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.

[Arterial spin labeling in assessment of interstitial fibrosis in renal allografts]

Objective: To explore the feasibility and application value of arterial spin labeling (ASL) in evaluating the degree of renal fibrosis after kidney transplantation. Methods: This is a cross-sectional study. Renal transplant recipients who received treatment at the First Affiliated Hospital of Soochow University from December 2021 to December 2022 were enrolled. All participants underwent ASL scan, and the values of renal cortical renal blood flow (RBF) were measured through post-processing software. The participants were divided into different groups according to the Banff interstitial fibrosis score (ci score) of the transplanted kidneys, and then relevant indicators were compared. One-way analysis of variance was conducted to compare the differences in renal cortical RBF among the groups. Spearman correlation analysis was employed to investigate the association between renal cortical RBF and ci score of the transplanted kidney. Receiver operating characteristic curve was used to analyze the diagnostic effectiveness of renal cortical RBF and laboratory indicators for distinguishing varying degrees of fibrosis in transplanted kidneys. The Delong test was utilized to compare the area under the curve (AUC). Results: A total of 60 patients (42 males and 18 females) were included in the study, with a mean age of (44.6±10.8) years. All patients were divided into 4 groups: ci0 group (ci score=0, 11 cases), ci1 group (ci score=1, 21 cases), ci2 group (ci score=2, 20 cases), and ci3 group (ci score=3, 8 cases). With an increase in the degree of fibrosis in the transplanted kidney, there was a corresponding decrease in the renal cortical RBF value. The differences in renal cortical RBF values among the 4 groups were statistically significant[ci0 group: (214.9±28.5) ml·(100 g)-1·min-1; ci1 group: (181.7±29.3) ml·(100 g)-1·min-1; ci2 group: (158.8±39.2) ml·(100 g)-1·min-1; ci3 group: (123.1±27.2) ml·(100 g)-1·min-1; F=14.02, P<0.001]. The renal cortical RBF was moderately negatively correlated with the ci score (r=-0.644, P<0.001). The AUC for discriminating between ci0 and ci1-3 of renal cortical RBF and 24-hour urine protein was 0.881 (95%CI: 0.772-0.950) and 0.680 (95%CI: 0.547-0.795), respectively. The AUC for renal cortical RBF was significantly higher than that for 24-hour urine protein (P=0.047). The renal cortical RBF can distinguish between ci0-1 and ci2-3, as well as ci0-2 and ci3, with the corresponding AUC value of 0.796 (95%CI: 0.673-0.889) and 0.900 (95%CI: 0.795-0.963), respectively. Conclusion: ASL can quantitatively assess renal blood perfusion in transplanted kidneys and demonstrates high operational efficacy in distinguishing varying degrees of fibrosis in the transplanted kidneys.

Myokines and Biomarkers of Frailty in Older Inpatients with Undernutrition: A Prospective Study

BACKGROUND

Population aging might increase the prevalence of undernutrition in older people, which increases the risk of frailty. Numerous studies have indicated that myokines are released by skeletal myocytes in response to muscular contractions and might be associated with frailty. This study aimed to evaluate whether myokines are biomarkers of frailty in older inpatients with undernutrition.

METHODS

The frailty biomarkers were extracted from the Gene Expression Omnibus and Genecards datasets. Relevant myokines and health-related variables were assessed in 55 inpatients aged ≥ 65 years from the Peking Union Medical College Hospital prospective longitudinal frailty study. Serum was prepared for enzyme-linked immunosorbent assay using the appropriate kits. Correlations between biomarkers and frailty status were calculated by Spearman's correlation analysis. Multiple linear regression was performed to investigate the association between factors and frailty scores.

RESULTS

The prevalence of frailty was 13.21%. The bioinformatics analysis indicated that leptin, adenosine 5'-monophosphate-activated protein kinase (AMPK), irisin, decorin, and myostatin were potential biomarkers of frailty. The frailty group had significantly higher concentrations of leptin, AMPK, and MSTN than the robust group (p < 0.05). AMPK was significantly positively correlated with frailty (p < 0.05). The pre-frailty and frailty groups had significantly lower concentrations of irisin than the robust group (p < 0.05), whereas the DCN concentration did not differ among the groups. Multiple linear regression suggested that the 15 factors influencing the coefficients of association, the top 50% were the ADL score, MNA-SF score, serum albumin concentration, urination function, hearing function, leptin concentration, GDS-15 score, and MSTN concentration.

CONCLUSIONS

Proinflammatory myokines, particularly leptin, myostatin, and AMPK, negatively affect muscle mass and strength in older adults. ADL and nutritional status play major roles in the development of frailty. Our results confirm that identification of frailty relies upon clinical variables, myokine concentrations, and functional parameters, which might enable the identification and monitoring of frailty.

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.

[Sequential treatment of oral and maxillofacial deformities with hemifacial microsomia]

The incidence of the first and second branchial arch syndrome namely hemifacial microsomia (HFM) is the second only to cleft lip and palate, and it is a very common craniofacial developmental deformity. This congenital condition affects the development of the orbit, ear, and mandible, and the clinical manifestations of each patient are significantly heterogeneous. Clinical treatment needs to formulate corresponding treatment measures according to different degrees of tissue deformity at different ages. This article puts forward personal suggestions for the sequential treatment of oral and maxillofacial deformities of HFM from the perspective of patient age and classification.

[Clinicopathological features of thyroid-like low-grade nasopharyngeal papillary adenocarcinoma]

Objective: To investigate the clinicopathological features, immunophenotype and gene alterations of thyroid-like low-grade nasopharyngeal papillary adenocarcinoma (TL-LGNPPA). Methods: Fifteen case of TL-LGNPPA diagnosed at Zhejiang Cancer Hospital (5 cases) and the First Affiliated Hospital, Zhejiang University School of Medicine (10 cases) from November 2011 to August 2020 were collected. Clinical and pathological examinations, immunohistochemical staining and next-generation sequencing were performed. The clinicopathological and molecular characteristics were summarized, and relevant literature was reviewed. Results: Fifteen patients were identified and included. Their median age was 36 years (range, 20-60 years). The male-female ratio was 1.0∶1.1. The most common symptoms were epistaxis and nasal obstruction. The neoplasms were located on the roof of the nasopharynx or the posterior margin of the nasal septum. The pathological features included complex papillary and glandular structures mainly composed of single or pseudostratified cubic and columnar cells, with mild to moderate cytological atypia. In some cases, spindle cell features, nuclear grooves, ground glass nuclei, squamous metaplasia, or scattered psammoma bodies were identified. In addition, nuclear polar reversal cells, hobnail cells and micropapillary structures were found, but have not been reported in previous literature. Immunohistochemistry showed that the tumor cells were diffusely positive for TTF1, CK7, vimentin and CKpan; focally positive for p40, CK5/6 and p16; and negative for Tg, NapsinA, CK20, CDX2, S-100 and PAX8. The Ki-67 positive rates ranged from 1% to 20% and were≤10% in thirteen cases (13/15). EBER in situ hybridization was negative in all cases. DNA sequencing of 6 specimens was performed and all specimens were found harboring gene mutations (EWSR1, SMAD2, ROS1, JAK3, GRIN2A, ERRCC5, STAT3, and TET2), but no hot spot gene alterations were found. No MSI-H and MMR related gene changes were detected. All tumors showed low tumor mutation burden. All 15 patients underwent endoscopic surgery, and only 1 of them underwent radiotherapy postoperatively. All patients were recurrence free and alive at the end of follow-up periods (range: 23 to 129 months). Conclusions: TL-LGNPPA is a rare indolent tumor of the nasopharynx and exhibits a unique morphology and immunophenotype. Endoscopic resection is an effective treatment for TL-LGNPPA with excellent overall prognosis.

[Association between chronic lung diseases and the risk of lung cancer in UK Biobank: observational and Mendelian randomization analyses]

Objective: To investigate the association between chronic lung diseases and the risk of lung cancer. Methods: Using UK Biobank (UKB) survey data, 472 397 participants who had not previously been diagnosed with cancer and whose self-reported sex was consistent with their genetic sex were studied. Information on the prevalence of previous chronic lung diseases, general demographic characteristics and the prevalence of lung cancer was collected using baseline questionnaires and national health system data. The multivariate Cox proportional risk regression model was used to analyze the association between four previous chronic lung diseases (asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis and interstitial pulmonary disease) and the risk of lung cancer. A total of 458 526 participants with genotype data in the observational study were selected as research objects, and the closely related and independent genetic loci with four chronic lung diseases were selected as instrumental variables, and the association between four chronic lung diseases and the risk of lung cancer was analyzed by Mendelian randomization (MR). The dose-response relationship between genetic risk score and the risk of lung cancer in different chronic lung diseases was evaluated using a restricted cubic spline function. Results: The age [M (Q1, Q3)] of the subjects was 57 (50, 63) years old, and there were 3 516 new cases of lung cancer (0.74%) during follow-up. The multivariate Cox proportional hazard regression model analysis showed that previous chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis were associated with the risk of lung cancer, about 1.61 (1.49-1.75) and 2.61 (1.24-5.49), respectively. MR Studies showed that genetically predicted chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis were associated with the risk of lung cancer, with HR (95%CI) of 1.10 (1.03-1.19) and 1.04 (1.01-1.08), respectively. The results of restricted cubic spline function analysis showed that the risk of lung cancer increased linearly with the increase of genetic risk scores for chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis (P<0.05). Neither observational studies nor Mendelian randomization analysis found an association between previous asthma or interstitial lung disease and the risk of lung cancer (both P values>0.05). Conclusion: Chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis are potential risk factors for lung cancer.

A binary pulsar in a 53-minute orbit

Spider pulsars are neutron stars that have a companion star in a close orbit. The companion star sheds material to the neutron star, spinning it up to millisecond rotation periods, while the orbit shortens to hours. The companion is eventually ablated and destroyed by the pulsar wind and radiation1,2. Spider pulsars are key for studying the evolutionary link between accreting X-ray pulsars and isolated millisecond pulsars, pulsar irradiation effects and the birth of massive neutron stars3-6. Black widow pulsars in extremely compact orbits (as short as 62 minutes7) have companions with masses much smaller than 0.1 M⊙. They may have evolved from redback pulsars with companion masses of about 0.1-0.4 M⊙ and orbital periods of less than 1 day8. If this is true, then there should be a population of millisecond pulsars with moderate-mass companions and very short orbital periods9, but, hitherto, no such system was known. Here we report radio observations of the binary millisecond pulsar PSR J1953+1844 (M71E) that show it to have an orbital period of 53.3 minutes and a companion with a mass of around 0.07 M⊙. It is a faint X-ray source and located 2.5 arcminutes from the centre of the globular cluster M71.

[Molecular pathological mechanism of liver metabolic disorder in mice with severe spinal muscular atrophy]

OBJECTIVE

To explore the molecular pathological mechanism of liver metabolic disorder in severe spinal muscular atrophy (SMA).

METHODS

The transgenic mice with type Ⅰ SMA (Smn^-/- SMN2^0tg/2tg) and littermate control mice (Smn^+/- SMN2^0tg/2tg) were observed for milk suckling behavior and body weight changes after birth. The mice with type Ⅰ SMA mice were given an intraperitoneal injection of 20% glucose solution or saline (15 μL/12 h), and their survival time was recorded. GO enrichment analysis was performed using the RNA-Seq data of the liver of type Ⅰ SMA and littermate control mice, and the results were verified using quantitative real-time PCR. Bisulfite sequencing was performed to examine CpG island methylation level in Fasn gene promoter region in the liver of the neonatal mice.

RESULTS

The neonatal mice with type Ⅰ SMA showed normal milk suckling behavior but had lower body weight than the littermate control mice on the second day after birth. Intraperitoneal injection of glucose solution every 12 h significantly improved the median survival time of type Ⅰ SMA mice from 9±1.3 to 11± 1.5 days (P < 0.05). Analysis of the RNA-Seq data of the liver showed that the expression of the target genes of PPARα related to lipid metabolism and mitochondrial β oxidation were down-regulated in the liver of type Ⅰ SMA mice. Type Ⅰ SMA mice had higher methylation level of the Fasn promoter region in the liver than the littermate control mice (76.44% vs 58.67%). In primary cultures of hepatocytes from type Ⅰ SMA mice, treatment with 5-AzaC significantly up-regulated the expressions of the genes related to lipid metabolism by over 1 fold (P < 0.01).

CONCLUSION

Type Ⅰ SMA mice have liver metabolic disorder, and the down-regulation of the target genes of PPARα related to lipid and glucose metabolism due to persistent DNA methylation contributes to the progression of SMA.

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.

Effects of UV radiation on natural and synthetic materials

The deleterious effects of solar ultraviolet (UV) radiation on construction materials, especially wood and plastics, and the consequent impacts on their useful lifetimes, are well documented in scientific literature. Any future increase in solar UV radiation and ambient temperature due to climate change will therefore shorten service lifetimes of materials, which will require higher levels of stabilisation or other interventions to maintain their lifetimes at the present levels. The implementation of the Montreal Protocol and its amendments on substances that deplete the ozone layer, controls the solar UV-B radiation received on Earth. This current quadrennial assessment provides a comprehensive update on the deleterious effects of solar UV radiation on the durability of natural and synthetic materials, as well as recent innovations in better stabilising of materials against solar UV radiation-induced damage. Pertinent emerging technologies for wood and plastics used in construction, composite materials used in construction, textile fibres, comfort fabric, and photovoltaic materials, are addressed in detail. Also addressed are the trends in technology designed to increase sustainability via replacing toxic, unsustainable, legacy additives with 'greener' benign substitutes that may indirectly affect the UV stability of the redesigned materials. An emerging class of efficient photostabilisers are the nanoscale particles that include oxide fillers and nanocarbons used in high-performance composites, which provide good UV stability to materials. They also allow the design of UV-shielding fabric materials with impressive UV protection factors. An emerging environmental issue related to the photodegradation of plastics is the generation of ubiquitous micro-scale particles from plastic litter exposed to solar UV radiation.

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.

Three-dimensional quantification of fibrosis and ossification after cochlear implantation via virtual re-sectioning: Potential implications for residual hearing

Hearing preservation may be achieved initially in the majority of patients after cochlear implantation, however, a significant proportion of these patients experience delayed hearing loss months or years later. A prior histological report in a case of delayed hearing loss suggested a potential cochlear mechanical origin of this hearing loss due to tissue fibrosis, and older case series highlight the frequent findings of post-implantation fibrosis and neoosteogenesis though without a focus on the impact on residual hearing. Here we present the largest series (N = 20) of 3-dimensionally reconstructed cochleae based on digitally scanned histologic sections from patients who were implanted during their lifetime. All patients were implanted with multichannel electrodes via a cochleostomy or an extended round window insertion. A quantified analysis of intracochlear tissue formation was carried out via virtual re-sectioning orthogonal to the cochlear spiral. Intracochlear tissue formation was present in every case. On average 33% (SD 14%) of the total cochlear volume was occupied by new tissue formation, consisting of 26% (SD 12%) fibrous and 7% (SD 6%) bony tissue. The round window was completely covered by fibro-osseous tissue in 85% of cases and was associated with an obstruction of the cochlear aqueduct in 100%. The basal part of the basilar membrane was at least partially abutted by the electrode or new tissue formation in every case, while the apical region, corresponding with a characteristic frequency of < 500 Hz, appeared normal in 89%. This quantitative analysis shows that after cochlear implantation via extended round window or cochleostomy, intracochlear fibrosis and neoossification are present in all cases at anatomical locations that could impact normal inner ear mechanics.

Serum SIRT6 Levels Are Associated with Frailty in Older Adults

OBJECTIVES

Frailty is one of the major health problems facing aging societies worldwide. We investigated the association between serum SIRT6 and frailty in older adults.

DESIGN

Cross-sectional analysis of associations of serum SIRT6 and frailty in older people.

SETTING

Enrolled community-dwelling and hospital outpatient clinic adults older than 65 years old in Wuhan City, Hubei Province, China.

PARTICIPANTS

A total of 540 community-dwelling older adults (age ≥ 65 years) in Wuhan were included in the study.

MEASURES

We used Frailty Phenotype criteria for classifying participants based on their frailty status. Serum SIRT6 was measured using an ELISA kit.

RESULTS

A total of 540 older adults were included in this cross-sectional study. Serum SIRT6 was lower in the slowness group (7.23±1.81 vs 5.89±1.74, p<0.001), weakness group (6.87±1.88 vs 5.68±1.64, p<0.001), and exhaustion group (6.73±1.90 vs 5.88±1.74, p<0.001) compare with the normal group. ROC curves were used to assess the efficiency of SIRT6 in predicting frailty in older adults. The AUC for SIRT6 was 0.792 (95% CI: 0.7514 to 0.8325), with the highest sensitivity of 68.0% and the specificity of 91.9%, and the optimal critical value of 4.65ng/ml according to Youden's index. Multivariate logistic regression analysis showed that serum SIRT6 level was independently associated with frailty in older people.

CONCLUSION

In conclusion, serum SIRT6 was decreased in frailty compared with robust older adults. A decreased serum SIRT6 was independently associated with an increased risk of frailty. SIRT6 may be a potential target for the treatment of patients with frailty.

[Mediation effect of smoking and healthy diet score on the association between educational level and the risk of lung cancer incidence]

Objective: To evaluate the possible mediation effect of smoking and healthy diet score on the association between educational level and the risk of lung cancer incidence. Methods: After excluding individuals with missing educational levels and cancer information at baseline, 446 772 participants in the UK Biobank (UKB) prospective cohort study were included. Cox regression models were used to investigate the associations of educational level and smoking and healthy diet score with the incidence of lung cancer. Mediating effect analysis was conducted to analyze the mediating effect of smoking and healthy diet score on the correlation between educational level and lung cancer. Results: During a median follow-up of 7.13 years, 1 994 new- onset lung cancer cases were observed. Per 1 standard deviation (5 years) increase in educational level was associated with a 12% lower risk of lung cancer (HR=0.88, 95%CI: 0.84-0.92). The corresponding level 1-5 in the International Standard Classification for Education (ISCED) were mapped to UKB self-report highest qualification to estimate the educational level. A higher rank means a higher educational level. Compared with level ISCED-1, the HR(95%CI) of level ISCED-2, ISCED-3, ISCED-4 and ISCED-5 were respectively 0.83 (0.72-0.94), 0.67 (0.53-0.85), 0.76 (0.65-0.89) and 0.72 (0.64-0.80) for lung cancer. Education years were negatively correlated with smoking, with β coefficients (95%CI) being -0.079 (-0.081- -0.077), but positively correlated with healthy diet score (β=0.042, 95%CI: 0.039-0.045). Analysis of mediating effect indicated that the association of educational level with lung cancer risk was mediated by smoking and healthy diet score, the proportions of mediating effect were 38.952% (95%CI: 31.802%-51.659%) and 1.784% (95%CI: 0.405%-3.713%), respectively. Conclusion: Smoking and healthy diet score might mediate the effect of educational level on the incidence of lung cancer, indicating that improving the level of education can reduce the risk of lung cancer by changing lifestyles such as smoking and diet.

[Application study of stool-based methylated SDC2 test in the screening of colorectal neoplasms for physical examination population]

Objective: To investigate the value of stool-based methylated SDC2 test in physical examination population for the screening of colorectal neoplasms. Methods: Using the prospective cohort study method, from December 2020 to November 2021, 2 107 participants from the First People's Hospital of Xiushui County, Jiangxi Province were enrolled, consisted of 1 012 males and 1 094 females, aged 20-90 years with the median age of 49 years old. Fresh stool samples were collected and SDC2 DNA methylation tests were carried out as the primary screening method. The participants with positive results were recommended to undergo colonoscopy, and those who were negative were followed up by telephone. The positive rate of screening, the compliance of colonoscopy, and the detection of colorectal lesions were analyzed by chi-square test. Combined the follow-up results of negative subjects, the value of SDC2 DNA methylation test for the screening of colorectal neoplasms was evaluated. Results: Among the 2 107 participants, 2 106 completed the SDC2 methylation test. 113 participants (5.4%) were positive. The positive rate of primary screening increased with age significantly (χ²=32.135, P<0.001). Out of 113 cases, 72 (63.7%) underwent colonoscopy examinations. Finally, 3 (4.2%) cases of colorectal cancer, 12 (16.7%) cases of advanced adenoma, 31 (43.1%) cases of non-advanced adenoma, and 16 (22.2%) cases of non-adenomatous polyp were detected. The positive predictive value (PPV) of stool-based SDC2 DNA methylation test for intestinal lesions and colorectal neoplasms were 86.1% and 63.9%, respectively. Among the 1 374 follow-up participants, the negative predictive value (NPV) of this test for intestinal lesions and colorectal neoplasms were 97.7% and 99.4%, respectively. Conclusion: Primary stool-based SDC2 DNA methylation test and subsequent colonoscopy examination can effectively find colorectal neoplasms. This strategy may be a potential tool for the screening of colorectal neoplasms in general risk population.

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.

[Effects and mechanism of water-soluble chitosan hydrogel on infected full-thickness skin defect wounds in diabetic mice]

Objective: To explore the effects and mechanism of water-soluble chitosan hydrogel on infected full-thickness skin defect wounds in diabetic mice. Methods: The experimental research method was adopted. The control hydrogel composed of polyvinyl alcohol and gelatin, and the water-soluble chitosan hydrogel composed of the aforementioned two materials and water-soluble chitosan were prepared by the cyclic freeze-thaw method. The fluidity of the two dressings in test tube before and after the first freeze-thawing was generally observed, and the difference in appearance of the final state of two dressings in 12-well plates were compared. According to random number table (the same grouping method below), the cell strains of L929 and HaCaT were both divided into water-soluble chitosan hydrogel group and control hydrogel group, respectively. After adding corresponding dressings and culturing for 24 h, the cell proliferation activity was measured using cell counting kit 8. Rabbit blood erythrocyte suspensions were divided into normal saline group, polyethylene glycol octyl phenyl ether (Triton X-100) group, water-soluble chitosan hydrogel group, and control hydrogel group, which were treated accordingly and incubated for 1 hour, and then the hemolysis degree of erythrocyte was detected by a microplate reader. Twenty-four female db/db mice aged 11-14 weeks were selected, and full-thickness skin defect wounds on their backs were inflicted and inoculated with the methicillin-resistant Staphylococcus aureus (MRSA), 72 h later, the mice were divided into blank control group, sulfadiazine silver hydrogel group, control hydrogel group, and water-soluble chitosan hydrogel group, which were treated accordingly. On post injury day (PID) 0 (immediately), 7, 14, and 21, the healing of the wound was observed. On PID 14 and 21, the wound healing rate was calculated. On PID 14, MRSA concentration in wounds was determined. On PID 21, the wounds were histologically analyzed by hematoxylin and eosin staining; the expression of CD31 in the wounds was detected by immunofluorescence method, and its positive percentage was calculated. Raw264.7 cells were taken and divided into interleukin-4 (IL-4) group, blank control group, control hydrogel group, and water-soluble chitosan hydrogel group, which were treated accordingly. At 48 h of culture, the percentages of CD206 positive cells were detected by flow cytometry. The number of samples was all 3. Data were statistically analyzed with independent sample t test, one-way analysis of variance, analysis of variance for repeated measurement, least significant difference test, and Dunnett T3 test. Results: Two dressings in test tube had certain fluidity before freeze-thawing and formed semi-solid gels after freeze-thawing for once. The final forms of two dressings in 12-well plates were basically stable and translucent sheets, with little difference in transparency. At 24 h of culture, the cell proliferation activities of L929 and HaCaT in water-soluble chitosan hydrogel group were significantly higher than those in control hydrogel group (with t values of 6.37 and 7.50, respectively, P<0.01). At 1 h of incubation, the hemolysis degree of erythrocyte in water-soluble chitosan hydrogel group was significantly lower than that in Triton X-100 group (P<0.01), but similar to that in normal saline group and control hydrogel group (P>0.05). On PID 0, the traumatic conditions of mice in the 4 groups were similar. On PID 7, more yellowish exudates were observed inside the wound in blank control group and control hydrogel group, while a small amount of exudates were observed in the wound in sulfadiazine silver hydrogel group and water-soluble chitosan hydrogel group. On PID 14, the wounds in blank control group and control hydrogel group were dry and crusted without obvious epithelial coverage; in sulfadiazine silver hydrogel group, the scabs fell off and purulent exudate was visible on the wound; in water-soluble chitosan hydrogel group, the base of wound was light red and obvious epithelial coverage could be observed on the wound. On PID 14, the wound healing rate in water-soluble chitosan hydrogel group was significantly higher than that in the other 3 groups (all P<0.01). On PID 21, the wound in water-soluble chitosan hydrogel group was completely closed, while the wounds in the other 3 groups were not completely healed; the wound healing rate in water-soluble chitosan hydrogel group was significantly higher than that in the other 3 groups (all P<0.01). On PID 14, the concentration of MRSA in the wound in water-soluble chitosan hydrogel group was significantly lower than that in blank control group (P<0.01), but similar to that in control hydrogel group and sulfadiazine silver hydrogel group (P>0.05). On PID 21, the new epidermis was severely damaged in blank control group; the epidermis on the wound in control hydrogel group also had a large area of defect; complete new epidermis had not yet being formed on the wound in sulfadiazine silver hydrogel group; the wound in water-soluble chitosan hydrogel group was not only completely covered by the new epidermis, the basal cells of the new epidermis were also regularly aligned. On PID 21, the percentage of CD31 positivity in the wound in water-soluble chitosan hydrogel group was (2.19±0.35)%, which was significantly higher than (0.18±0.05)% in blank control group, (0.23±0.06)% in control hydrogel group, and (0.62±0.25)% in sulfadiazine silver hydrogel group, all P<0.01. At 48 h of culture, the percentage of CD206 positive Raw264.7 cells in water-soluble chitosan hydrogel group was lower than that in IL-4 group (P>0.01) but significantly higher than that in blank control group and control hydrogel group (P<0.05 or P<0.01). Conclusions: The water-soluble chitosan hydrogel has good biosafety and can induce higher level of macrophage M2 polarization than control hydrogel without water-soluble chitosan, so it can enhance the repair effect of MRSA-infected full-thickness skin defect wounds in diabetic mice and promote rapid wound healing.

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01420-1.

Hierarchical hollow superstructure cobalt selenide bird nests for high-performance lithium storage

The inferior cycling performance caused by large volume variation is the main problem that restricts the application of cobalt selenides in lithium-ion batteries. Herein, we synthesize raspberry-like Co-ethylene glycol precursor. It is further selenized into the hierarchical hollow superstructure CoSe₂/CoSe bird nests that are assembled by the hollow nanosphere units of CoSe₂ and CoSe nanocrystalline. CoSe₂/CoSe bird nests achieve excellent cycling performance, high reversible capacity and satisfactory rate capability (1361 mAh/g at 1 A/g after 1000 cycles, 579 mAh/g at 2 A/g after 2000 cycles, 315 mAh/g at 5 A/g after 1000 cycles). Electrochemical kinetics analyses and ex-situ material characterization reveal that the surface capacitive behavior controls the electrochemical reaction, and the composite has low reaction impedance, fast and stable Li⁺ diffusion, and superior structural stability. The superior lithium storage performance is attributed to the unique superstructure bird nest. Large specific surface area, abundant hierarchical pores and the opening mouth result in high electrochemical activity, which induces high reversible capacity. The small hollow nanosphere units, the sufficiently thick hierarchical porous superstructure shell and the large hollow interior bring about the strong synergistic effect to improve cycling performance. The intimately coupling of CoSe₂/CoSe nanocrystalline and the hollow nanosphere units guarantees high conductivity. This work has greatly enriched the understanding of structure design of high-performance cobalt selenide anodes.

P-382 Decrease of serum estradiol prior to human chorionic gonadotrophin administration have an impact on live birth in IVF/ICSI cycles

Study question

Whether decrease of serum estradiol prior to human chorionic gonadotrophin administration have an impact on live birth in IVF/ICSI cycles?

Summary answer

The E2 change before the day of hCG administration had significant correlation with live birth. The live birth rate decreased with decreasing serum E2 level.

What is known already

The objective of this study was to assess the effects of a decrease of estradiol (E2) levels on the day of human chorionic gonadotrophin (hCG) administration on in vitro fertilization /intracytoplasmic sperm injection (IVF/ICSI) outcomes, including cycles with long, antagonist and micro stimulus protocols.

Study design, size, duration

In this retrospective cohort study, 1303 patients who received IVF/ICSI non-donor treatment were identified. Patients were divided into two groups according to live birth and the characteristics of IVF/ICSI cycles were compared between groups, including baseline infertility parameters, ovarian stimulation characteristics and embryo laboratory manipulation parameters.

Participants/materials, setting, methods

In this retrospective cohort study, 1303 patients who received IVF/ICSI non-donor treatment were identified. Patients were divided into two groups according to live birth and the characteristics of IVF/ICSI cycles were compared between groups, including baseline infertility parameters, ovarian stimulation characteristics and embryo laboratory manipulation parameters. The multivariate logistic regression model was performed to adjust potential confounders and assess correlation between E2 dynamics before hCG administration and live birth.

Main results and the role of chance

Our results revealed that patients without live birth had higher age (32.13 ± 4.33 vs. 30.21 ± 3.71, P &lt; 0.001) and pervious miscarriages (0.57 ± 0.95 vs. 0.46 ± 0.83, P = 0.0295), while had lower number of oocytes retrieved (8.95 ± 4.69 vs. 12.36 ± 5.54, P &lt; 0.001), day of hCG E2 (8269.53 ± 4104.22 vs. 9580.71 ± 3534.11, P &lt; 0.001) and endometrium thickness (10.37 ± 3.66 vs. 11.50 ± 3.40, P &lt; 0.001) compared with patients with live birth. Additionally, the multivariate logistic regression analysis displayed significant impact of serum E2 change on the live birth, and the achievement of live birth [OR (95%CI) 0.81 (0.71, 0.92), P = 0.001] decreased with the decreasing level of serum E2 before hCG trigger day. Estradiol stratification analyses displayed the OR and 95% CI for the association between △E2 and live birth among patients with different levels of estradiol decline (&lt;25%, 25%–50%, 50%–75%, &gt;75%). Compared with the &lt;25% decline and 25%–50% decline groups, the ORs of 50%–75% and &gt;75% decline groups were 1.66 (95% CI: 1.12-2.45, P = 0.012) and 2.00 (95% CI: 1.39-2.89, P &lt; 0.001), respectively, after adjusting potential confounders.

Limitations, reasons for caution

There was concealment of randomization and blinding of outcome assessments reducing the risk of selection and measurement bias.

Wider implications of the findings

In summary, the E2 change before the day of hCG administration had significant correlation with live birth, and the live birth decreased with the decreasing level of serum E2 before hCG trigger day. The patients with a greater decline in the E2 level more likely to had poor clinical outcomes.

Trial registration number

Chi CTR1900026088

[Isobavachalcone induces cell death through multiple pathways in human breast cancer MCF-7 cells]

OBJECTIVE

To explore the effects of isobavachalcone (IBC) on cell death of human breast cancer MCF-7 cells and explore the possible mechanism.

METHODS

MCF-7 cells were treated with different concentrations of IBC, and the changes in cell proliferation were assessed using MTT assay. Apoptosis of MCF-7 cells following treatment with 10, 20, and 40 μmol/L IBC was analyzed using flow cytometry with annexin V-FITC/PI double staining and fluorescence microscopy, and the expressions of apoptosis- and autophagy-related proteins (Bax, Bcl-2, Akt, p-Akt, p62, and LC3) were detected with Western blotting. Electron microscopy was used to observe the changes in submicrostructure of the cells following treatment with 40 μmol/L IBC. JC-1 assay kit, ATP assay kit, and reactive oxygen species (ROS) kit were used to determine the effect of IBC on mitochondrial function of the cells.

RESULTS

MTT assay showed that IBC significantly inhibited the proliferation of MCF-7 cells in a concentration- and time-dependent manner, with IC₅₀ values of 38.46, 31.31, and 28.26 μmol/L at 24, 48, and 72 h, respectively. IBC also concentration-dependently induced apoptosis of MCF-7 cells. IBC-induced cell death was inhibited by z-VAD-fmk, a caspase inhibitor (P < 0.05), but not by the necroptosis inhibitor necrostatin-1 (Nec-1). Western blotting showed that IBC-induced MCF-7 cell apoptosis by increasing Bax expression and down-regulating the expressions of Bcl-2, Akt and p-Akt-473 (all P < 0.05). With the increase of IBC concentration, the expression of autophagy-related protein p62 and the LC3-II/I ratio increased progressively. Electron microscopy revealed the presence of autophagic bodies in IBC-treated MCF-7 cells. IBC treatment also resulted in decreased mitochondrial membrane potential and intracellular ATP level and increased ROS accumulation in MCF-7 cells (P < 0.05).

CONCLUSION

IBC is capable of inducing both apoptosis and autophagy in MCF-7 cells, suggesting the potential value of IBC as a lead compound in the development of anti-breast cancer agents.

[Low-dose helical CT projection data restoration using noise estimation]

OBJECTIVE

To build a helical CT projection data restoration model at random low-dose levels.

METHODS

We used a noise estimation module to achieve noise estimation and obtained a low-dose projection noise variance map, which was used to guide projection data recovery by the projection data restoration module. A filtering back-projection algorithm (FBP) was finally used to reconstruct the images. The 3D wavelet group residual dense network (3DWGRDN) was adopted to build the network architecture of the noise estimation and projection data restoration module using asymmetric loss and total variational regularization. For validation of the model, 1/10 and 1/15 of normal dose helical CT images were restored using the proposed model and 3 other restoration models (IRLNet, REDCNN and MWResNet), and the results were visually and quantitatively compared.

RESULTS

Quantitative comparisons of the restored images showed that the proposed helical CT projection data restoration model increased the structural similarity index by 5.79% to 17.46% compared with the other restoration algorithms (P < 0.05). The image quality scores of the proposed method rated by clinical radiologists ranged from 7.19% to 17.38%, significantly higher than the other restoration algorithms (P < 0.05).

CONCLUSION

The proposed method can effectively suppress noises and reduce artifacts in the projection data at different low-dose levels while preserving the integrity of the edges and fine details of the reconstructed CT images.

[An adaptive CT metal artifact reduction algorithm that combines projection interpolation and physical correction]

OBJECTIVE

To propose an adaptive weighted CT metal artifact reduce algorithm that combines projection interpolation and physical correction.

METHODS

A normalized metal projection interpolation algorithm was used to obtain the initial corrected projection data. A metal physical correction model was then introduced to obtain the physically corrected projection data. To verify the effectiveness of the method, we conducted experiments using simulation data and clinical data. For the simulation data, the quantitative indicators PSNR and SSIM were used for evaluation, while for the clinical data, the resultant images were evaluated by imaging experts to compare the artifact-reducing performance of different methods.

RESULTS

For the simulation data, the proposed method improved the PSNR value by at least 0.2 dB and resulted in the highest SSIM value among the methods for comparison. The experiment with the clinical data showed that the imaging experts gave the highest scores of 3.616±0.338 (in a 5-point scale) to the images processed using the proposed method, which had significant better artifact-reducing performance than the other methods (P < 0.001).

CONCLUSION

The metal artifact reduction algorithm proposed herein can effectively reduce metal artifacts while preserving the tissue structure information and reducing the generation of new artifacts.

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.

[Potential transmission risk of key parasitic diseases and responses to the risk during the construction of an ecological city in Shanghai Municipality]

A blueprint on Shanghai's ecological space design between 2021 and 2035 was released in 2021, aiming to build an ecological city and improve the development of ecological civilization. The transmission of parasitic diseases is strongly associated with climate and ecological environments. Currently, the prevalence of parasitic diseases has been maintained at extremely low-transmission levels, and there are almost no local cases; however, the alteration of ecological environments may results in a potential transmission risk of parasitic diseases. Hereby, the current status of key parasitic diseases in Shanghai Municipality was described, and the potential transmission risk of parasitic diseases and responses to this risk were analyzed during the construction of an ecological city in Shanghai Municipality. In addition, the suggestions pertaining to surveillance and management of parasitic diseases were proposed during the mid- and long-term construction of an ecological city in Shanghai Municipality.

[Relationship between body mass index and sexual development in Chinese children]

Objective: To investigate the relationship between body mass index (BMI) and sexual development in Chinese children. Methods: A nationwide multicenter and population-based large cross-sectional study was conducted in 13 provinces, autonomous regions and municipalities of China from January 2017 to December 2018. Data on sex, age, height, weight were collected, BMI was calculated and sexual characteristics were analyzed. The subjects were divided into four groups based on age, including ages 3-<6 years, 6-<10 years, 10-<15 years and 15-<18 years. Multiple Logistic regression models were used for evaluating the associations of BMI with sexual development in children. Dichotomous Logistic regression was used to compare the differences in the distribution of early and non-early puberty among normal weight, overweight and obese groups. Curves were drawn to analyze the relationship between the percentage of early puberty and BMI distribution in girls and boys at different Tanner stages. Results: A total of 208 179 healthy children (96 471 girls and 111 708 boys) were enrolled in this study. The OR values of B2, B3 and B4+ in overweight girls were 1.72 (95%CI: 1.56-1.89), 3.19 (95%CI: 2.86-3.57), 7.14 (95%CI: 6.33-8.05) and in obese girls were 2.05 (95%CI: 1.88-2.24), 4.98 (95%CI: 4.49-5.53), 11.21 (95%CI: 9.98-12.59), respectively; while the OR values of G2, G3, G4+ in overweight boys were 1.27 (95%CI: 1.17-1.38), 1.52 (95%CI: 1.36-1.70), 1.88 (95%CI: 1.66-2.14) and in obese boys were 1.27 (95%CI: 1.17-1.37), 1.59 (95%CI: 1.43-1.78), and 1.93 (95%CI: 1.70-2.18) (compared with normal weight Tanner 1 group,all P<0.01). Analysis in different age groups found that OR values of obese girls at B2 stage and boys at G2 stage were 2.02 (95%CI: 1.06-3.86) and 2.32 (95%CI:1.05-5.12) in preschool children aged 3-<6 years, respectively (both P<0.05). And in the age group of 6-10 years, overweight girls had a 5.45-fold risk and obese girls had a 12.54-fold risk of B3 stage compared to girls with normal BMI. Compared with normal weight children, the risk of early puberty was 2.67 times higher in overweight girls, 3.63 times higher in obese girls, and 1.22 times higher in overweight boys, 1.35 times higher in obese boys (all P<0.01). Among the children at each Tanner stages, the percentage of early puberty increased with the increase of BMI, from 5.7% (80/1 397), 16.1% (48/299), 13.8% (27/195) to 25.7% (198/769), 65.1% (209/321), 65.4% (157/240) in girls aged 8-<9, 10-<11 and 11-<12 years, and 6.6% (34/513), 18.7% (51/273), 21.6% (57/264) to 13.3% (96/722), 46.4% (140/302), 47.5% (105/221) in boys aged 9-<10, 12-<13 and 13-<14 years, respectively. Conclusions: BMI is positively correlated with sexual development in both Chinese boys and girls, and the correlation is stronger in girls. Obesity is a risk factor for precocious puberty in preschool children aged 3-<6 years, and 6-<10 years of age is a high risk period for early development in obese girls.

Environmental effects of stratospheric ozone depletion, UV radiation, and interactions with climate change: UNEP Environmental Effects Assessment Panel, Update 2021

The Environmental Effects Assessment Panel of the Montreal Protocol under the United Nations Environment Programme evaluates effects on the environment and human health that arise from changes in the stratospheric ozone layer and concomitant variations in ultraviolet (UV) radiation at the Earth’s surface. The current update is based on scientific advances that have accumulated since our last assessment (Photochem and Photobiol Sci 20(1):1–67, 2021). We also discuss how climate change affects stratospheric ozone depletion and ultraviolet radiation, and how stratospheric ozone depletion affects climate change. The resulting interlinking effects of stratospheric ozone depletion, UV radiation, and climate change are assessed in terms of air quality, carbon sinks, ecosystems, human health, and natural and synthetic materials. We further highlight potential impacts on the biosphere from extreme climate events that are occurring with increasing frequency as a consequence of climate change. These and other interactive effects are examined with respect to the benefits that the Montreal Protocol and its Amendments are providing to life on Earth by controlling the production of various substances that contribute to both stratospheric ozone depletion and climate change.

Charge density waves and Fermi surface reconstruction in the clean overdoped cuprate superconductor Tl2Ba2CuO6+δ

Hall effect and quantum oscillation measurements on high temperature cuprate superconductors show that underdoped compositions have small Fermi surface pockets whereas when heavily overdoped, a single much larger pocket is found. The origin of this change in electronic structure has been unclear, but may be related to the high temperature superconductivity. Here we show that the clean overdoped single-layer cuprate Tl₂Ba₂CuO_6+δ (Tl2201) displays CDW order with a remarkably long correlation length ξ ≈ 200 Å which disappears above a hole doping of p_CDW ≈ 0.265. We show that the evolution of the electronic properties of Tl2201 as the doping is lowered may be explained by a Fermi surface reconstruction which accompanies the emergence of the CDW below p_CDW. Our results demonstrate importance of CDW correlations in understanding the electronic properties of overdoped cuprates.

The origin of the Fermi surface reconstruction that occurs in cuprate superconductors as hole doping increases remains unclear. Here, the authors observe long range charge density wave (CDW) order in the overdoped single-layer cuprate Tl₂Ba₂CuO_6+δ, which then disappears above a hole concentration 0.265, suggesting a correlation between Fermi surface reconstruction and the emergence of the CDW.

Predictive Value of Geriatric Nutritional Risk Index in Older Adult Cancer Patients

BACKGROUND AND AIMS

To compare the association of geriatric nutritional risk index (GNRI) and controlling nutritional status (CONUT) scores with malnutrition, and to study their association with clinical outcomes in older adult cancer patients.

METHODS

This retrospective analysis was conducted on 854 older adult cancer patients collected from 34 hospitals in 18 cities in China between June and September 2014. Anthropometric and hematological examination results at admission were collected, and subjective global assessment was used. Clinical outcomes, such as complications, length of hospital stays, and hospital costs, were recorded. Receiver operating characteristic curves were used to evaluate the accuracy of the two nutritional assessment tools for malnutrition. The association between GNRI and CONUT score and clinical outcomes was analyzed using the chi-square test, t-test, or rank sum test.

RESULTS

Among 854 patients with cancer, the prevalence of malnutrition was 42.7%. Compared with subjective global assessment, the GNRI had a significantly higher accuracy than the CONUT score in predicting malnutrition (area under the curve 0.704, 95% confidence interval, 0.658 - 0.750, P < 0.001). The GNRI was significantly associated with the occurrence of complications (χ2 = 4.985, P = 0.026), and low GNRI (≤98) was associated with a longer length of hospital stay (t = -2.179, P = 0.030).

CONCLUSIONS

The GNRI may be used to assess malnutrition in older adult cancer patients and can predict poor clinical outcomes in these patients.

Sex-specific plasticity in CRF regulation of inhibitory control in central amygdala CRF1 neurons after chronic voluntary alcohol drinking

Despite strong preclinical evidence for the ability of corticotropin releasing factor 1 (CRF1) antagonists to regulate alcohol consumption, clinical trials have not yet demonstrated therapeutic effects of these compounds in alcohol use disorder (AUD) patients. Several confounding factors may limit the translation of preclinical CRF1 research to patients, including reliance on experimenter-administered alcohol instead of voluntary consumption, a preponderance of evidence collected in male subjects only and an inability to assess the effects of alcohol on specific brain circuits. A population of particular interest is the CRF1-containing neurons of the central amygdala (CeA). CRF1 CeA neurons are sensitive to ethanol, but the effects of alcohol drinking on CRF signalling within this population are unknown. In the present study, we assessed the effects of voluntary alcohol drinking on inhibitory control of CRF1+ CeA neurons from male and female CRF1:GFP mice using ex vivo electrophysiology and determined the contributions of CRF1 signalling to inhibitory control and voluntary alcohol drinking. Chronic alcohol drinking produced neuroadaptations in CRF1+ neurons that increased the sensitivity of GABA_A receptor-mediated sIPSCs to the acute effects of alcohol, CRF and the CRF1 antagonist R121919, but these adaptations were more pronounced in male versus female mice. The CRF1 antagonist CP-154,526 reduced voluntary alcohol drinking in both sexes and abolished sex differences in alcohol drinking. The lack of alcohol-induced adaptation in the female CRF1 system may be related to the elevated alcohol intake exhibited by female mice and could contribute to the ineffectiveness of CRF1 antagonists in female AUD patients.

[Prevalence of Clonorchis sinensis infections in freshwater fish in mainland China: A meta-analysis]

OBJECTIVE

To understand the real prevalence of Clonorchis sinensis infections in the freshwater fish in mainland China, so as to provide insights into clonorchiasis control and detection of freshwater fish.

METHODS

All literatures reporting the prevalence of C. sinensis infections in the freshwater fish, the second intermediate host of the parasite, were jointly retrieved in Chinese and English electronic databases from January 1, 2010 to December 31, 2020, including Wanfang Data, CNKI, PubMed, Web of Science, Embase and Cochrane Library. All studies were screened based on inclusion and exclusion criteria, and the quality of all enrolled literatures was evaluated. The pooled prevalence of C. sinensis infections in freshwater fish and its 95% confidence interval (CI) were estimated using the software Stata version 15.0, and subgroup analyses were performed to investigate the region-, season- and sample source-specific pooled prevalence of C. sinensis infections in freshwater fish. In addition, the sensitivity and publication bias of all included studies were analyzed.

RESULTS

A total of 40 eligible literatures were included in this study, including 37 Chinese literatures and 3 English literatures, and there were 10 high-quality literatures, 27 moderate-quality literatures and 3 low-quality literatures. A total of 53 species containing 37 959 freshwater fish were reported in these 40 studies, and 73.58% (39/53) of freshwater fish species were identified with C. sinensis infections. Meta-analysis showed 23.5% [95% CI: (0.19, 0.28)] pooled prevalence of C. sinensis infections in freshwater fish in mainland China, and subgroup analyses higher prevalence of C. sinensis infections in freshwater fish in northeastern China [35.7%, 95% CI: (0.22, 0.50)] than in central [25.9%, 95% CI: (0.04, 0.48)] and southern China [20.6%, 95% CI: (0.09, 0.32)], higher prevalence of C. sinensis infections in freshwater fish sampled in spring [44.1%, 95% CI: (0.35, 0.53)] than in autumn [6.7%, 95% CI: (0.05, 0.08)] and summer [3.3%, 95% CI: (-0.01, 0.07)], and higher prevalence of C. sinensis infections in freshwater fish sampled from natural water [25.2%, 95% CI: (0.17, 0.33)] than from retail trades [22.2%, 95% CI: (0.17, 0.28)] and breeding chain [12.3%, 95% CI: (0.03, 0.22)]. However, all included studies had a publication bias with a low sensitivity.

CONCLUSIONS

The prevalence of C. sinensis infections is high in freshwater fish in mainland China, and there are still challenges for clonorchiasis control. Reinforcement of health education, diagnostics development and food safety supervision is recommended in future clonorchiasis control programs.

Characterization of genetic fundamentals for piglet mortality at birth in Yorkshire, Landrace, and Duroc sows

Piglet mortality is an economically important complex trait that impacts sow prolificacy. Genetic analyses for piglet mortality at weaning have been reported in dozens of studies, but not for piglet mortality at birth. In this study, we used multi-breed data sets from Yorkshire, Landrace, and Duroc sows to characterize the genetic fundamentals of piglet mortality at birth. The heritabilities from parity I to III were estimated to be 0.0630, 0.1031, and 0.1140 respectively. By using a combined strategy, a total of 21 SNPs were detected in three parities, of which six were observed in parity I, five in parity II and 10 in parity III. Genome annotation revealed that these SNPs were harbored within or close to 19 candidate genes. The candidate genes were found to associate with the reproductive system and embryonic development in the tissue expression database, which are reasonably related to piglet mortality. These findings are expected to provide much information for understanding the genetic and genomic fundamentals of farrowing mortality.

Integrating genome-wide association and transcriptome prediction model identifies novel target genes for osteoporosis

In this study, we integrated large-scale GWAS summary data and used the predicted transcriptome-wide association study method to discover novel genes associated with osteoporosis. We identified 204 candidate genes, which provide novel clues for understanding the genetic mechanism of osteoporosis and indicate potential therapeutic targets.

INTRODUCTION

Osteoporosis is a highly polygenetic disease characterized by low bone mass and deterioration of the bone microarchitecture. Our objective was to discover novel candidate genes associated with osteoporosis.

METHODS

To identify potential causal genes of the associated loci, we investigated trait-gene expression associations using the transcriptome-wide association study (TWAS) method. This method directly imputes gene expression effects from genome-wide association study (GWAS) data using a statistical prediction model trained on GTEx reference transcriptome data. We then performed a colocalization analysis to evaluate the posterior probability of biological patterns: associations characterized by a single causal variant or multiple distinct causal variants. Finally, a functional enrichment analysis of gene sets was performed using the VarElect and CluePedia tools, which assess the causal relationships between genes and a disease and search for potential gene's functional pathways. The osteoporosis-associated genes were further confirmed based on the differentially expressed genes profiled from mRNA expression data of bone tissue.

RESULTS

Our analysis identified 204 candidate genes, including 154 genes that have been previously associated with osteoporosis, 50 genes that have not been previously discovered. A biological function analysis found that 20 of the candidate genes were directly associated with osteoporosis. Further analysis of multiple gene expression profiles showed that 15 genes were differentially expressed in patients with osteoporosis. Among these, SLC11A2, MAP2K5, NFATC4, and HSP90B1 were enriched in four pathways, namely, mineral absorption pathway, MAPK signaling pathway, Wnt signaling pathway, and PI3K-Akt signaling pathway, which indicates a causal relationship with the occurrence of osteoporosis.

CONCLUSIONS

We demonstrated that transcriptome fine-mapping identifies more osteoporosis-related genes and provides key insight into the development of novel targeted therapeutics for the treatment of osteoporosis.

The dUTPase of caprine arthritis-encephalitis virus negatively regulates interferon signaling pathway

Background

Deoxyuracil triphosphate nucleotide (dUTP) pyrophosphatase (dUTPase, DU) is an enzyme of caprine arthritis-encephalitis virus (CAEV) that minimizes incorporation of dUTP into the DNA. Caprine arthritis-encephalitis virus relies partly on its ability to escape from innate immunity to cause persistent infections. Interferon β (IFN-β) is an important marker for evaluating the innate immune system, and it has a broad spectrum of antiviral activity.

Aims

This study was conducted to investigate the details of the IFN-β response to CAEV infection.

Methods

The expression of IFN-β and the proliferation of Sendai virus (SeV) and vesicular stomatitis virus (VSV) were determined by real-time quantitative polymerase chain reaction (qPCR). The effect of DU on the IFN signaling pathway was evaluated using luciferase reporter assays.

Results

In our study, the expression of IFN-β was significantly inhibited and the proliferation of SeV and VSV was promoted in cells overexpressing CAEV-DU. DU affected interferon stimulated response element (ISRE) and IFN-β promoter activities induced by RIG-I/MDA5/MAVS/TBK1 pathway, while did not affect them induced by interferon regulatory factor 3 (IRF3-5D).

Conclusion

DU protein downregulated the production of IFN-β by inhibiting the activity of the signal transduction molecules upstream of IRF3, thereby, helping CAEV escape innate immunity. Findings of this work provide an evidence to understand the persistent infection and multiple system inflammation of CAEV.