Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs-paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.].

Extensive Defect Reconstruction With Pre-expanded Anterolateral Thigh Flap: Tissue Expansion of the "Outskirts".

BACKGROUND: Previously reported pre-expansion techniques of the anterolateral thigh flap are mainly perforator-based. The expansion will interfere with the flap harvest if the requisite perforator is found unsuitable as a pedicle. Expansion of the peripheral territories of the flap donor site can minimize the interference from the expansion. METHODS: Forty-eight peripheral pre-expansions of the anterolateral thigh flap were retrospectively reviewed in 38 patients from 2012 to 2021. The reconstructive outcomes, including flap success, increase in flap size, donor-site closure, and complications, were assessed. In addition, subgroup analysis was performed based on the expanded territories. RESULTS: Rate of successful flap elevation of 100% and flap survival rate of 97.9% were achieved. One patient had total flap necrosis, which was salvaged with skin grafting. Peripheral expansion attained a mean 55.5% ± 19.6% increase in flap width. Primary donor-site closure was accomplished in 95.8% of flaps and fascial restoration in 97.9% of the donor sites. Three patients developed major expansion-related complications, which required surgical intervention. One patient had wound dehiscence in the donor site, which healed by secondary intention. Compared with other subgroups, the lateral-and-medial-side expansion provided a larger flap for reconstruction (P = 0.001). CONCLUSIONS: If time is not of the essence, peripheral pre-expansion permits direct donor-site closure with size augment of the anterolateral thigh flap. In addition, it preserves the reliability and versatility of the anterolateral thigh flap.

Abiotic Niche Divergence of Hybrid Species from Their Progenitors.

AbstractAlthough more frequently discussed recently than previously, the role of ecology in homoploid hybrid and allopolyploid speciation has not been subjected to comparative analysis. We examined abiotic niche divergence of 22 assumed homoploid hybrid species and 60 allopolyploid species from that of their progenitors. Ecological niche modeling was employed in an analysis of each species' fundamental niche, and ordination methods were used in an analysis of realized niches. Both analyses utilized 100,000 georeferenced records. From estimates of niche overlap and niche breadth, we identified for both types of hybrid species four niche divergence patterns: niche novelty, niche contraction, niche intermediacy, and niche expansion. Niche shifts involving niche novelty were common and considered likely to play an important role in the establishment of both types of hybrid species, although more so for homoploid hybrid species than for allopolyploid species. Approximately 70% of homoploid hybrid species versus 37% of allopolyploid species showed shifts in the fundamental niche from their parents, and ∼86% versus ∼52%, respectively, exhibited shifts in the realized niche. Climate was shown to contribute more than soil and landform to niche shifts in both types of hybrid species. Overall, our results highlight the significance of abiotic niche divergence for hybrid speciation, especially without genome duplication.

Synergistic effects of myogenic cells and fibroblasts on the promotion of engineered tendon regeneration with muscle derived cells.

AIMS: Tendon development requires the coordinated interaction of muscles and tendons. Muscle-derived cells (MDCs), a mixed cell population containing both myogenic and fibroblastic cell subsets, have been found to be ideal seed cells for tendon regeneration. However, the necessity of these cell types for tendon regeneration has not yet been tested. In this study, we aim to explore the possible synergistic effects of myogenic cells and fibroblasts in engineered tendon regeneration. METHODS: MDCs were separated into rapidly adhering cell (RAC; fibroblasts) and slowly adhering cell (SAC; myogenic cells) populations. Myogenic- and tenogenic-related molecules were analyzed by immunofluorescent staining, RT-PCR and real-time PCR. The proliferative abilities of MDCs, RACs and SACs were also evaluated. Cell-scaffold constructs were implanted into nude mice, and subsequently evaluated for their histologic, ultrastructure, gene expression, and biomechanical characteristics. RESULTS: MDCs have better proliferative activity than RAC and SAC population. RACs could express higher levels of tenogenic-related molecules tenomodulin (TNMD) and scleraxis (SCX) than SACs. Whereas SACs only expressed myogenic-related molecules MyoD. In contrast to the tendons engineered using RACs and SACs, the tendons engineered using MDCs exhibited a relatively more mature and well-organized tissue structure and ultrastructure as well as better mechanical properties. CONCLUSIONS: Fibroblasts in muscle may be the primary cell population involved in tendon regeneration and that myogenic cells are an important component of the niche and control the fibroblast activity during tendon regeneration. The synergistic effects between fibroblasts and myogenic cells significantly contribute to efficient and effective regeneration of engineered tendons.

Continuous tension reduction technique in facial scar management: A comparison of W-plasty and straight-line closure on aesthetic effects in Asian patients.

W-plasty is a very popular scar excisional revision technique. The core of the technique is to break up the scar margins into small triangular components, so as to cause light scattering and make the scar less noticeable. However, due to skin tension, facial incision scars tend to spread. Applying W-plasty alone cannot achieve the ideal repair effect of facial scars. In this study, we proposed a scar revision technique combined W-plasty with continuous tension-reduction (CTR) technique to improve the appearance of facial scars. Sixty patients with facial scar were comprised in this retrospective study. Scars were assessed independently using the scar scale before and at 12-month follow-up. Clinical results showed a significant difference in scar appearance between different groups at 12-month follow-up. Vancouver scar scale (VSS), visual analogue scale (VAS) scores, and patient satisfaction were significant better in W-plasty and CTR than other groups at 12-month follow-up. No severe complications were reported. The application of the tension offloading device provides an environment where the tension is continuously reduced, which could greatly decrease tension on the surgical incision. Combined with W-plasty, this technique could significantly improve the scar's aesthetic appearance.

Periorbital and Perioral Defect Reconstruction Using the Split Pre-Expanded Medial Arm Flap Aided by Using Indocyanine Green Angiography.

ABSTRACT: The pre-expanded medial arm flap provides suitable skin for the resurfacing of a periorbital or perioral defect. However, the flap must be intraoperatively split to imitate the appearance of the oral or ophthalmic fissure, which can compromise flap perfusion. This study aimed to evaluate the safety and effectiveness of splitting pre-expanded medial arm flaps with the aid of indocyanine green angiography. All 8 patients underwent periorbital or perioral soft tissue reconstruction using a split pre-expanded medial arm flap. Flap splitting was aided by indocyanine green angiography. It was used during 2 stages of the procedure, tissue expander placement and flap transfer. The pedicle was divided 3 weeks later, and the flaps were used to resurface the defect. The distal portion of the flap was split into a fishmouth pattern in 5 patients and a window pattern in 3 patients. The donor sites were closed directly or by using a latissimus dorsi myocutaneous flap. There were no perioperative complications or flap necrosis. A pre-expanded split medial arm flap could be an option for the reconstruction of periorbital and perioral defects. With the assistance of indocyanine green angiography, vessel distribution and distal flap perfusion can be reliably evaluated, facilitating the safe splitting of the flap for the reconstruction of defects.

Use of Indocyanine Green Imaging for Perforator Identification in Preexpanded Brachial Artery Perforator Flaps.

The tissues of the medial arm as a donor site for perforator flap design have several advantages. However, they are relatively underused with limited reports, partly due to unreliable perforator anatomy. Therefore, we aimed to review our preliminary experience using indocyanine green (ICG) angiography to design and elevate preexpanded pedicled brachial artery perforator (BAP) flaps for regional reconstruction. All patients underwent soft tissue reconstructions using a preexpanded BAP flap in two or three stages. ICG angiography was used to localize perforators during both expander insertion and flap elevation. The pedicle was divided at the third stage 3 weeks following flap elevation for head and neck cases. Sixteen patients underwent reconstructions of the head and neck (n = 13) or shoulder/trunk (n = 3) using 14 perforator-plus and 2 propeller BAP flaps. In total, 50 perforators were identified using ICG imaging, all of which were appreciable during both expander placement and flap elevation. Thirty-five perforators were directly visualized during flap elevation, and an additional 15 perforators were not explored but incorporated into the flap. All flaps survived without necrosis, and the donor sites healed uneventfully without complications. The medial arm provides thin and pliable skin for the resurfacing of regional defects with relatively minimal donor-site morbidity. With the assistance of ICG angiography, perforators of the brachial artery can be reliably identified, facilitating the preexpansion and elevation of pedicled BAP flaps for use in head-neck and trunk reconstruction.

Comparison of the impact of single-port laparoscopic and conventional laparoscopic ovarian cystectomy on the ovarian reserve in adult patients with benign ovarian cysts.

Objective: The surgical approach, hemostatic approach, histologic findings, and cyst size and location may have a role in reducing the ovarian reserve. The aim of this study was to investigate the impact of single-port laparoscopic cystectomy (SLC) and conventional laparoscopic cystectomy (CLC) on the ovarian reserve based on serum anti-Mullerian hormone (AMH) concentrations.Material and methods: This non-randomized concurrent control trial enrolled 79 female patients aged 18-45 years with benign ovarian cysts, including 47 patients in the SLC group and 32 patients in the CLC group. Outcome measures, including hospital stay, operative time, blood loss, analgesic use, body temperature, hospitalization cost, and serum AMH concentration, were evaluated preoperatively, two to three days postoperatively, and four to six weeks postoperatively.Results: The reduction in the AMH concentration after cystectomy was significantly different preoperatively, two to three days postoperatively (p < .001), and four weeks postoperatively (p < .001) regardless of the surgical approach (SLC or CLC) [F (1.00,31.00) = 0.026, p = .873]. Moreover, the hemostatic approach and histologic findings yielded significant differences in the serum AMH concentration regardless of the surgical approach (p < .05). The serum AMH concentration was higher in unilateral cysts (2.70 ± 1.80 ng/mL) than in bilateral cysts (1.73 ± 1.11 ng/mL) postoperatively (p < .05). In the SLC group, the serum AMH concentration in the patients with ovarian endometriomas (1.58 ± 1.39 ng/mL) was significantly lower than that in the patients with other cysts (3.22 ± 1.68 ng/mL) postoperatively (p < .05).Conclusion: The serum AMH concentration decreased over time postoperatively but did not significantly differ between SLC and CLC.

Single-Trial Phase Entrainment of Theta Oscillations in Sensory Regions Predicts Human Associative Memory Performance.

Episodic memories are rich in sensory information and often contain integrated information from different sensory modalities. For instance, we can store memories of a recent concert with visual and auditory impressions being integrated in one episode. Theta oscillations have recently been implicated in playing a causal role synchronizing and effectively binding the different modalities together in memory. However, an open question is whether momentary fluctuations in theta synchronization predict the likelihood of associative memory formation for multisensory events. To address this question we entrained the visual and auditory cortex at theta frequency (4 Hz) and in a synchronous or asynchronous manner by modulating the luminance and volume of movies and sounds at 4 Hz, with a phase offset at 0° or 180°. EEG activity from human subjects (both sexes) was recorded while they memorized the association between a movie and a sound. Associative memory performance was significantly enhanced in the 0° compared with the 180° condition. Source-level analysis demonstrated that the physical stimuli effectively entrained their respective cortical areas with a corresponding phase offset. The findings suggested a successful replication of a previous study (Clouter et al., 2017). Importantly, the strength of entrainment during encoding correlated with the efficacy of associative memory such that small phase differences between visual and auditory cortex predicted a high likelihood of correct retrieval in a later recall test. These findings suggest that theta oscillations serve a specific function in the episodic memory system: binding the contents of different modalities into coherent memory episodes.SIGNIFICANCE STATEMENT How multisensory experiences are bound to form a coherent episodic memory representation is one of the fundamental questions in human episodic memory research. Evidence from animal literature suggests that the relative timing between an input and theta oscillations in the hippocampus is crucial for memory formation. We precisely controlled the timing between visual and auditory stimuli and the neural oscillations at 4 Hz using a multisensory entrainment paradigm. Human associative memory formation depends on coincident timing between sensory streams processed by the corresponding brain regions. We provide evidence for a significant role of relative timing of neural theta activity in human episodic memory on a single-trial level, which reveals a crucial mechanism underlying human episodic memory.

Surgical Site Infections Caused by Highly Virulent Methicillin-Resistant Staphylococcus aureus Sequence Type 398, China.

We identified 2 methicillin-resistant Staphylococcus aureus strains of sequence type 398 from surgical site infections in China. Genetic analysis and clinical data from these strains suggested that they were human-related but sporadic. Hemolysis analysis and mouse-skin infection models indicated a high virulence potential for these strains.

Does theta synchronicity of sensory information enhance associative memory? Replicating the theta-induced memory effect.

The binding of information from different sensory or neural sources is critical for associative memory. Previous research in animals suggested that the timing of theta oscillations in the hippocampus is critical for long-term potentiation, which underlies associative and episodic memory. Studies with human participants showed correlations between theta oscillations in medial temporal lobe and episodic memory. Clouter et al. directly investigated this link by modulating the intensity of the luminance and the sound of the video clips so that they 'flickered' at certain frequencies and with varying synchronicity between the visual and auditory streams. Across several experiments, better memory was found for stimuli that flickered synchronously at theta frequency compared with no-flicker, asynchronous theta, or synchronous alpha and delta frequencies. This effect - which they called the theta-induced memory effect - is consistent with the importance of theta synchronicity for long-term potentiation. In addition, electroencephalography data showed entrainment of cortical regions to the visual and auditory flicker, and that synchronicity was achieved in neuronal oscillations (with a fixed delay between visual and auditory streams). The theoretical importance, large effect size, and potential application to enhance real-world memory mean that a replication of theta-induced memory effect would be highly valuable. The present study aimed to replicate the key differences among synchronous theta, asynchronous theta, synchronous delta, and no-flicker conditions, but within a single experiment. The results do not show evidence of improved memory for theta synchronicity in any of the comparisons. We suggest a reinterpretation of theta-induced memory effect to accommodate this non-replication.