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Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.

ObjectiveTo investigate the clinical manifestations, molecular genetics and gonadal pathology characteristics of patients with disorders of sex development (DSD), and to summarize the clinical experience of identifying rare diseases from common symptoms.MethodsThe clinical data of 416 patients with DSD diagnosed and treated in the multidisciplinary center of DSD of Guangzhou Women and Children′s Medical Center from May 2018 to August 2023 were retrospectively analyzed, summarized and discussed.ResultsAccording to chromosome karyotype, 416 cases of DSD were classified into three types: 92 cases(22.1%) of abnormal sex chromosome karyotype, 285 cases(68.5%) of 46, XY karyotype and 39 cases(9.4%) of 46, XX karyotype. Among the 92 patients with abnormal sex chromosome karyotype, 59 cases were raised as males, 18 cases (30.5%) complained of short penis with hypospadias and cryptorchidism. The most common karyotype was 45, X/46, XY(58 cases, 63.0%).Among the 285 patients with 46, XY karyotype, 238 cases were raised as males, and 63 cases(26.5%)complained of short penis and hypospadias; 47 cases were raised as females, and 13 cases(27.7%) complained of inguinal mass. A total of 216 patients with 46, XY karyotype were subjected to whole exome gene detection, and 155 cases(71.8%) were found to have molecular pathogenesis with the clinical phenotype. Among the 39 patients with 46, XX karyotype, 19 cases were raised as males, and 8 cases(42.1%) complained of short penis and hypospadias. In the 18 cases of gonad biopsy, 17 cases showed testicular tissue in gonads. Whole exome sequencing was performed in 14 cases. NR5A1 gene heterozygous mutation, SRY gene mutation and SOX3 gene mutation were found in 2 cases, respectively(14.3%). Twenty cases were raised as females, and 14 cases(70.0%) complained of clitoral hypertrophy. Gonad biopsy was performed in 8 cases, with 7 cases of ovotestis(87.5%) and 1 case of NR5A1 gene heterozygous mutation(14.3%).ConclusionsThe etiologies of DSD are complex and diverse, and the clinical manifestations are various, which can be manifested as hypospadias, micropenis, cryptorchidism and other common symptoms of the urinary system. Different etiologies have different treatment options. Therefore, chromosome karyotype, molecular genetic testing and gonadal pathology can be used to clarify the cause of disease, especially for rare diseases, improve the detection rate, reduce the rate of missed diagnosis, and ensure reasonable treatment, especially sex selection.

[Objective] The Late Devonian Frasnian-Famennian (F-F) transition is a critical time interval in geological history. This period saw major simultaneous marine ecological system changes that led to one of the Big Five mass extinctions in the Phanerozoic. The F-F event (also referred to as the Kellwasser event) was characterized by severe losses of low-latitude shallow-water benthic faunas, notably reef-dwelling coral and stromatoporoids. High-latitude, deep-sea and terrestrial faunas were the least affected. Various separate or combined hypotheses have been proposed as the causes of this mass extinction (sea-level change, marine anoxia, climate change, volcanic/hydrothermal activities, and bolide impact) . Of these, climate change and marine anoxia have been the most intensively researched and discussed hypotheses based on the Web of Science in recent years. However, some controversies remain, and the interactions of certain factors are still unclear. [Methods] This study systematically reviews available reports on the paleoclimatic and paleo-oceanic changes during the F-F transition and discusses the anoxic model during this critical period, based on related case studies in southern China. [Results and Conclusions] Conodont oxygen and strontium isotopes, as well as the carbon isotope records for carbonates, collectively suggest a cold climate during the F-F transition interval, with several rapid warming-cooling fluctuations. Conodont oxygen isotopes suggest that the sea-sur face temperature (SST) dropped by 5 ° C-8 ° C. Strontium isotopes also imply that the temperature fluctuations were due to frequent, short-duration volcanism. Palynological data and carbonate platform exposure/karstification are also suggestive of coeval climate cooling. Additionally, marine anoxia has been extensively hypothesized as a possible killing mechanism in the F-F mass extinction, based initially on the presence of bituminous limestones (or black shales), named the lower and upper Kellwasser horizons. Studies of pyrite framboids, biomarker compounds, trace elements, isotopes of nitrogen, sulfur and uranium, and iron speciation have variously suggested the existence of the Kellwasser anoxic events. However, these generally occurred in geographically specific environments notably in the pericontinental basins/sub-basins proximal to source hinterlands. Moreover, the range and degree of anoxia in the F-F transition also reportedly differed between study sections around the world. With regard to the anoxic model, studies have suggested that the Kellwasser anoxic events were caused by the increased nutrient input related to enhanced continental weathering. Marine anoxic studies from three F-F sections comprising different depositional facies in southern China also support this "top down" anoxic model. Clearly, the F-F biotic crisis was not caused by any single factor. Frequent short-term volcanic activity may have enhanced continental weathering and associated greenhouse gas emission, leading to frequent warming-cooling climate fluctuations and also increased oceanic nutrient input. In the latter case, eutrophication and anoxia would have occurred in shallow water, and the mutual interaction of the various environmental factors may have exerted biological pressure in the low-latitude shallow sea, and eventually led to the F-F biotic crisis. [ABSTRACT FROM AUTHOR]