Thermal ablation with and without adjuvant systemic therapy: a nationwide multicenter observational cohort study of solitary colorectal liver metastases.

BACKGROUND: Thermal ablation is routinely used for solitary colorectal liver metastases (SCLM), but the added value of adjuvant systemic therapy in SCLM remains unclear. This study aimed to compare the long-term outcomes for SCLM treated by ablation alone (AB) versus ablation plus systemic therapy (AS). METHODS: This multicenter retrospective study using nationwide data from fourteen institutions between October 2010 and May 2023, 369 patients with initial SCLM smaller than 5 cm, no extrahepatic metastases, and colorectal cancer R0 resection treated by thermal ablation were included. The crude analysis was used to analyze eligible cases between the two groups. The propensity score matching (PSM) to control for potential confounders in each matched group. Subgroup analyses were performed to identify specific survival benefits. RESULTS: 61.2% (226/369) of eligible patients were treated with AS and 38.8% (143/369) with AB. During the median follow-up period of 8.8 years, 1-/3-/5-year DFS/OS rates did not differ between the two groups, when analyzed via PSM (P=0.52/0.08). Subgroup analysis revealed that AS was significantly associated with better OS than AB in patients with plasma CEA >5 ug/L (P=0.036), T (III-IV) category of primary cancer (P=0.034), or clinical risk score (1-2) (P=0.041). In each matched group, we did find a significant difference in drug-related adverse events (P<0.001) between AS group (24.1%, 28/116) and AB group (0.0%, 0/116). CONCLUSIONS: For patients with plasma CEA >5 ug/L, T (III-IV) category of primary cancer, or clinical risk score (1-2), thermal ablation plus systemic therapy appeared to be associated with improved overall survival. Thermal ablation was equally effective in disease-free survival for treating solitary colorectal liver metastasis, whether with or without adjuvant systemic therapy.

Gliotoxin elicits immunotoxicity in the early innate immune system of ducks.

Gliotoxin (GT) belongs to the epipolythiodioxopiperazine (ETP) family, which is considered a crucial virulence determinant among the secondary metabolites produced by Aspergillus fumigatus. The metabolites are commonly found in food and feed, contributing to the invasion and immune escape of Aspergillus fumigatus, thereby posing a significant threat to the health of livestock, poultry, and humans. Heterophil extracellular traps (HETs), a novel form of innate immune defense, have been documented in the chicken's innate immune systems for capturing and eliminating invading microbes. However, the effects and mechanisms of GT on the production of duck HETs in vitro remain unknown. In this study, we first confirmed the presence of HETs in duck innate immune systems and further investigated the molecular mechanism underlying GT-induced HETs release. Our results demonstrate that GT can trigger typical release of HETs in duck. The structures of GT-induced HETs structures were characterized by DNA decoration, citrullinated histones 3, and elastase. Furthermore, NADPH oxidase, glycolysis, ERK1/2 and p38 signaling pathway were found to regulate GT-induced HETs. In summary, our findings reveal that gliotoxin activates HETs release in the early innate immune system of duck while providing new insights into the immunotoxicity of GT towards ducks.

Molecular and metabolic responses to immune stress in the jejunum of broiler chickens: transcriptomic and metabolomic analysis.

In the large poultry industry, where farmed chickens are fed at high density, the prevalence of pathogens and repeated vaccinations induce immune stress, which can significantly decrease the production performance and increase the mortality. This study was designed to shed light on the molecular mechanisms and metabolic pathways involved in immune stress through an in-depth analysis of transcriptomic and metabolomic changes in jejunum samples from the broilers. Two groups were established for the experiment: a control group and an LPS group. LPS group received an intraperitoneal injection of LPS solution at a dose of 250 µg per kg at 12, 14, 33, and 35 d of age, whereas the control group received a sterile saline injection. The severity of immune stress was assessed using the Disease Activity Index. A jejunal section was collected to measure the intestinal villus structure (villus length and crypt depth). RNA sequencing and metabolomics data analysis were conducted to reveal differentially expressed genes and metabolites. The results showed that the DAI index was increased and jejunal villus height/crypt depth was decreased in the LPS group. A total of 96 differentially expressed genes and 672 differentially accumulating metabolites were detected in the jejunum by LPS group compared to the control group. The comprehensive analysis of metabolomic and transcriptomic data showed that 23 pathways were enriched in the jejunum and that appetite, nutrient absorption, energy and substance metabolism disorders and ferroptosis play an important role in immune stress in broilers. Our findings provide a deeper understanding of the molecular and metabolic responses in broilers to LPS-induced immune stress, suggesting potential targets for therapeutic strategies to improve the production performance of broiler chickens.

A multicenter case-controlled study on laparoscopic hepatectomy versus microwave ablation as first-line therapy for 3-5 cm hepatocellular carcinoma in patients aged 60 and older.

BACKGROUND: There is currently a lack of convincing evidence for microwave ablation (MWA) and laparoscopic liver resection (LLR) for patients ≥60 years old with 3-5 cm hepatocellular carcinoma. MATERIALS AND METHODS: Patients were divided into three cohorts based on restricted cubic spline analysis: 60-64, 65-72, and ≥73 years. Propensity score matching (PSM) was performed to balance the baseline variables in a 1:1 ratio. Overall survival (OS) and disease-free survival (DFS) were assessed, followed by a comparison of complications, hospitalization, and cost. RESULTS: Among 672 patients, the median age was 66 (IQR 62-71) years. After PSM, two groups of 210 patients each were selected. During the 36.0 (20.4-52.4) month follow-up period, the 1-year, 3-year, and 5-year OS rates in the MWA group were 97.6, 80.9, and 65.3% and 95.5, 78.7, and 60.4% in the LLR group (HR 0.98, P =0.900). The corresponding DFS rates were 78.6, 49.6, and 37.5% and 82.8, 67.8, and 52.9% (HR 1.52, P =0.007). The 60-64 age cohort involved 176 patients, with no a significant difference in OS between the MWA and LLR groups (HR 1.25, P =0.370), MWA was associated with a higher recurrence rate (HR 1.94, P =0.004). A total of 146 patients were matched in the 65-72 age cohort, with no significant differences in OS and DFS between the two groups (OS (HR 1.04, P =0.900), DFS (HR 1.56, P =0.110)). In 76 patients aged ≥73 years after PSM, MWA provided better OS for patients (HR 0.27, P =0.015), and there were no significant differences in DFS between the two groups (HR 1.41, P =0.380). Taken together, for patients older than 65 years, the recurrence rate of MWA was comparable with LLR. Safety analysis indicated that LLR was associated with more postoperative bleeding ( P =0.032) and hypoproteinemia ( P =0.024). CONCLUSIONS: MWA was comparable to LLR in patients aged 65 years and older. MWA could be an alternative for the oldest old or the ill patients who cannot afford LLR, while LLR is still the first option of treatments for early-stage 3-5 cm hepatocellular carcinoma in capable elderly's.

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains.

Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).

BACKGROUND: Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary. RESULTS: Here we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression. CONCLUSIONS: Collectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.

Construction of a Soft Antifouling PAA/PSBMA Hydrogel Coating with High Toughness and Low Swelling through the Dynamic Coordination Bonding Provided by Al(OH)3 Nanoparticles.

Marine biofouling, resulting from the adhesion of marine organisms to ship surfaces, has long been a significant issue in the maritime industry. In this paper, we focused on utilizing soft and hydrophilic hydrogels as a potential approach for antifouling (AF) coatings. Acrylic acid (AA) with a polyelectrolyte effect and N-(3-sulfopropyl)-N-(methacryloxyethyl)-N,N-dimethylammonium betaine (SBMA) with an antipolyelectrolyte effect were selected as monomers. By adjusting the monomer ratio, we were able to create hydrogel coatings that exhibited low swelling ratio in both fresh water and seawater. The Al(OH)3 nanoparticle, as a physical cross-linker, provided better mechanical properties (higher tensile strength and larger elongation at break) than the chemical cross-linker through the dynamic coordination bonds and plentiful hydrogen bonds. Additionally, we incorporated trehalose into the hydrogel, enabling the repair of the hydrogel network through covalent-like hydrogen bonding. The zwitterion compound SBMA endowed the hydrogel with excellent AF performance. It was found that the highest SBMA content did not lead to the best antibacterial performance, as bacterial adhesion quantity was also influenced by the charge of the hydrogel. The hydrogel with appropriate SBMA content being close to electrical neutrality exhibits the strongest zwitterionic property of PSBMA chains, resulting in the best antibacterial adhesion performance. Furthermore, the pronounced hydrophilicity of SBMA enhanced the lubrication of the hydrogel surface, thereby reducing the friction resistance when applied to the hull surface during ship navigation.

CT-Net: Asymmetric compound branch Transformer for medical image segmentation.

The Transformer architecture has been widely applied in the field of image segmentation due to its powerful ability to capture long-range dependencies. However, its ability to capture local features is relatively weak and it requires a large amount of data for training. Medical image segmentation tasks, on the other hand, demand high requirements for local features and are often applied to small datasets. Therefore, existing Transformer networks show a significant decrease in performance when applied directly to this task. To address these issues, we have designed a new medical image segmentation architecture called CT-Net. It effectively extracts local and global representations using an asymmetric asynchronous branch parallel structure, while reducing unnecessary computational costs. In addition, we propose a high-density information fusion strategy that efficiently fuses the features of two branches using a fusion module of only 0.05M. This strategy ensures high portability and provides conditions for directly applying transfer learning to solve dataset dependency issues. Finally, we have designed a parameter-adjustable multi-perceptive loss function for this architecture to optimize the training process from both pixel-level and global perspectives. We have tested this network on 5 different tasks with 9 datasets, and compared to SwinUNet, CT-Net improves the IoU by 7.3% and 1.8% on Glas and MoNuSeg datasets respectively. Moreover, compared to SwinUNet, the average DSC on the Synapse dataset is improved by 3.5%.

CR-Conformer: a fusion network for clinical skin lesion classification.

Deep convolutional neural network (DCNN) models have been widely used to diagnose skin lesions, and some of them have achieved diagnostic results comparable to or even better than dermatologists. Most publicly available skin lesion datasets used to train DCNN were dermoscopic images. Expensive dermoscopic equipment is rarely available in rural clinics or small hospitals in remote areas. Therefore, it is of great significance to rely on clinical images for computer-aided diagnosis of skin lesions. This paper proposes an improved dual-branch fusion network called CR-Conformer. It integrates a DCNN branch that can effectively extract local features and a Transformer branch that can extract global features to capture more valuable features in clinical skin lesion images. In addition, we improved the DCNN branch to extract enhanced features in four directions through the convolutional rotation operation, further improving the classification performance of clinical skin lesion images. To verify the effectiveness of our proposed method, we conducted comprehensive tests on a private dataset named XJUSL, which contains ten types of clinical skin lesions. The test results indicate that our proposed method reduced the number of parameters by 11.17 M and improved the accuracy of clinical skin lesion image classification by 1.08%. It has the potential to realize automatic diagnosis of skin lesions in mobile devices.

Class key feature extraction and fusion for 2D medical image segmentation.

BACKGROUND: The size variation, complex semantic environment and high similarity in medical images often prevent deep learning models from achieving good performance. PURPOSE: To overcome these problems and improve the model segmentation performance and generalizability. METHODS: We propose the key class feature reconstruction module (KCRM), which ranks channel weights and selects key features (KFs) that contribute more to the segmentation results for each class. Meanwhile, KCRM reconstructs all local features to establish the dependence relationship from local features to KFs. In addition, we propose the spatial gating module (SGM), which employs KFs to generate two spatial maps to suppress irrelevant regions, strengthening the ability to locate semantic objects. Finally, we enable the model to adapt to size variations by diversifying the receptive field. RESULTS: We integrate these modules into class key feature extraction and fusion network (CKFFNet) and validate its performance on three public medical datasets: CHAOS, UW-Madison, and ISIC2017. The experimental results show that our method achieves better segmentation results and generalizability than those of mainstream methods. CONCLUSION: Through quantitative and qualitative research, the proposed module improves the segmentation results and enhances the model generalizability, making it suitable for application and expansion.

Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae).

Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which - in combination - support the following tree topology: (((E. godlewskii, E. cia), E. cioides), E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.

Effect of plant polysaccharides (Poria cocos and Astragalus polysaccharides) on immune responses and intestinal microbiota of Dabry's sturgeons.

Searching for non-toxic and harmless feed ingredients that can improve growth performance and host immunity has always been the focus of attention in the protected areas for artificially bred Dabry's sturgeons. The present study explored the effect of dietary Poria cocos and Astragalus polysaccharides on the antioxidant status, expression of immune related genes, and composition and putative functions of gut bacterial communities in Dabry's sturgeons for the first time. In this study, Dabry's sturgeons were randomly divided into 3 groups and fed diets of normal, P. cocos polysaccharide-added (200 mg/kg), and Astragalus polysaccharide-added (200 mg/kg) food for 14 days. The results indicated that dietary Astragalus polysaccharide can increase the final body weight of Dabry's sturgeon. Compared with normal breeding individuals, feeding diets containing the P. cocos and Astragalus polysaccharides up-regulated the activity of superoxide dismutase, lysozyme, catalase, and glutathione peroxidase while also decreasing the levels of malondialdehyde. In addition, the Astragalus polysaccharide group had higher gene expression of two inflammatory cytokines, tumor necrosis factor alpha and immunoglobulin M, than the control group. Analysis of intestinal microbiota revealed that the dietary Astragalus polysaccharide improved the richness and diversity of major gut microbiota in Dabry's sturgeons, while the structure in the P. cocos polysaccharide group was clearly distinguished from that of the control group. Our results preliminarily indicated that dietary supplementation of P. cocos and Astragalus polysaccharides may contribute to better performance in growth, development, and inflammatory response for Dabry's sturgeons, and they provide basic guidance for plant polysaccharide additives in artificial breeding of sturgeons.

Outcomes Following Different Thermal Ablation Strategies in Patients with Unresectable Colorectal Liver Metastases.

Background For patients with unresectable colorectal liver metastases (CRLM), clinical guidelines recommend imaging-guided thermal ablation combined with systemic therapy. However, the optimal thermal ablation strategy remains unclear. Purpose To compare long-term outcomes between patients who underwent upfront ablation or delayed ablation for unresectable CRLM. Materials and Methods This retrospective study included patients with unresectable CRLM (three or fewer lesions; diameter, <3 cm) admitted to one of seven hospitals between October 2009 and December 2020. Upfront ablation was performed 2-4 weeks before the start of systemic therapy, and delayed ablation was performed 2-3 months after the start of systemic therapy. Propensity score matching was applied to adjust for differences in baseline variables between groups. Disease-free survival (DFS) was the primary outcome. Overall survival (OS), complications, and adverse events were secondary outcomes. Outcomes were compared between groups by using the log-rank test. Results In total, 255 patients who underwent delayed ablation (mean age, 57 years ± 11 [SD]; 184 men [72%]) and 103 patients who underwent upfront ablation (mean age, 56 years ± 12; 72 men [70%]) were included. After propensity score matching (n = 100 in both groups), the 5-year DFS for patients who underwent upfront ablation was better compared with patients who underwent delayed ablation (36% vs 21%; P = .02). For 5-year OS, no evidence of a difference was observed between ablation strategies (delayed ablation, 59% vs upfront ablation, 64%; P = .49). Additionally, no differences were observed between ablation strategies with respect to the rates of ablative complications (delayed ablation, 6% vs upfront ablation, 5%; P = .76) or drug-related adverse events (delayed and upfront ablation both 9%; P = .99). Conclusion In patients with relatively few (three or fewer) and small (<3 cm) unresectable CRLM, upfront thermal ablation combined with adjuvant systemic therapy led to better DFS compared with delayed ablation. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Georgiades in this issue.

Disseminated visceral Kaposi's sarcoma after allogeneic hematopoietic stem cell transplantation: a case report.

Cases of disseminated visceral Kaposi's sarcoma (KS) after allogenic hematopoietic stem cell transplantation (HSCT) are very rare worldwide, and disseminated visceral KS is often rapidly progressive and life-threatening, especially in paediatric patients. Here, the case of a 6-year-old female patient with disseminated visceral KS after allogeneic HSCT for treating severe aplastic anaemia is presented. The authors encountered difficulties in making the diagnosis due to lack of experience, but the diagnosis was achieved relatively quickly and accurately using metagenomic next-generation sequencing. After tapering and withdrawal of immunosuppressant drugs, the patient's condition was controlled. In conclusion, although HSCT-related KS is very rare, it should be considered during differential diagnosis.

miR-665 overexpression inhibits the apoptosis of luteal cells in small ruminants suppressing HPGDS.

Evidence has shown that microRNA-665 (miR-665) is highly expressed in the mid-luteal phase compared with the early and end-luteal phase of the corpus luteum (CL) life cycle. However, whether miR-665 is a positive regulator of the life span of the CL is still unknown. The objective of this study is to explore the effect of miR-665 on the structural luteolysis in the ovarian CL. In this study, the targeting relationship between miR-665 and hematopoietic prostaglandin synthase (HPGDS) was firstly verified by dual luciferase reporter assay. Then, quantitative real-time PCR (qRT-PCR) was used to detect the expression of miR-665 and HPGDS in luteal cells. Following miR-665 overexpression, the apoptosis rate of the luteal cells was determined using flow cytometry; B-cell lymphoma-2 (BCL-2) and caspase-3 mRNA and protein were measured using qRT-PCR and Western blot (WB) analysis. Finally, the DP1 and CRTH2 receptors of PGD2, a synthetic product of HPGDS, were localized using immunofluorescence. Results confirmed that HPGDS was a direct target gene of miR-665, and miR-665 expression was negatively correlated with HPGDS mRNA expression in luteal cells. Meanwhile, after miR-665 was overexpressed, the apoptotic rate of the luteal cells showed a significant decrease (P < 0.05) and this was accompanied by elevated expression levels of anti-apoptotic factor BCL-2 mRNA and protein and decreased expression levels of apoptotic factor caspase-3 mRNA and protein (P < 0.01). Moreover, the immune fluorescence staining results showed that the DP1 receptor was also significantly decreased (P < 0.05), but the CRTH2 receptor was significantly increased (P < 0.05) in luteal cells. Overall, these results indicate that miR-665 reduces the apoptosis of luteal cells via inhibiting caspase-3 expression and promoting BCL-2 expression, and the biological function of miR-665 may be attributed to its target gene HPGDS which regulates the balance of DP1 and CRTH2 receptors expression in luteal cells. As a consequence, this study suggests that miR-665 might be a positive regulator of the life span of the CL rather than destroy the integrity of CL in small ruminants.

Improve L-isoleucine production in Corynebacterium glutamicum WM001 by destructing the biosynthesis of trehalose dicorynomycolate.

Trehalose dicorynomycolates are structurally important constituents of the cell envelope in Corynebacterium glutamicum. The genes treS, treY, otsA, mytA and mytB are necessary for the biosynthesis of trehalose dicorynomycolates. In this study, the effect of biosynthesis of trehalose dicorynomycolates on L-isoleucine production in C. glutamicum has been investigated by deleting the genes treS, treY, otsA, mytA, and mytB in the L-isoleucine producing C. glutamicum WM001. L-isoleucine production was slightly improved in the mutants ΔtreY, ΔotsA, and ΔtreYA, and not improved in the single deletion mutant ΔtreS , but significantly improved in the triple deletion mutant ΔtreSYA. Deletion of mytA or mytB in ΔtreSYA could further improve L-isoleucine production. However, deletion of both mytA and mytB in ΔtreSYA significantly decreased L-isoleucine production. The final L-isoleucine producing C. glutamicum WL001 was constructed by deletion of treS, treY, otsA, and mytB, insertion of lrp, and replacement of the native promoter of ilvA with the L-isoleucine sensitive promoter PbrnFE7. WL001 grew worse than the control WM001, but produced 36.1% more L-isoleucine after 72 h shake flask cultivation than WM001.

Recurrent selection and reduction in recombination shape the genomic landscape of divergence across multiple population pairs of Green-backed Tit.

Speciation is fundamental for building and maintaining biodiversity. The formation of the highly differentiated genomic regions between diverging taxa has been interpreted as a result of divergence with gene flow, linked selection, and reduction in recombination. It is challenging to unravel these nonexclusive processes in shaping genomic divergence. Here, we investigate the relative roles of these processes in shaping genomic differentiation in a montane bird, the Green-backed Tit (Parus monticolus). Our genetic structure and demographic analyses identify that four genetic lineages diverge between 838 and 113 thousand years ago and there is evidence of secondary gene flow. The highly divergent genomic regions do not increase with the divergence time, as we found that the old lineages show relatively fewer numbers and smaller sizes of highly differentiated regions than the young divergent lineages (numbers, 118-138 vs. 156-289; sizes, 5.9-6.9 vs. 7.8-14.5 megabase). Across the genome, the outlier windows show a reduction in nucleotide diversity, absolute genetic divergence, and recombination rate, suggesting recurrent selection in regions with low recombination being the major driver of genomic divergence. Finally, we show that secondary gene flow tends to affect the highly differentiated genomic regions if these regions are less likely to be the targets of selection. Altogether, our study shows how common ancestry, recurrent selection, low recombination rate, and gene flow have contributed to the emergence of genomic islands at different stages of speciation.

Limited Song Mixing Without Genomic Gene Flow in a Contact Zone Between Two Songbird Species.

Song is considered to play an important role in the maintenance of prezygotic reproductive isolation between closely related songbird species. Therefore, song mixing in a contact zone between closely related species is often considered as evidence of hybridization. The Sichuan Leaf Warbler Phylloscopus forresti and the Gansu Leaf Warbler Phylloscopus kansuensis, which diverged 2 million years ago, have formed a contact zone in the south of the Gansu Province of China, where mixed songs have been observed. In this study, we investigated the potential causes and consequences of song mixing by integrating bioacoustic, morphological, mitochondrial, and genomic data with field ecological observations. We found that the two species display no apparent morphological differences, whereas their songs differ dramatically. We demonstrated that ∼11% of the males in the contact zone sang mixed songs. Two males singing mixed song were genotyped, and both were found to be P. kansuensis. Despite the presence of mixed singers, population genomic analyses detected no signs of recent gene flow between the two species, although two possible cases of mitochondrial introgression were identified. We conclude that the rather limited song mixing does not lead to, or result from, hybridization, and hence does not result in the breakdown of reproductive barriers between these cryptic species.

FaxMatch: Multi-Curriculum Pseudo-Labeling for semi-supervised medical image classification.

BACKGROUND: Semi-supervised learning (SSL) can effectively use information from unlabeled data to improve model performance, which has great significance in medical imaging tasks. Pseudo-labeling is a classical SSL method that uses a model to predict unlabeled samples and selects the prediction with the highest confidence level as the pseudo-labels and then uses the generated pseudo-labels to train the model. Most of the current pseudo-label-based SSL algorithms use predefined fixed thresholds for all classes to select unlabeled data. PURPOSE: However, data imbalance is a common problem in medical image tasks, where the use of fixed threshold to generate pseudo-labels ignores different classes of learning status and learning difficulties. The aim of this study is to develop an algorithm to solve this problem. METHODS: In this work, we propose Multi-Curriculum Pseudo-Labeling (MCPL), which evaluates the learning status of the model for each class at each epoch and automatically adjusts the thresholds for each class. We apply MCPL to FixMatch and propose a new SSL framework for medical image classification, which we call the improved algorithm FaxMatch. To mitigate the impact of incorrect pseudo-labels on the model, we use label smoothing (LS) strategy to generate soft labels (SL) for pseudo-labels. RESULTS: We have conducted extensive experiments to evaluate our method on two public benchmark medical image classification datasets: the ISIC 2018 skin lesion analysis and COVID-CT datasets. Experimental results show that our method outperforms fully supervised baseline, which uses only labeled data to train the model. Moreover, our method also outperforms other state-of-the-art methods. CONCLUSIONS: We propose MCPL and construct a semi-supervised medical image classification framework to reduce the reliance of the model on a large number of labeled images and reduce the manual workload of labeling medical image data.