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The management of papillary thyroid carcinoma (PTC) concurrent with Hashimoto’s thyroiditis (HT) lacks standardized guidelines, especially concerning surgical strategies. This study aimed to compare unilateral thyroidectomy (UT) with total thyroidectomy (TT) in PTC-HT patients to optimize clinical management and improve postoperative outcomes. This retrospective study included PTC-HT patients undergoing thyroid surgery at a tertiary academic medical institution from January 2018 to August 2023. The patients were grouped according to the quartiles of preoperative thyroid peroxidase antibody (TPOAB) levels at the last follow-up. Additionally, patients were divided into UT and TT groups, with propensity score matching (PSM) to ensure comparability. Patients were also stratified by TPOAB levels (L: 100–400, M: 400–1000, H: >1000). Patient-reported outcomes (PROMs), including quality of life and fatigue, were compared between UT and TT groups within each TPOAB subgroup (ΔPROMs = UT-TT). 246 patients were included. Those with higher TPOAB levels at the last follow-up reported increased physical fatigue scores. After PSM, there were no significant demographic differences between UT and TT groups. During a median follow-up of 16 months for UT and 20 months for TT, no recurrence or metastasis occurred. Compared to the UT group, the TT group exhibited lower TPOAB levels at the last follow-up (65.7 ± 78 vs. 374.6 ± 331.9, p < 0.001), and lower physical fatigue scores (3.6 ± 2.5 vs. 4.5 ± 2.8, p = 0.039). However, TT was associated with a higher incidence of transient hypoparathyroidism (7.8% vs. 1.1%, p = 0.030). Stratified analysis by preoperative TPOAB levels revealed significant differences in ΔPROMs (Physical fatigue) between L and H groups (0.2 ± 3.5 vs. 4.6 ± 2, p = 0.004) and between M and H groups (0.6 ± 4.5 vs. 4.6 ± 2, p = 0.037). ΔPROMs (Mental fatigue) also significantly differed between L and H groups (0 ± 1.8 vs. 1.6 ± 0.9, p = 0.026). For PTC-HT patients, particularly those with high preoperative TPOAB levels, TT offers advantages in alleviating fatigue symptoms but carries a higher risk of complications. Therefore, clinical decision-making should consider patient-specific factors, particularly preoperative TPOAB levels, to determine the optimal surgical approach. Trial registration: Chinese Clinical Trial Registry. ID ChiCTR2300069240.

Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis -regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis -regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression. Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.

Estuarine hydrodynamics, governing the interplay between riverine inputs, tidal currents, and coastal processes, are critical to understanding material transport, ecosystem dynamics, and anthropogenic impacts in transitional coastal zones. This study uses a high-resolution Coupled-Ocean-Atmosphere-Wave-Sediment Transport Modeling System (COAWST) to investigate the wave-current interactions in the shallow Pearl River Estuary during the winter, focusing on two typical tidal phases: maximum flood and maximum ebb. The results indicate that tidal currents significantly modulate the significant wave height, wave direction, and absolute mean bottom period within the estuary, with stronger modulation during maximum ebb. The wave-enhanced bottom friction notably weakens both maximum flood and ebb tidal currents, causes phase delays in the water level, and enhances tidal energy dissipation, which results in a reduction of water level amplitudes, especially at the estuary head. Wave-enhanced mixing and 3D wave forces cause significant adjustments in the current field nearby the plume front. The adjustments in the current field by the wave-enhanced bottom stress restrict more freshwater near the river mouths, lowering the salinity at the estuary head while increasing the salinity south of Qi’ao Island, significantly influencing the location of the plume front. Additionally, wave-enhanced mixing and wave forces significantly influence the position of the plume front. This study provides new insights into the wave-current interactions in the Pearl River Estuary and their impact on the dynamics of the freshwater plume.

Manakins are a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family has served as a good model for the study of sexual selection. Here we present genome assemblies of four manakin species, including Cryptopipo holochlora, Dixiphia pipra (also known as Pseudopipra pipra ), Machaeropterus deliciosus and Masius chrysopterus , generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 29 Mb and contig N50 of 169 Kb. On average, 12,055 protein-coding genes were annotated in the genomes, and 9.79% of the genomes were annotated as repetitive elements. We further identified 75 Mb of Z-linked sequences in manakins, containing 585 to 751 genes and an ~600 Kb pseudoautosomal region (PAR). One notable finding from these Z-linked sequences is that a possible Z-to-autosome/PAR reversal could have occurred in M. chrysopterus . These de novo genomes will contribute to a deeper understanding of evolutionary history and sexual selection in manakins. Measurement(s) whole genome sequencing Technology Type(s) BGISEQ-500 Sequencing Sample Characteristic - Organism Pipridae

Alleles that cause advantageous phenotypes with positive selection contribute to adaptive evolution. Investigations of positive selection in protein-coding genes rely on the accuracy of orthology, models, the quality of assemblies, and alignment. Here, based on the latest genome assemblies and gene annotations, we present a comparative analysis on positive selection in four great ape species and identify 211 high-confidence positively selected genes (PSGs). Even the differences in population size among these closely related great apes have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments, we found that they experienced comparable numbers of positive selection. We also uncovered that more than half of multigene families exhibited signals of positive selection, suggesting that imbalanced positive selection resulted in the functional divergence of duplicates. Moreover, at the expression level, although positive selection led to a more non-uniform pattern across tissues, the correlation between positive selection and expression patterns is diverse. Overall, this updated list of PSGs is of great significance for the further study of the phenotypic evolution in great apes.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions 1 – 3 . Here we address these issues by analysing the genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies. Using intergenic regions and coalescent methods to analyse the genomes of 363 bird species, the authors present a well-supported tree confirming that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary.

Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.

Forages generally suffer more severe nutrition stress than other crops, but the corresponding theoretical studies still lag behind. In this study, metabo- lites in tall fescue leaves under normal and low nitrogen conditions were analyzed with LC-ESI-MS （ liquid chromatography-electrospray ionization-mass spectrome- try）. A total of 1 424 and 1 251 metabolites were detected from two groups of samples respectively using OPLS-DA （orthogonal partial least squares discriminant analysis）. The content of 13 major metabolites changed under low nitrogen stress, including auxin （indale acetic acid, IAA）. Quantitative real-time PCR （qRT- PCR） showed that eight genes related to IAA signaling pathway were up-regulated after nitrogen stress. Enzyme-linked immuno sorbent assay （ELISA） revealed that the IAA concentration was elevated in tall fescue leaves after nitrogen stress. Our research provides valuable information for studying the response mechanisms of tall feseue to low nitrogen. The results suggest that application of IAA could be used to alleviate the harmful effects of nitrogen deficiency.

Good genes theories of sexual selection predict that polygamy will be associated with more efficient removal of deleterious alleles (purifying selection), due to the alignment of sexual selection with natural selection. On the other hand, runaway selection theories expect no such alignment of natural and sexual selection, and may instead predict less efficient purifying selection in polygamous species due to higher reproductive variance. In an analysis of polymorphism data extracted from 150-bird genome assemblies, we show that polygamous species carry significantly fewer nonsynonymous polymorphisms, relative to synonymous polymorphisms, than monogamous bird species (p = .0005). We also show that this effect is independent of effective population size, consistent with the alignment of natural selection with sexual selection and “good genes” theories of sexual selection. Further analyses found no impact of polygamy on genetic diversity, while polygamy in females (polyandry) had a marginally significant impact (p = .045). We also recapitulate previous findings that smaller body mass and greater geographic range size are associated with more efficient purifying selection, more intense GC-biased gene conversion, and greater genetic diversity.

Migration allows animals to exploit spatially separated and seasonally available resources at a continental to global scale. However, responding to global climatic changes might prove challenging, especially for long-distance intercontinental migrants. During glacial periods, when conditions became too harsh for breeding in the north, avian migrants have been hypothesized to retract their distribution to reside within small refugial areas. Here, we present data showing that an Afro-Palearctic migrant continued seasonal migration, largely within Africa, during previous glacial–interglacial cycles with no obvious impact on population size. Using individual migratory track data to hindcast monthly bioclimatic habitat availability maps through the last 120,000 y, we show altered seasonal use of suitable areas through time. Independently derived effective population sizes indicate a growing population through the last 40,000 y. We conclude that the migratory lifestyle enabled adaptation to shifting climate conditions. This indicates that populations of resource-tracking, long-distance migratory species could expand successfully during warming periods in the past, which could also be the case under future climate scenarios.