different fields.Further analysis of 143 papers suspected of plagiarism was also performed from the perspective of sections containing duplication and according to the field of research.Findings:Papers in the field of pharmacology and pharmacy had the highest similarity index(8.67±5.92%),which was significantly higher than that in other fields,except health management.The similarity index of review articles(9.77±10.28%)was significantly higher than that of research articles(7.41±6.26%).In total,143 papers were suspected of plagiarism(5.80%)with similarity indices≥15%;most were papers on health management(78,54.55%),followed by public health and preventive medicine(38,26.58%);90.21%of the 143 papers had duplication in multiple sections,while only 9.79%had duplication in a single section.The distribution of sections with duplication varied among different fields;papers in pharmacology and pharmacy were more likely to have duplication in the data/methods and introduction/background sections,however,papers in health management were more likely to contain duplication in the introduction/background or results/discussion sections.Different structures for papers in different fields may have caused these differences.Research limitations:There were three limitations to our research.Firstly,we observed that a small number of papers have been checked early.It is unknown who conducted the plagiarism check as this can be included in other evaluations,such as applications for Science and technology projects or awards.If the authors carried out the check,text with high similarity indices may have been excluded before submission,meaning the similarity index in our research may have been lower than the original value.Secondly,there were only four medical fields included in our research.Additional analysis on a wider scale is required in the future.Thirdly,only a general similarity index was calculated in our study;other similarity indices were not tested.Practical implications:A comprehensive analysis of similarity indices in four medical fields was performed.We made several recommendations for the supervision of medical academic misconduct and the formation of criteria for defining suspected plagiarism for medical papers,as well as for the improved accuracy of text duplication checks.Originality/value:We quantified the differences between the AMLC general similarity index and the corrected index,described the situation around text duplication and plagiarism in papers from four medical fields,and revealed differences in similarity indices between different article types.We also revealed differences in the sections containing duplication for papers with suspected plagiarism among different fields.

An Automatic Threshold Selection Using ALO for Healthcare Duplicate Record Detection with Reciprocal Neuro-Fuzzy Inference System

ESystems based on EHRs(Electronic health records)have been in use for many years and their amplified realizations have been felt recently.They still have been pioneering collections of massive volumes of health data.Duplicate detections involve discovering records referring to the same practical components,indicating tasks,which are generally dependent on several input parameters that experts yield.Record linkage specifies the issue of finding identical records across various data sources.The similarity existing between two records is characterized based on domain-based similarity functions over different features.De-duplication of one dataset or the linkage of multiple data sets has become a highly significant operation in the data processing stages of different data mining programmes.The objective is to match all the records associated with the same entity.Various measures have been in use for representing the quality and complexity about data linkage algorithms,and many other novel metrics have been introduced.An outline of the problem existing in themeasurement of data linkage and de-duplication quality and complexity is presented.This article focuses on the reprocessing of health data that is horizontally divided among data custodians,with the purpose of custodians giving similar features to sets of patients.The first step in this technique is about an automatic selection of training examples with superior quality from the compared record pairs and the second step involves training the reciprocal neuro-fuzzy inference system(RANFIS)classifier.Using the Optimal Threshold classifier,it is presumed that there is information about the original match status for all compared record pairs(i.e.,Ant Lion Optimization),and therefore an optimal threshold can be computed based on the respective RANFIS.Febrl,Clinical Decision(CD),and Cork Open Research Archive(CORA)data repository help analyze the proposed method with evaluated benchmarks with current techniques.

Cecal duplication cyst in an infant presenting as shock:A case report

BACKGROUND Although intestinal obstruction is one of the most common surgical emergencies in an infant,it is difficult to diagnose neonatal enteric duplication cysts(EDC)preoperatively owing to their rarity as a cause of intestinal obstruction.We describe a case report of a neonatal EDC presenting intestinal obstruction and shock.CASE SUMMARY A 32-d-old male infant with a prenatal sonographic finding of bladder distension was admitted to our hospital for a severely distended abdomen,fever,and oliguria.The first diagnostic hypothesis was septic shock and intestinal obstruction.The patient’s symptoms worsened;following an emergency surgical exploratory laparotomy and histopathological findings,the final diagnosis of cecal duplication cyst was confirmed.The patient’s postoperative course was uneventful,and on the fifth postoperative day,oral feeding restarted.Twenty days later,the patient was discharged from the hospital.CONCLUSION Although EDC located in the cecum is exceptional,it should be considered when evaluating suspected intestinal obstruction and shock.

A case of duplicated inferior vena cava with bilateral iliac vein compression

Duplicated inferior vena cava with bilateral iliac vein compression is extremely rare.We report a case of an 87-year-old man presented with bilateral lower extremity swelling,who was noted to have duplicated inferior vena cava,as revealed by computed tomography angiography(CTA).This revealed bilateral iliac vein compression caused by surrounding structures.Anticoagulant treatment combined with stent implantation completely alleviated this chronic debilitating condition during the follow-up of 2 months with no recurrence.

New treatment for gastric duplication cyst:Endoscopic ultrasonography-guided fine-needle aspiration combined with lauromacrogol sclerotherapy:A case report

BACKGROUND Gastric duplication cysts are very rare disease that are mainly diagnosed by endoscopic ultrasonographic fine-needle aspiration biopsy.In the past,this disease was usually treated with traditional surgery and rarely with minimally invasive endoscopic surgery.However,minimally invasive endoscopic therapy has many advantages,such as no skin wound,organ preservation,postoperative pain reduction,early food intake,fewer postoperative complications,and shorter post-procedure hospitalization.CASE SUMMARY We report a case of endoscopic ultrasonography-guided fine-needle aspiration(EUS-FNA)combined with lauromacrogol sclerotherapy for pyloric obstruction due to gastric duplication cysts.CONCLUSION EUS-FNA combined with lauromacrogol sclerotherapy provides a new option for the treatment of gastrointestinal duplication cysts.

Methyl-CpG-Binding protein 2 duplication syndrome in a Chinese patient:A case report and review of the literature

BACKGROUND Chromosomal Xq28 region duplication encompassing methyl-CpG-binding protein 2(MECP2)results in an identifiable phenotype and global developmental delay known as MECP2 duplication syndrome(MDS).This syndrome has a wide range of clinical manifestations,including abnormalities in appearance,neurodevelopment,and gastrointestinal motility;recurrent infections;and spasticity.Here,we report a case of confirmed MDS at our institution.CASE SUMMARY A 12-year-old Chinese boy presented with intellectual disability(poor intellectual[reasoning,judgment,abstract thinking,and learning]and adaptive[lack of communication and absent social skills,apraxia,and ataxia]functioning)and dysmorphism.He had no history of recurrent infections,seizures,or bowel dysfunction,which is different from that in reported cases.Microarray comparative genomic hybridization confirmed MECP2 duplication in the patient and his mother who is a carrier.The duplication size was the same in the patient and his mother.No prophylactic antibiotic or anti-seizure therapy was offered to the patient or his mother before or after the consultation.CONCLUSION MDS is rare and has various clinical presentations.Clinical suspicion is critical in patients presenting with developmental delays.

Confusing finding of quantitative fluorescent polymerase chain reaction analysis in invasive prenatal genetic diagnosis:A case report

BACKGROUND Quantitative fluorescent polymerase chain reaction(QF-PCR)is a rapid prenatal diagnostic method for abnormalities on chromosomes 21,18,and 13 and sex chromosomal aneuploidy.However,the value of QF-PCR in diagnosing chromosomal structural abnormalities is limited.In this article,we report a confusing QF-PCR finding in a pregnant woman who underwent amniocentesis.CASE SUMMARY The short tandem repeat marker AMXY(Xp22.2/Yp11.2)located on the sex chromosome exhibited a trisomic biallelic pattern,indicating that the karyotype of the fetus might be 47,XYY.Chromosome analysis performed on cultured amniocytes showed a normal male karyotype of the fetus.Copy number variation sequencing confirmed a 500 kb duplication at Yp11.2-Yp11.2(chrY:6610001_7110000)and a 250 kb duplication at Yp11.2-Yp11.2(chrY:7110001_7360000).CONCLUSION In conclusion,the comprehensive application of different methods could achieve a higher detection rate and accuracy for the prenatal diagnosis of chromosomal disorders through chromosomal testing.

Complete Ureteral Duplicity Complicated by Lithiasis with Right Ureterohydronephrosis with Left Renal Excretion Defect: Apropos of a Clinical Case

Ureteral duplication is a congenital malformative uropathy that occurs most often in children. Complete ureteral duplication is defined by a kidney that has two ureters with two orifices that communicate to the bladder through two ureteral meati. It is an anatomical variant that remains rare. Its early discovery is due to a lack of diagnostic means, hence the occurrence of long-term complications. To this end, we observe an increased importance of the morbidity linked to the late diagnosis of this duplicity. Our objective was to show the importance of the morbidity linked to the late diagnosis of this anomaly, the incidence of the infection and the complications that this pathology poses as a problem. It was a clinical case of fortuitous discovery taken care of by a general surgeon in the general surgery department of the hospital “Mother Child” Le Luxembourg Bamako Mali. We report a case of complete ureteral duplication complicated by ureterohydronephrosis on a lithiasis wedged in the uretero-vesical junction of one of the left ureters in its lower portion which required a uretero-lithotomy with bladder reimplantation of the left ureters and secondly to a uretero-lithotomy with bladder reimplantation after two months. The postoperative course was simple.