A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/without login requirements.

An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK+ support. It displays two-dimensional (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK+package is freely available.

We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the compar-ison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.

Objective:To investigate the similarities and differences of chondrolaryngoplasty between female and male-to-female transgender patients.Methods:A retrospective analysis focused on the case with chondrolaryngoplasty in Peking University Third Hospital from March 2016 to September 2019.Patients were followed up an average 14mths with an eleven-point Likert scale. We assigned patients into a female ( n=11) and transgender women( n=12) groups, using SPSS 22.0 tool to process and analyze data. The paired sample t test is conducted to compare pre-and postoperative differences, while independent sample t test is to compare between groups; a P-value less than 0.05 is considered to have statistical significance. Results:A total of 23 patients were enrolled, including 11 female patients and 12 transgender patients, aged 18 to 37 years old (mean 26.87±5.54 years old). Satisfaction with surgery is 95.65% (22/23 patients), satisfaction with the appearance of laryngeal prominence is 82.61% (19/23 patients). After the operation, the Self-Estimate Laryngeal Prominence Score improves from 6.57±2.45 to 2.22±2.09, the Social Ability Restriction Score improves from 6.30±3.02 to 1.52±2.54, the Phycological Burden Score decrease from 7.70±2.44 to 1.83±2.62, all data have statistical significances ( P<0.01). The improvement value of the previous two scores is greater than the transgender women group with statistical significances ( P<0.05). Conclusions:Chondrolaryngoplasty can remarkably improve the appearance of laryngeal prominence of patients. Transgenders women can obtain better social and phycological improvement than female patients after chondrolaryngoplasty.

Objective:To investigate the similarities and differences of chondrolaryngoplasty between female and male-to-female transgender patients.Methods:A retrospective analysis focused on the case with chondrolaryngoplasty in Peking University Third Hospital from March 2016 to September 2019.Patients were followed up an average 14mths with an eleven-point Likert scale. We assigned patients into a female ( n=11) and transgender women( n=12) groups, using SPSS 22.0 tool to process and analyze data. The paired sample t test is conducted to compare pre-and postoperative differences, while independent sample t test is to compare between groups; a P-value less than 0.05 is considered to have statistical significance. Results:A total of 23 patients were enrolled, including 11 female patients and 12 transgender patients, aged 18 to 37 years old (mean 26.87±5.54 years old). Satisfaction with surgery is 95.65% (22/23 patients), satisfaction with the appearance of laryngeal prominence is 82.61% (19/23 patients). After the operation, the Self-Estimate Laryngeal Prominence Score improves from 6.57±2.45 to 2.22±2.09, the Social Ability Restriction Score improves from 6.30±3.02 to 1.52±2.54, the Phycological Burden Score decrease from 7.70±2.44 to 1.83±2.62, all data have statistical significances ( P<0.01). The improvement value of the previous two scores is greater than the transgender women group with statistical significances ( P<0.05). Conclusions:Chondrolaryngoplasty can remarkably improve the appearance of laryngeal prominence of patients. Transgenders women can obtain better social and phycological improvement than female patients after chondrolaryngoplasty.

Objective:To prove the effect of double V-Y procedure for paramedian tubercles plasty in patients with thin lower lips and dissatisfied appearance of lower lips.Methods:From 2013 to 2019, 127 Chinese cases of thin and dissatisfied appearance of lower lips were included. A double V-Y procedure for paramedian tubercles plasty was performed. Objective data of lip morphology before and after operation were measured, and subjective satisfaction survey and long-term follow-up were conducted.Results:The midline lower red lip height, the height of paramedian tubercles of lower-lip and the protrusion of lower-lip were significantly higher than that before the operation. The time of apocatastasis, scar softening of incision, natural expression recovery and local numbness relief were evaluated by following up at 7 d, and 3-24 months after operation, and it showed 73.2% of subjective satisfaction. The time of detumescence was 6-32 (15.2±3.5) days; the time of incision scar softening was 2-10 (5.1±2.3) months; the time of expression recovery was 1-7 (3.1±0.9) months; the time of numbness disappearance was 5 d-2 years (158.2±82.6) days.Conclusions:The double V-Y advancement of vermilion mucosa flap procedure for paramedian tubercles plasty displays a significant effect in improving volume and shape of lower lips. It is recommended for further clinical application.

Objective:To observe and evaluate reductional M-shaped plasty method in patients with thick lips and dissatisfied lip appearance.Methods:From 2013 to 2019, 415 Chinese cases of thick upperlip without clear vermilion curve and tubercle were included. A reduction method for upper lip M-shaped plasty was performed. Objective data of lip morphology before and after operation were measured, and subjective satisfaction survey and long-term follow-up were conducted.Results:According to the statistics of 415 patients, the time of detumescence was 3-21 (11.8±2.6) days; the time of incision scar softening was 1-24 (2.6±0.8) months; the time of expression recovery was 1-24 (3.1±1.4) months; the time of numbness disappearance was 1-2 years. Three months after the operation, there was no significant change in the height of the central part of the upper red lip compared with that before the operation, the height of the red lip at the peak of the lip was significantly reduced, the height of the red lip was (13.3±2.2) mm before the operation, and (11.4±1.7) mm after the operation; the relative height of the dome point was significantly increased, the height was (0.4±1.0) mm before the operation, and the height was (2.1±0.5) mm after the operation. After more than 6 months of follow-up, patients' satisfaction rate of one operation was 72.0%, the satisfactory rate of upper lip shape was 75.4%, the long-term complications included obvious scars or discomfort (3.6%), local numbness (1.7%), and unnatural expression (0.7%).Conclusions:The reduction method for upper lip M-shaped plasty displays a significant effect in improving the shape of upper vermilion with thick and normal lips. The complications are slight and repairable. This lip cosmetology and rejuvenation procedure is recommended for further clinical application.

Composition vector trees(CVTrees)are inferred from whole-genome data by an alignment-free and parameter-free method.The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny.In this work,we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach.Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach.Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
Genome ; Genomics ; Phylogeny ; RNA, Ribosomal, 16S ; genetics ; Sequence Analysis, DNA

Objective: To summarize and update the terminology of the lip and perioral morphological aesthetic subunits and aesthetic landmarks in the domestic medical aesthetics field. Methods: 36 English literatures, 13 Chinese literatures, 3 foreign academic compositions, 2 domestic academic compositions, 1 domestic medical aesthetics textbook, and 14 websites of the medical aesthetic field have been included. We summarized the commonly seen terminology of the lip and perioral morphological aesthetic subunits and aesthetic landmarks. Moreover, for the aesthetic subunits and aesthetic landmarks which are commonly used in clinical practice but have not yet been named in Chinese term are named following the current Chinese terminology rule. We summarized not only the terminology of lips but also the anatomical acknowledge of the commonly used aesthetic subunits. Results: There are 17 standard nomenclatures for aesthetic subunits, 8 standard nomenclatures with abbreviations for aesthetic surface landmarks, 20 standard terms for aesthetic measurement and distance. Moreover, we named 5 aesthetic subunits and 6 aesthetic surface landmarks for which there are no standard Chinese medical terms. Conclusions The standard terminology for the aesthetic subunits and landmarks is the foundation for the lip and perioral measurement and evaluation. Besides, it also provides a reference basis for the development of lip cosmetic and perioral rejuvenation treatment programs.