Score-based Counterfactual Generation for Interpretable Medical Image Classification and Lesion Localization.

Deep neural networks (DNNs) have immense potential for precise clinical decision-making in the field of biomedical imaging. However, accessing high-quality data is crucial for ensuring the high-performance of DNNs. Obtaining medical imaging data is often challenging in terms of both quantity and quality. To address these issues, we propose a score-based counterfactual generation (SCG) framework to create counterfactual images from latent space, to compensate for scarcity and imbalance of data. In addition, some uncertainties in external physical factors may introduce unnatural features and further affect the estimation of the true data distribution. Therefore, we integrated a learnable FuzzyBlock into the classifier of the proposed framework to manage these uncertainties. The proposed SCG framework can be applied to both classification and lesion localization tasks. The experimental results revealed a remarkable performance boost in classification tasks, achieving an average performance enhancement of 3-5% compared to previous state-of-the-art (SOTA) methods in interpretable lesion localization.

A Statistical Physics Perspective: Understanding the Causality Behind Convolutional Neural Network Adversarial Vulnerability.

The adversarial vulnerability of convolutional neural networks (CNNs) refers to the performance degradation of CNNs under adversarial attacks, leading to incorrect decisions. However, the causes of adversarial vulnerability in CNNs remain unknown. To address this issue, we propose a unique cross-scale analytical approach from a statistical physics perspective. It reveals that the huge amount of nonlinear effects inherent in CNNs is the fundamental cause for the formation and evolution of system vulnerability. Vulnerability is spontaneously formed on the macroscopic level after the symmetry of the system is broken through the nonlinear interaction between microscopic state order parameters. We develop a cascade failure algorithm, visualizing how micro perturbations on neurons' activation can cascade and influence macro decision paths. Our empirical results demonstrate the interplay between microlevel activation maps and macrolevel decision-making and provide a statistical physics perspective to understand the causality behind CNN vulnerability. Our work will help subsequent research to improve the adversarial robustness of CNNs.

A sequence-aware merger of genomic structural variations at population scale.

Merging structural variations (SVs) at the population level presents a significant challenge, yet it is essential for conducting comprehensive genotypic analyses, especially in the era of pangenomics. Here, we introduce PanPop, a tool that utilizes an advanced sequence-aware SV merging algorithm to efficiently merge SVs of various types. We demonstrate that PanPop can merge and optimize the majority of multiallelic SVs into informative biallelic variants. We show its superior precision and lower rates of missing data compared to alternative software solutions. Our approach not only enables the filtering of SVs by leveraging multiple SV callers for enhanced accuracy but also facilitates the accurate merging of large-scale population SVs. These capabilities of PanPop will help to accelerate future SV-related studies.

Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum.

Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.

The pan-genome and local adaptation of Arabidopsis thaliana.

Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.

SeqNovo: De Novo Peptide Sequencing Prediction in IoMT via Seq2Seq.

In the Internet of Medical Things (IoMT), de novo peptide sequencing prediction is one of the most important techniques for the fields of disease prediction, diagnosis, and treatment. Recently, deep-learning-based peptide sequencing prediction has been a new trend. However, most popular deep learning models for peptide sequencing prediction suffer from poor interpretability and poor ability to capture long-range dependencies. To solve these issues, we propose a model named SeqNovo, which has the encoding-decoding structure of sequence to sequence (Seq2Seq), the highly nonlinear properties of multilayer perceptron (MLP), and the ability of the attention mechanism to capture long-range dependencies. SeqNovo use MLP to improve the feature extraction and utilize the attention mechanism to discover key information. A series of experiments have been conducted to show that the SeqNovo is superior to the Seq2Seq benchmark model, DeepNovo. SeqNovo improves both the accuracy and interpretability of the predictions, which will be expected to support more related research.

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis.

Rhubarb is the collective name for various perennial plants from the genus Rheum L. and the Polygonaceae family. They are one of the most ancient, commonly used, and important herbs in traditional Chinese medicine. Rhubarb is a major source of anthraquinones, but how they are synthesized remains largely unknown. Here, we generate a genome sequence assembly of one important medicinal rhubarb R. tanguticum at the chromosome level, with 2.76 Gb assembled into 11 chromosomes. The genome is shaped by two recent whole-genome duplication events and recent bursts of retrotransposons. Metabolic analyses show that the major anthraquinones are mainly synthesized in its roots. Transcriptomic analysis reveals a co-expression module with a high correlation to anthraquinone biosynthesis that includes key chalcone synthase genes. One CHS, four CYP450 and two BGL genes involved in secondary metabolism show significantly upregulated expression levels in roots compared with other tissues and clustered in the co-expression module, which implies that they may also act as candidate genes for anthraquinone biosynthesis. This study provides valuable insights into the genetic bases of anthraquinone biosynthesis that will facilitate improved breeding practices and agronomic properties for rhubarb in the future.

The C2 H2 -type zinc finger transcription factor OSIC1 positively regulates stomatal closure under osmotic stress in poplar.

Salt and drought impair plant osmotic homeostasis and greatly limit plant growth and development. Plants decrease stomatal aperture to reduce water loss and maintain osmotic homeostasis, leading to improved stress tolerance. Herein, we identified the C2 H2 transcription factor gene OSMOTIC STRESS INDUCED C2 H2 1 (OSIC1) from Populus alba var. pyramidalis to be induced by salt, drought, polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). Overexpression of OSIC1 conferred transgenic poplar more tolerance to high salinity, drought and PEG6000 treatment by reducing stomatal aperture, while its mutant generated by the CRISPR/Cas9 system showed the opposite phenotype. Furthermore, OSIC1 directly up-regulates PalCuAOζ in vitro and in vivo, encoding a copper-containing polyamine oxidase, to enhance H2 O2 accumulation in guard cells and thus modulates stomatal closure when stresses occur. Additionally, ABA-, drought- and salt-induced PalMPK3 phosphorylates OSIC1 to increase its transcriptional activity to PalCuAOζ. This regulation of OSIC1 at the transcriptional and protein levels guarantees rapid stomatal closure when poplar responds to osmotic stress. Our results revealed a novel transcriptional regulatory mechanism of H2 O2 production in guard cells mediated by the OSIC1-PalCuAOζ module. These findings deepen our understanding of how perennial woody plants, like poplar, respond to osmotic stress caused by salt and drought and provide potential targets for breeding.

Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau.

Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. Numerous genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.

Somatic mutations during rapid clonal domestication of Populus alba var. pyramidalis.

For many clonally propagated species, the accumulation of somatic mutations is the principal driver of declines in yield and quality. However, somatic mutations may also promote genetic diversification. Thus, elucidating somatic mutation rates and patterns is important to understand the genetic basis undergirding the emergence of commercially valuable traits and developmental processes. In this study, we studied the effect of short-time clonal domestication of Populus alba var. pyramidalis, a species that has been propagated by cutting for the last 67 years. We found that: (1) the somatic mutation rate for P. alba var. pyramidalis is 9.24 × 10-9, which is higher than rates observed in related species; (2) there were more mutations near heterozygous regions, and a larger proportion of CpG and CHG sites were associated with somatic mutations, which may be related to the blocking of DNA repair by methylation; and (3) deleterious mutations were not shared by multiple individuals, and all occurred in heterozygous states, demonstrating the strong selective pressures that act against deleterious mutations. Taken together, the results of our study provide a global view of somatic mutation that will aid efforts to understand the genetic basis of commercially valuable traits and to improve clonally breeding species.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots.

BACKGROUND: Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. RESULTS: Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. CONCLUSIONS: Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots.

Defining Key Performance Indicators for the California COVID-19 Exposure Notification System (CA Notify).

OBJECTIVES: Toward common methods for system monitoring and evaluation, we proposed a key performance indicator framework and discussed lessons learned while implementing a statewide exposure notification (EN) system in California during the COVID-19 epidemic. MATERIALS AND METHODS: California deployed the Google Apple Exposure Notification framework, branded CA Notify, on December 10, 2020, to supplement traditional COVID-19 contact tracing programs. For system evaluation, we defined 6 key performance indicators: adoption, retention, sharing of unique codes, identification of potential contacts, behavior change, and impact. We aggregated and analyzed data from December 10, 2020, to July 1, 2021, in compliance with the CA Notify privacy policy. RESULTS: We estimated CA Notify adoption at nearly 11 million smartphone activations during the study period. Among 1 654 201 CA Notify users who received a positive test result for SARS-CoV-2, 446 634 (27%) shared their unique code, leading to ENs for other CA Notify users who were in close proximity to the SARS-CoV-2-positive individual. We identified at least 122 970 CA Notify users as contacts through this process. Contact identification occurred a median of 4 days after symptom onset or specimen collection date of the user who received a positive test result for SARS-CoV-2. PRACTICE IMPLICATIONS: Smartphone-based EN systems are promising new tools to supplement traditional contact tracing and public health interventions, particularly when efficient scaling is not feasible for other approaches. Methods to collect and interpret appropriate measures of system performance must be refined while maintaining trust and privacy.

Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae).

BACKGROUND: Bretschneidera sinensis is an endangered relic tree species in the Akaniaceae family and is sporadically distributed in eastern Asia. As opposed to its current narrow and rare distribution, the fossil pollen of B. sinensis has been found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. B. sinensis is also a typical mycorrhizal plant, and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. The chromosome-level high-quality genome of B. sinensis will help us to more deeply understand the survival and demographic histories of this relic species. RESULTS: A total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of B. sinensis, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The identified transposable elements account for 55.21% of the genome. A total of 45,839 protein-coding genes were predicted in B. sinensis. A lineage-specific whole-genome duplication was detected, and 7,283 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified. The historical effective population size (Ne) of B. sinensis was found to oscillate greatly in response to Quaternary climatic changes. The Ne of B. sinensis has decreased rapidly in the recent past, making its extant Ne extremely lower. Our additional evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of B. sinensis. CONCLUSION: This is a detailed report of the genome sequences for the family Akaniaceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource may provide critical clues for comparative genomics studies of this family in the future.

Establishment and Verification of UPLC-MS/MS Technique for Pharmacokinetic Drug-Drug Interactions of Selinexor with Posaconazole in Rats.

BACKGROUND: A method for the determination of selinexor by UPLC-MS/MS was established to study the effect of posaconazole on the pharmacokinetics of selinexor in rats. METHODS: The experiment rats were divided into group A (0.5% CMC-Na) and group B (posaconazole, 20 mg/kg), 6 rats in each group. 30 minutes after administration of 0.5% CMC-Na or posaconazole, all the rats were given selinexor (8 mg/kg), and plasma samples were collected. The plasma samples underwent acetonitrile protein precipitation, and were separated by UPLC on an Acquity UPLC BEH C18 column with gradient elution. Acetonitrile and 0.1% formic acid were used as the mobile phases. The analyte detection was used a Xevo TQ-S triple quadrupole tandem mass spectrometer and multiple reaction monitoring (MRM) for analyte monitoring. We use acetonitrile for protein precipitation. RESULTS: Selinexor had good linearity (1.0-1000 ng/mL, r2 =0.996 2), and the accuracy and precision, recovery rate and matrix effects(ME) were also met the FDA approval guidelines. Compared with group A, the Cmax, AUC(0-t) and AUC(0-∞) of selinexor in group B increased by 60.33%, 48.28% and 48.27%, and Tmax increased by 53.92%, CLz/F reduced by 32.08%. CONCLUSION: This bioanalysis method had been applied to the study of drug interactions in rats. It was found that posaconazole significantly increased the concentration of selinexor in rats. Therefore, when selinexor and posaconazole are combined, we should pay attention to the possible drug-drug interactions to reduce adverse reactions.

Which factors contribute most to genome size variation within angiosperms?

Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It has been reported that many factors correlate with the variation in genome size, but few studies have systematically explored this at the genomic level. Here, we scan genomic information for 74 species from 74 families in 38 orders covering the major groups of angiosperms (the taxonomic information was acquired from the latest Angiosperm Phylogeny Group (APG IV) system) to evaluate the correlation between genome size variation and different genome characteristics: polyploidization, different types of repeat sequence content, and the dynamics of long terminal repeat retrotransposons (LTRs). Surprisingly, we found that polyploidization shows no significant correlation with genome size, while LTR content demonstrates a significantly positive correlation. This may be due to genome instability after polyploidization, and since LTRs occupy most of the genome content, it may directly result in most of the genome variation. We found that the LTR insertion time is significantly negatively correlated with genome size, which may reflect the competition between insertion and deletion of LTRs in each genome, and that the old insertions are usually easy to recognize and eliminate. We also noticed that most of the LTR burst occurred within the last 3 million years, a timeframe consistent with the violent climate fluctuations in the Pleistocene. Our findings enhance our understanding of genome size evolution within angiosperms, and our methods offer immediate implications for corresponding research in other datasets.

Adrenomedullin(27-52) inhibits vascular calcification in rats.

Adrenomedullin (ADM) has the vasodilatory properties and involves in the pathogenesis of vascular calcification. ADM could be degraded into more than six fragments in the body, including ADM(27-52), and we suppose the degrading fragments from ADM do the same bioactivities as derived peptides from pro-adrenomedullin. The present study carries forward by assessing the effects on vascular calcification of the systemic administration of ADM(27-52). The rat vascular calcific model was replicated with vitamin D3 and nicotine. ADM or/and ADM(27-52) were systemically administrated with mini-osmotic pump beginning at seventh day after the model replication for 25 days. Vascular calcific nodules histomorphometry, vascular calcium content, vascular calcium uptake, alkaline phosphatase activity, and osteopontin-mRNA quantification in aorta were assessed. ADM limited 40.2% vascular calcific nodules (P<0.01), did not effect on calcium content (P>0.05), reduced 44.4% calcium uptake (P<0.01), lowered 21.1% alkaline phosphatase activity (P<0.01), and regulated 40.9% downwards osteopontin-mRNA expression (P<0.01) in the aorta of rats with vascular calcification. ADM(27-52) receded 32.0% vascular calcific nodules (P<0.01), taken from 55.5% calcium content (P<0.01), did not affect calcium uptake (P>0.05), inhibited 22.5% alkaline phosphatase activity (P<0.01), and restrained 21.9% osteopontin-mRNA expression (P<0.01) in the aorta of rats with vascular calcification. Both of ADM and ADM(27-52) did interact on vascular calcification each other. ADM could partially antagonize the effects of ADM(27-52) in taking from calcium content (17.5%, P<0.01) and in receding vascular calcific nodules (18.6%, P<0.01). ADM could obviously enhance the action of ADM(27-52) in inhibiting alkaline phosphatase activity (14.4%, P<0.01) and in reducing calcium uptake (11.4%, P<0.01). ADM(27-52) could partially antagonize the effects of ADM on regulating downwards osteopontin-mRNA expression (17.0%, P<0.01). It is concluded that ADM(27-52) derived from ADM acts as an inhibitory agent on vascular calcification, with special mechanisms different from ADM derived from ADM progenitor molecule.