PeerJ最新文献

{"title":"Spontaneous space closure after extraction of young first permanent molar. Retrospective cohort study.","authors":"Heba Jafar Sabbagh, Ahmad Adnan Samara, Shoroog Hassan Agou, Jihan Turkistani, Manal Ibrahim Al Malik, Hadeel Abdulatief Alotaibi, Abrar Shimi Dhaifallah Alsolami, Nada Othman Bamashmous","doi":"10.7717/peerj.18276","DOIUrl":"10.7717/peerj.18276","url":null,"abstract":"<p><strong>Background: </strong>Early compromised first-permanent-molar (FPM) extraction can adversely affect occlusion. However, the current literature does not provide sufficient support for definitive early extraction outcome. This cohort study aimed to evaluate the pattern of post-FPM extraction spontaneous space closure and its pre-extraction indicators.</p><p><strong>Methods: </strong>Patients of 7-13 years, with compromised FPM at three-tertiary-centers between 2015 and 2019 were retrospectively screened. Pre-extraction indicators were evaluated (extraction location, direction of the second permanent molar (SPM) long-axis, and SPM Demirjian development stage). Spontaneous space closure pattern was evaluated clinically and radiographically using the American Board of Orthodontics (ABO) grading system.</p><p><strong>Results: </strong>In total, 112 FPMs (73-patients) were identified and five (4.5%) of the extraction sites showed favorable combined-ABO-scores. Distal direction of the SPM long-axis in the maxillary arch significantly decreased the relative risk (RR) of having a SPM rotation/alignment ABO score-1 (<i>P</i> = 0.002; RR = 0.64). For the mandibular arch, Demirjian stage D and E significantly decreased the RR of having ABO score-1 for spacing between the SPMs and second premolars (<i>P</i> = 0.029; RR:0.57, <i>P</i> = 0.004; RR:0.53, respectively) and vertical dimension (<i>P</i> = 0.02; RR = 0.53).</p><p><strong>Conclusions: </strong>The direction of the SPM long-axis and its developmental stage are key indicators of the favorable outcome pattern of spontaneous space closure after FPM early extraction.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11512553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association between plain ropivacaine dose and spinal hypotension for cesarean delivery: a retrospective study.","authors":"Min Li, Guohao Xie, Lihua Chu, Xiangming Fang","doi":"10.7717/peerj.18398","DOIUrl":"10.7717/peerj.18398","url":null,"abstract":"<p><strong>Background: </strong>Data on the association between the plain ropivacaine dose and maternal hypotension during cesarean delivery are limited. Thus, this study aimed to explore this association.</p><p><strong>Methods: </strong>This retrospective study included patients undergoing cesarean sections under spinal or combined spinal-epidural anesthesia with plain ropivacaine at The First Hospital of Fuyang, Hangzhou, China, between 2018 and 2022. Data were obtained from the anesthesia information management system. Liner trend tests were used to distinguish the linear relationship between spinal hypotension and the plain ropivacaine dose, and receiver operating characteristic curves were used to calculate the dose threshold. Logistic regression was used to adjust for confounders. Sensitivity analyses were performed to evaluate the stability of the results. The secondary outcome was vasopressor use (metaraminol and ephedrine).</p><p><strong>Results: </strong>In total, 1,219 women were included. The incidence of hypotension linearly correlated with the plain ropivacaine dose (adjusted <i>P</i>-value for trend, <i>P</i> < 0.001). Thus, we used a dose threshold of 17.5 mg to compare the dose as a binary variable (≥17.5 mg <i>vs.</i> < 17.5 mg). Plain ropivacaine doses of ≥17.5 mg were associated with a higher incidence of spinal hypotension (adjusted odds ratio: 2.71; 95% confidence interval [1.85-3.95]; <i>P</i> < 0.001). The sensitivity analyses yielded similar results. The plain ropivacaine dose also correlated with metaraminol use but not ephedrine use.</p><p><strong>Conclusions: </strong>The incidence of spinal-induced hypotension in women undergoing cesarean section linearly correlated with the plain ropivacaine dose. The dose threshold for hypotension risk was 17.5 mg.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11512552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface-functionalized PAN fiber membranes for the sensitive detection of airborne specific markers.","authors":"Leontyna Varvarovska, Bruno Sopko, Dana Gaskova, Tomas Bartl, Evzen Amler, Tatana Jarosikova","doi":"10.7717/peerj.18077","DOIUrl":"10.7717/peerj.18077","url":null,"abstract":"<p><p>PAN fibers are characterized by having a large surface-to-volume ratio and small pores, which are beneficial for applications in filtration and specific molecular detection systems. Naturally, larger items are filtered, and a lower ratio between specific and nonspecific binding is expected since small pores do not allow larger elements to penetrate through membranes; thus, nonspecific binding is enhanced. We prepared and tested fiber membranes (diameter cca 700 nm) functionalized with a specific antibody to prove that even microscopic systems such as bacteria could be specifically identified. In addition, we established a methodology that enabled the effective binding of bacteria in not only an aqueous environment but also air. Our data clearly prove that even large systems such as bacteria could be specifically identified by fiber membranes surface-functionalized with a specific antibody. This research opens the door to the construction of biosensors for the fast, inexpensive, and sensitive identification of airborne bacterial contaminants and other airborne pollutants.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11512550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecological and taxonomic dissimilarity in species and higher taxa of reptiles in western Mexico.","authors":"Jaime Manuel Calderón-Patrón, Jorge Téllez-López, Eréndira Canales-Gómez, Karen Elizabeth Peña-Joya","doi":"10.7717/peerj.18343","DOIUrl":"10.7717/peerj.18343","url":null,"abstract":"<p><p>Reptiles are one of the most diverse groups of vertebrates in the world that are distributed in almost all ecosystems. Many of these studies have focused on exploring their diversity patterns across different environments; and recent studies on reptile alpha and beta diversity have incorporated a multifaceted approach into their analysis to have more comprehensive evaluations. This study presents an assessment of the taxonomic diversity of reptile patterns using methods that incorporate the assessment of higher taxa. Likewise, the taxonomic dissimilarities between reptile communities in the physiographic regions of the state of Jalisco were analyzed. Evaluations for the groups of snakes and lizards independently are presented. We use the taxonomic distinctiveness index that assesses the complexity of the taxonomic structure of communities through hierarchical classification above the species level to measure the relationships between taxa. The dissimilarity of the taxonomic structure in each community was also analyzed. Beta diversity partitions were performed to identify the contribution of turnover and the differences in richness. We determined that alpha diversity of species and higher taxa maintain different patterns, indicating that Jalisco presents regions with overrepresentation of reptile families and genera, as well as regions with an opposite trend. The representation of higher taxa is higher in the lizard group, although in terms of species richness snakes are the most prominent group. The turnover is the most important component at species and higher taxa, with similar values for lizards and snakes. The findings presented show that incorporating phylogenetic information about species through taxonomic relationships provides complementary information that species diversity <i>per se</i>, especially at the level of alpha diversity.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying a <i>cis-element</i> in PtoCP1 promoter for efficiently controlling constitutive gene expression in <i>Populus tomentosa</i>.","authors":"Yu Peng, Xueqin Guo, Yawei Fan, Han Liu, Leiqian Sun, Di Liu, Hui Li, Xin Wang, Hongli Guo, Hai Lu","doi":"10.7717/peerj.18292","DOIUrl":"10.7717/peerj.18292","url":null,"abstract":"<p><p>Gene expression is regulated by transcription factors binding to <i>cis-elements</i> in promoters. However, efficient <i>cis-elements</i> for genetic engineering are rarely reported. In this study, we identified an 11 bp <i>cis-element</i> in the PtoCP1 promoter that drives strong constitutive gene expression in <i>Populus tomentosa</i>. A 2,270 bp promoter region upstream of the <i>PtoCP1</i> gene's translation start site was cloned and named ProPtoCP1. This promoter controls GUS reporter gene expression in the roots, leaves, and stems of <i>Arabidopsis</i> seedlings. Based on the location and density of <i>cis-elements</i>, the PtoCP1 promoter was divided into four fragments by 5'-end deletions. GUS staining and RT-qPCR revealed a key <i>cis-element</i> at -466 to -441 bp essential for gene expression. Further analysis showed that the MYB-TGACG <i>cis-element</i> is a positive regulator, whereas neither MYB nor TGACG alone drove gene expression. This study enhances our understanding of gene expression regulation by <i>cis-elements</i> and provides a valuable tool for genetic engineering.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Muscle synergies during the walk-run and run-walk transitions.","authors":"Leonardo Lagos-Hausheer, Samuel Vergara, Victor Munoz-Martel, Germán Pequera, Renata L Bona, Carlo M Biancardi","doi":"10.7717/peerj.18162","DOIUrl":"10.7717/peerj.18162","url":null,"abstract":"<p><strong>Background: </strong>Muscular synergies could represent the patterns of muscular activation used by the central nervous system (CNS) to simplify the production of movement. Studies in walking-running transitions described up to nine synergy modules, and an earlier activation of flexor and extension ankle muscular groups compared to running or walking. Our project aims to study the behaviour of muscle synergies in different stance and swing variations of walking-running (WRT) and running-walking (RWT) transitions.</p><p><strong>Methods: </strong>Twenty-four trained men participated in this study. A variable speed protocol on a treadmill was developed to record the activity of 14 muscle during walking, running and relative transitions. The protocol was based on five ramps of 50 seconds each around ± 10 and 20% of the WRT speed. WRT and RWT were identified according to an abrupt change of the duty factor. Analysing surface electromyography using non-negative matrix factorization (NMF) we obtained synergy modules and temporal activation profiles. Alpha threshold for statistical tests set at 0.05.</p><p><strong>Results: </strong>We described four different transition strides, two for increasing speed transitions, and two for decreasing speed transitions. Four to six synergy modules were found in each condition. According to the maximum cosine similarity results, the two identified WRT conditions shared five modules, while the two RWT conditions shared four modules. WRT and RWT overall shared 4.33 ± 0.58 modules. The activation profiles and centres of activation revealed differences among conditions.</p><p><strong>Discussion: </strong>Transition occurred at step level, and transition strides were composed by walk-like and run-like steps. Compared with previous studies in running and walking, both transitions needed earlier activation of a comparable number of synergy modules. Synergies were affected by acceleration: during RWT the need to dissipate energy, to decrease the speed, was achieved by increasing the number of co-activating muscles. This was reflected in fewer synergy modules and different activation profiles compared to WRT. We believe that our results could be enforced in different applied fields, like clinical gait analysis, physiotherapy and rehabilitation, where plans including co-activation of specific muscular groups could be useful. Gait transitions are common in different sports, and therefore also application in training and sport science would be possible.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mitochondrial genome sequences of eleven leafhopper species of <i>Batracomorphus</i> (Hemiptera: Cicadellidae: Iassinae) reveal new gene rearrangements and phylogenetic implications.","authors":"Jikai Lu, Jiajia Wang, Renhuai Dai, Xianyi Wang","doi":"10.7717/peerj.18352","DOIUrl":"10.7717/peerj.18352","url":null,"abstract":"<p><p><i>Batracomorphus</i> is the most diverse and widely distributed genus of Iassinae. Nevertheless, there has been no systematic analysis of the genome structure and phylogenetic relationships of the genus. To determine the characteristics of the mitogenomes of <i>Batracomorphus</i> species as well as the phylogenetic relationships between them, we sequenced and compared the mitogenomes of 11 representative <i>Batracomorphus</i> species. The results revealed that the mitogenomes of the 11 <i>Batracomorphus</i> species exhibited highly similar gene and nucleotide composition, and codon usage compared with other reported mitogenomes of Iassinae. Of these 11 species, we found that the mitogenomes of four species were rearranged in the region from <i>trnI</i>-<i>trnQ</i>-<i>trnM</i> to <i>trnQ</i>-<i>trnI</i>-<i>trnM</i>, whereas the remaining species presented a typical gene order. The topologies of six phylogenetic trees were in agreement. Eurymelinae consistently formed paraphyletic groups. Ledrinae and Evacanthinae formed sister taxa within the same clade. Similarly, Typhlocybinae and Mileewinae consistently clustered together. All phylogenetic trees supported the monophyly of Iassinae, indicating its evolutionary distinctiveness while also revealing its sister relationship with Coelidiinae. Notably, the nodes for all species of the genus <i>Batracomorphus</i> were well supported and these taxa clustered into a large branch that indicated monophyly. Within this large branch, four <i>Batracomorphus</i> species with a gene rearrangement (<i>trnQ</i>-<i>trnI</i>-<i>trnM</i>) exhibited distinctive clustering, which divided the large branch into three minor branches. These findings expand our understanding of the taxonomy, evolution, genetics, and systematics of the genus <i>Batracomorphus</i> and broader Iassinae groups.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatiotemporal gait characteristics post-total hip arthroplasty and its impact on locomotive syndrome: a before-after comparative study in hip osteoarthritis patients.","authors":"Shigeaki Miyazaki, Yoshinori Fujii, Kurumi Tsuruta, Saori Yoshinaga, Amy Hombu, Taro Funamoto, Takero Sakamoto, Takuya Tajima, Hideki Arakawa, Tsubasa Kawaguchi, Jun Nakatake, Etsuo Chosa","doi":"10.7717/peerj.18351","DOIUrl":"10.7717/peerj.18351","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Understanding the gait pattern of patients eligible for total hip arthroplasty (THA) due to hip osteoarthritis (OA) offers valuable information for improving locomotive syndrome (LS). This study aims to measure the gait patterns of THA-eligible patients using an optical motion capture system and to analyze these patterns using principal component analysis (PCA). Additionally, this study examines the relationship between THA-induced gait patterns and LS.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;This before-after study included 237 patients who underwent unilateral primary THA due to hip OA. The primary outcome measures were spatiotemporal gait parameters. Secondary outcome measures included three LS risk tests: a stand-up test, a two-step test, a 25-question Geriatric Locomotive Function Scale (GLFS-25), and total clinical decision limits stages. PCA was performed using 16 spatiotemporal gait parameters collected before and three months after THA. Principal components (PC) were selected to achieve a cumulative contribution rate of 90% (0.9) or higher. Each summarized PC was compared using a paired &lt;i&gt;t&lt;/i&gt;-test before and three months after THA. Furthermore, multiple regression analysis was conducted to determine how changes in each PC between before and three months after THA related to changes in the four LS evaluation items.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;PCA identified three principal components (PC1, PC2, PC3) that accounted for a cumulative contribution rate of 0.910 using 16 spatiotemporal gait parameters. When comparing before and three months after THA for all three PCs, significant differences were observed in each PC (&lt;i&gt;p&lt;/i&gt; &lt; 0.001), with overall walking ability and stance phase being higher three months after THA than before THA, while the asymmetry of support time was lower three months after THA. The results of multiple regression analysis revealed that PC1, PC2, and PC3 were the most influential factors in total clinical decision limits stage. For each LS risk test, the factors related to the stand-up test were identified as PC1, PC2, and PC3, while the factors related to the two-step test were identified as PC1 and PC2. The factors related to the GLFS-25 were also identified as PC1 and PC2.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;The most important findings of this study indicate that the three PCs represent over 90% of the 16 spatiotemporal gait parameters, which are associated with total clinical decision limits stage and LS risk tests. The present results suggest that PC1 represents overall walking ability, PC2 represents the stance phase, and PC3 represents asymmetry of support time. Gait pattern characteristics, such as overall walking ability, stance phase, and asymmetry of support time, were clearly defined by these PCs. Regarding the relationship between PC and LS, all three PCs are related to total clinical decision limits stage. In addition, PC1 and PC2 related to all three LS risk tests, and PC3 re","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A classification system for identifying persons with an unknown cardiovascular disease (CVD) status for a multiracial/ ethnic Caribbean population.","authors":"Amalia Hosein, Valerie Stoute, Natasha Singh","doi":"10.7717/peerj.17948","DOIUrl":"10.7717/peerj.17948","url":null,"abstract":"<p><strong>Background: </strong>The need for classification systems for cardiovascular disease (CVD) that is population-specific is important towards understanding the clinical disease and diagnostics associated with the disease. This paper presents the form and validation results of this classification system.</p><p><strong>Method: </strong>The survey data used was captured from 778 participants, 526 persons with no prior CVD, and 252 who reported prior CVD. Binomial logistic regression and Discriminant analysis were utilised to develop classification models. This classification system provided a general measure of severity of disease by utilising scores estimated from two algorithms developed from 13 routine physiologic measurements, along with demographic information of age and ethnicity, <i>inter alia</i>, and previous health status.</p><p><strong>Results: </strong>For each model, specific score ranges were identified, which gave the best classification for those with a prior CVD incident (higher scores) and for others labelled as non-CVD (lower scores). The two classification models (Logistic Regression Model and Discriminant Analysis Model) developed had high area under the receiver-operating characteristic (AUROC) values (98% & 99%) and sensitivity (86 and 90%), which improved discrimination between Non-CVD and CVD participants and, more importantly, correctly classified a greater proportion of CVD participants. New to this type of research was the estimation and detailed evaluation of a range of scores, labelled non-differentiating, which fell in the middle of the spectrum and which contained the higher-end scores for the non-CVD individuals and the lower-end scores for CVD patients, all of whom were incorrectly classified, based on their prior history.</p><p><strong>Conclusion: </strong>The classification system of scores is able to differentiate the CVD status of individuals, with good predictability, and could assist physicians with recommending different treatment plans. The two models in this classification system each individually outperformed the three established models in terms of the strength of their correct classifications of individuals with or without prior reported CVD incidents. More importantly, they have smaller non-differentiating ranges than the three known models and, in that range, the two new models have lower CVD/non-CVD ratios suggesting they are more likely to misclassify non-CVD individuals compared to CVD patients, which is a more benign misclassification. Further, when used in combination, the two models increased the sensitivity, in classifying individuals of different ethnicities, beyond that of either one used independently or of any of the three standard European/North American models. These efforts will be instrumental in advancing personalised CVD management strategies and improving health outcomes across diverse populations.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Python program to merge Sanger sequences: an update.","authors":"Shiming Lin, Bifang Huang, Li-Li Zhao, Fei Xu, Danni Pan, Xuanyang Chen, Shiqiang Lin","doi":"10.7717/peerj.18363","DOIUrl":"10.7717/peerj.18363","url":null,"abstract":"<p><p>Gene cloning is an important step in investigating gene structure and function. To verify gene sequence, Sanger sequencing is used, which may produce several overlapping sequencing files that need to be merged before alignment to the target gene sequence is performed. Previously, we reported the Python program to Merge Sanger sequences (https://peerj.com/articles/11354/), which ran in command line and relied heavily on EMBOSS suite. In this updated version of the program, we have made several remarkable improvements. It provides a graphical user interface (GUI) written with tkinter, which is convenient and stable. It does not require users to rename the input sequences before performing merging. With regard to the implementation, the updated version utilizes Python function (Align.PairwiseAligner) to align adjacent sequences, which is more flexible (can adjust program parameter <i>i.e.</i>, the number of first-time consecutive matching bases). The new version of the program makes merging Sanger sequences much more convenient and facilitates gene study.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142505375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}