A genomic and epigenomic atlas of prostate cancer in Asian populations.

Prostate cancer is the second most common cancer in men worldwide1. Over the past decade, large-scale integrative genomics efforts have enhanced our understanding of this disease by characterizing its genetic and epigenetic landscape in thousands of patients2,3. However, most tumours profiled in these studies were obtained from patients from Western populations. Here we produced and analysed whole-genome, whole-transcriptome and DNA methylation data for 208 pairs of tumour tissue samples and matched healthy control tissue from Chinese patients with primary prostate cancer. Systematic comparison with published data from 2,554 prostate tumours revealed that the genomic alteration signatures in Chinese patients were markedly distinct from those of Western cohorts: specifically, 41% of tumours contained mutations in FOXA1 and 18% each had deletions in ZNF292 and CHD1. Alterations of the genome and epigenome were correlated and were predictive of disease phenotype and progression. Coding and noncoding mutations, as well as epimutations, converged on pathways that are important for prostate cancer, providing insights into this devastating disease. These discoveries underscore the importance of including population context in constructing comprehensive genomic maps for disease.

Superconductivity and Charge-Density-Wave-Like Transition in Th2Cu4As5.

We report the synthesis, crystal structure, and physical properties of a novel ternary compound, Th2Cu4As5. The material crystallizes in a tetragonal structure with lattice parameters a = 4.0639(3) Å and c = 24.8221(17) Å. Its structure can be described as an alternating stacking of fluorite-type Th2As2 layers with antifluorite-type double-layered Cu4As3 slabs. The measurement of electrical resistivity, magnetic susceptibility, and specific heat reveals that Th2Cu4As5 undergoes bulk superconducting transition at 4.2 K. Additionally, all these physical quantities exhibit anomalies at 48 K, accompanied by a sign change in the Hall coefficient, suggesting a charge-density-wave-like (CDW) phase transition. Drawing from both experimental data and band calculations, we propose that the superconducting and CDW-like phase transitions are, respectively, associated with the Cu4As3 slabs and the As plane in the Th2As2 layers.

ThCr2Si2C: An Antiferromagnetic Metal with a Cr2C Square Lattice.

A quaternary compound, ThCr2Si2C, was synthesized by using the arc-melting technique. The compound adopts a tetragonal CeCr2Si2C-type crystal structure. The electronic resistivity and specific heat data exhibit metallic behavior, while the magnetic susceptibility displays a pronounced broad peak at around 370 K, indicating the antiferromagnetic phase transition. The first-principles calculations suggest A-type antiferromagnetic ordering of the Cr sublattice, which is confirmed by neutron diffraction experiments. By comparing the crystal structure of ThCr2Si2C with the isostructural Cr-based compounds, the magnetic state of Cr 3d orbital is discussed in terms of the band-filling effects and indirect spin exchange interaction.

Symbiotic status alters fungal eco-evolutionary offspring trajectories.

Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms.

Optimizing cropping systems to close the gap between economic profitability and environmental health.

Supporting food security while maintaining ecosystem sustainability is one of the most important global challenges for humanity. Optimization of cropping systems is expected to promote the ecosystem services of agroecosystems. Yet, how and why cropping system influences the trade-offs between economic profitability and multiple ecosystem services remain poorly understood. We investigate the influence of six cropping systems on trade-offs between economic profitability and multiple ecosystem services after considering 36 agricultural ecosystem properties using field experiment data from 2020 to 2022. We show that designing cropping system is a critical tool to closing the gap between ecosystem sustainability and commercial profitability. Cropping system with three harvests within 2 yr had higher performance in overall ecosystem multiple services through enhancement of supporting, regulating, and economic performance without compromising provisioning compared with four other systems. These systems diminished the trade-off among multiple services, resulting in a 'win-win' situation for economics and multiple services. By contrast, the monoculture and double cropping systems lead to a strong trade-off between pairwise services including ecosystem health and profitability. Our work illustrates the substantial potential of rotation systems with three harvests within 2 yr in enforcing ecosystem services and closing the trade-offs among multiple agricultural ecosystem services.

Full substitution of chemical fertilizer by organic manure decreases soil N2 O emissions driven by ammonia oxidizers and gross nitrogen transformations.

Replacing synthetic fertilizer by organic manure has been shown to reduce emissions of nitrous oxide (N2 O), but the specific roles of ammonia oxidizing microorganisms and gross nitrogen (N) transformation in regulating N2 O remain unclear. Here, we examined the effect of completely replacing chemical fertilizer with organic manure on N2 O emissions, ammonia oxidizers, gross N transformation rates using a 13-year field manipulation experiment. Our results showed that organic manure reduced cumulative N2 O emissions by 16.3%-210.3% compared to chemical fertilizer. The abundance of ammonia oxidizing bacteria (AOB) was significantly lower in organic manure compared with chemical fertilizer during three growth stages of maize. Organic manure also significantly decreased AOB alpha diversity and changed their community structure. However, organic manure substitution increased the abundance of ammonia oxidizing archaea and the alpha diversity of comammox Nitrospira compared to chemical fertilizer. Interestingly, organic manure decreased organic N mineralization by 23.2%-32.9%, and autotrophic nitrification rate by 10.5%-45.4%, when compared with chemical fertilizer. This study also found a positive correlation between AOB abundance, organic N mineralization and gross autotrophic nitrification rate with N2 O emission, and their contribution to N2 O emission was supported by random forest analysis. Our study highlights the key roles of ammonia oxidizers and N transformation rates in predicting cropland N2 O.

Identification of crucial genes related to heart failure based on GEO database.

BACKGROUND: The molecular biological mechanisms underlying heart failure (HF) remain poorly understood. Therefore, it is imperative to use innovative approaches, such as high-throughput sequencing and artificial intelligence, to investigate the pathogenesis, diagnosis, and potential treatment of HF. METHODS: First, we initially screened Two data sets (GSE3586 and GSE5406) from the GEO database containing HF and control samples from the GEO database to establish the Train group, and selected another dataset (GSE57345) to construct the Test group for verification. Next, we identified the genes with significantly different expression levels in patients with or without HF and performed functional and pathway enrichment analyses. HF-specific genes were identified, and an artificial neural network was constructed by Random Forest. The ROC curve was used to evaluate the accuracy and reliability of the constructed model in the Train and Test groups. Finally, immune cell infiltration was analyzed to determine the role of the inflammatory response and the immunological microenvironment in the pathogenesis of HF. RESULTS: In the Train group, 153 significant differentially expressed genes (DEGs) associated with HF were found to be abnormal, including 81 down-regulated genes and 72 up-regulated genes. GO and KEGG enrichment analyses revealed that the down-regulated genes were primarily enriched in organic anion transport, neutrophil activation, and the PI3K-Akt signaling pathway. The upregulated genes were mainly enriched in neutrophil activation and the calcium signaling. DEGs were identified using Random Forest, and finally, 16 HF-specific genes were obtained. In the ROC validation and evaluation, the area under the curve (AUC) of the Train and Test groups were 0.996 and 0.863, respectively. CONCLUSIONS: Our research revealed the potential functions and pathways implicated in the progression of HF, and designed an RNA diagnostic model for HF tissues using machine learning and artificial neural networks. Sensitivity, specificity, and stability were confirmed by ROC curves in the two different cohorts.

Impact of signs and symptoms on the prognosis of patients with HFmrEF.

BACKGROUND: Worsening of heart failure (HF) symptoms is the leading cause of medical contact and hospitalization of patients with mildly reduced ejection fraction (HFmrEF). The prognostic value of signs and symptoms for patients with HFmrEF is currently unclear. This study investigated the prognostic impact of signs and symptoms in HFmrEF patients. METHODS: A Cox proportional risk regression model analyzed the relationship between the number of signs/symptoms and outcomes in 1691 hospitalized HFmrEF patients. Ten significant signs and symptoms were included. Patients were divided into three groups (A: ≤2, B: 3-5, C: ≥6 signs/symptoms). Stratified analysis on male and female patients was performed. The primary endpoint was all-cause mortality, and the secondary outcome was a composite of cardiovascular death and heart failure readmission (CV events) post-discharge. RESULTS: After a median follow-up of 33 months, all-cause mortality occurred in 457 patients and CV events occurred in 977 patients. Incidence of all-cause mortality was 20.7%, 32.3%* and 49.4%*† in group A, B and C of male patients, (*P < 0.05 vs. A, †P < 0.05 vs. B) and 18.8%, 33.6% and 55.8%* in group A, B and C of female patients. Incidence of CV events was 64.8%, 70.1%* and 87.5%* in group A, B and C of male patients, 61.9%, 75.3%, and 86.1%* in group A, B and C of female patients. Multivariate Cox regression showed older age, renal insufficiency, higher number of signs and symptoms (≥ 3, hazard ratio [HR] 1.317, 95% confidence interval [CI] 1.070-1.621, P = 0.009; ≥6, HR 1.982, 95% CI 1.402-2.801, P < 0.001), myocardial infarction, stroke, faster heart rate on admission, and diabetes were independently associated with all-cause mortality(all P < 0.05). Similarly, higher number of signs and symptoms (≥ 3, HR 1.271, 95% CI 1.119-1.443, P < 0.001; ≥6, HR 1.955, 95% CI 1.524-2.508, P < 0.001), older age, renal insufficiency, atrial fibrillation, and diabetes were independently associated with cardiovascular events (all P < 0.05). CONCLUSIONS: Higher number of symptoms and signs is associated with increased risk of all-cause mortality and CV events in HFmrEF patients. Our results highlight the prognostic importance of careful inquiry on HF symptoms and related physical examination in HFmrEF patients.

Clinical Value and Mechanism of Long Non-Coding RNA UCA1 in Acute Respiratory Distress Syndrome Induced by Cardiopulmonary Bypass.

AIM: Long non-coding RNA (lncRNA) can be used as a biological marker for the diagnosis and treatment of various diseases. The study aimed to detect changes in the expression of lncRNA for urothelial carcinoma associated 1 (UCA1) in patients with cardiopulmonary bypass (CPB)-induced acute respiratory distress syndrome (ARDS). Clinical values and cell function in ARDS were explored. METHOD: In total, 195 patients without CPB-induced ARDS were included in the control group, and 85 patients with ARDS were included in the ARDS group. Serum UCA1 levels were measured by quantitative real-time polymerase chain reaction. A549 was used for the cell experiments by establishing oxygen-glucose deprivation/reperfusion (OGD/R) cell models, and the cell viability and apoptosis were tested. The concentration of inflammatory factors was tested by an enzyme-linked immunosorbent assay. A luciferase reporting assay was applied for target gene analysis. RESULTS: Quantitative real-time polymerase chain reaction revealed a gradual increase in serum UCA1 in both control and ARDS cases, and patients with ARDS had higher levels of UCA1 than those in the control group. Serum UCA1 was positively correlated with serum tumour necrosis factor-α and interleukin-6 concentration in patients with ARDS. UCA1 had the ability to distinguish patients with ARDS from those without it. UCA1 inhibition protected against lung injury and inhibited cell inflammation in vitro. MicroRNA (miR-182-5p) was downregulated in OGD/R-induced cell models and sponged by UCA1. CONCLUSIONS: Elevated expression of UCA1 may be associated with the occurrence of ARDS after CPB surgery. The regulatory role of UCA1 in ARDS might be related to inflammation and downregulated miR-182-5p in alveolar epithelial cells.

Conversion of natural grassland to cropland alters microbial community assembly across northern China.

To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have negative consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we investigated the diversity and community compositions of bacteria, archaea, fungi and protists, using a paired sampling of grassland and cropland soils across the agro-pastoral ecotone of northern China. Land-use conversion decreased α diversity of bacteria, fungi and protists, and altered the structures of the entire soil microbial community (archaea, bacteria, fungi and protists). The community assembly of archaea and bacteria was dominated by stochastic processes, and that of protists dominated by deterministic processes in both land-use types. By contrast, the fungal community was governed more strongly by stochastic processes in grassland soil, than by deterministic processes in cropland soil. Our findings support the 'size-plasticity' hypothesis that smaller body-sized microorganisms (archaea and bacteria) are more structured by stochastic processes, and larger one (protist) is more influenced by deterministic processes. Our study demonstrates that distinct ecological processes govern microbial community assembly, and land-use change regulates the balance between determinism and stochasticity.

Purcell Enhancement of a Cavity-Coupled Emitter in Hexagonal Boron Nitride.

Integration of solid-state quantum emitters into nanophotonic circuits is a critical step towards fully on-chip quantum photonic-based technologies. Among potential materials platforms, quantum emitters in hexagonal boron nitride (hBN) have emerged as a viable candidate over the last years. While the fundamental physical properties have been intensively studied, only a few works have focused on the emitter integration into photonic resonators. Yet, for a potential quantum photonic material platform, the integration with nanophotonic cavities is an important cornerstone, as it enables the deliberate tuning of the spontaneous emission and the improved readout of distinct transitions for a quantum emitter. In this work, the resonant tuning of a monolithic cavity integrated hBN quantum emitter is demonstrated through gas condensation at cryogenic temperature. In resonance, an emission enhancement and lifetime reduction are observed, with an estimate for the Purcell factor of ≈15.

Quasiparticle dynamics and phonon softening in FeSe0.9S0.1 superconductors.

The quasiparticle and longitudinal acoustic (LA) coherent phonon dynamics of the FeSe0.9S0.1 single crystal were investigated by femtosecond transient optical spectroscopy. The FeSe0.9S0.1 single crystal undergoes metal-superconductor transition at Tc = 9.5 K and structural phase transition at Ts = 72 K. To investigate the correlation between the quasiparticle/LA coherent phonon dynamics and the antiferromagnetic spin/nematic fluctuation, we measured the transient differential reflectivity ΔR(t)/R0 in time series (R is the reflectivity) between 4-130 K. The ΔR(t)/R0 time series showed a negative sign below Ts = 72 K, while its sign reversed from negative to positive above Ts. The ΔR(t)/R0 time series was contributed by a combination of two exponential decays and an oscillation term. The slow decay attributed to electron-phonon and phonon-phonon coupling showed a negative amplitude below Ts and a positive amplitude above Ts. A fast decay with positive amplitude appeared at T ≥ 55 K was induced by the electron-phonon coupling of the high-temperature orthorhombic phase FeSe0.9S0.1. The oscillation contributed by the LA coherent phonon emerged below Ts but was not observed above Ts, indicating that it was impacted by the nematic fluctuation of FeSe0.9S0.1.

Scalable and Deterministic Fabrication of Quantum Emitter Arrays from Hexagonal Boron Nitride.

We demonstrate the fabrication of large-scale arrays of single-photon emitters (SPEs) in hexagonal boron nitride (hBN). Bottom-up growth of hBN onto nanoscale arrays of dielectric pillars yields corresponding arrays of hBN emitters at the pillar sites. Statistical analysis shows that the pillar diameter is critical for isolating single defects, and diameters of ∼250 nm produce a near-unity yield of a single emitter at each pillar site. Our results constitute a promising route toward spatially controlled generation of hBN SPEs and provide an effective and efficient method to create large-scale SPE arrays. The results pave the way to scalability and high throughput fabrication of SPEs for advanced quantum photonic applications.

Bottom-Up Synthesis of Hexagonal Boron Nitride Nanoparticles with Intensity-Stabilized Quantum Emitters.

Fluorescent nanoparticles are widely utilized in a large range of nanoscale imaging and sensing applications. While ultra-small nanoparticles (size ≤10 nm) are highly desirable, at this size range, their photostability can be compromised due to effects such as intensity fluctuation and spectral diffusion caused by interaction with surface states. In this article, a facile, bottom-up technique for the fabrication of sub-10-nm hexagonal boron nitride (hBN) nanoparticles hosting photostable bright emitters via a catalyst-free hydrothermal reaction between boric acid and melamine is demonstrated. A simple stabilization protocol that significantly reduces intensity fluctuation by ≈85% and narrows the emission linewidth by ≈14% by employing a common sol-gel silica coating process is also implemented. This study advances a promising strategy for the scalable, bottom-up synthesis of high-quality quantum emitters in hBN nanoparticles.

Large-scale evidence for microbial response and associated carbon release after permafrost thaw.

Permafrost thaw could trigger the release of greenhouse gases through microbial decomposition of the large quantities of carbon (C) stored within frozen soils. However, accurate evaluation of soil C emissions from thawing permafrost is still a big challenge, partly due to our inadequate understanding about the response of microbial communities and their linkage with soil C release upon permafrost thaw. Based on a large-scale permafrost sampling across 24 sites on the Tibetan Plateau, we employed meta-genomic technologies (GeoChip and Illumina MiSeq sequencing) to explore the impacts of permafrost thaw (permafrost samples were incubated for 11 days at 5°C) on microbial taxonomic and functional communities, and then conducted a laboratory incubation to investigate the linkage of microbial taxonomic and functional diversity with soil C release after permafrost thaw. We found that bacterial and fungal α diversity decreased, but functional gene diversity and the normalized relative abundance of C degradation genes increased after permafrost thaw, reflecting the rapid microbial response to permafrost thaw. Moreover, both the microbial taxonomic and functional community structures differed between the thawed permafrost and formerly frozen soils. Furthermore, soil C release rate over five month incubation was associated with microbial functional diversity and C degradation gene abundances. By contrast, neither microbial taxonomic diversity nor community structure exhibited any significant effects on soil C release over the incubation period. These findings demonstrate that permafrost thaw could accelerate C emissions by altering the function potentials of microbial communities rather than taxonomic diversity, highlighting the crucial role of microbial functional genes in mediating the responses of permafrost C cycle to climate warming.

Altered microbial structure and function after thermokarst formation.

Permafrost thaw could induce substantial carbon (C) emissions to the atmosphere, and thus trigger a positive feedback to climate warming. As the engine of biogeochemical cycling, soil microorganisms exert a critical role in mediating the direction and strength of permafrost C-climate feedback. However, our understanding about the impacts of thermokarst (abrupt permafrost thaw) on microbial structure and function remains limited. Here we employed metagenomic sequencing to analyze changes in topsoil (0-15 cm) microbial communities and functional genes along a permafrost thaw sequence (1, 10, and 16 years since permafrost collapse) on the Tibetan Plateau. By combining laboratory incubation and a two-pool model, we then explored changes in soil labile and stable C decomposition along the thaw sequence. Our results showed that topsoil microbial α-diversity decreased, while the community structure and functional gene abundance did not exhibit any significant change at the early stage of collapse (1 year since collapse) relative to non-collapsed control. However, as the time since the collapse increased, both the topsoil microbial community structure and functional genes differed from the control. Abundances of functional genes involved in labile C degradation decreased while those for stable C degradation increased at the late stage of collapse (16 years since collapse), largely driven by changes in substrate properties along the thaw sequence. Accordingly, faster stable C decomposition occurred at the late stage of collapse compared to the control, which was associated with the increase in relative abundance of functional genes for stable C degradation. These results suggest that upland thermokarst alters microbial structure and function, particularly enhances soil stable C decomposition by modulating microbial functional genes, which could reinforce a warmer climate over the decadal timescale.

Improving the Surgical Effect for Primary Liver Cancer with Intraoperative Fluorescence Navigation Compared with Intraoperative Ultrasound.

BACKGROUND This study aimed to compare the application value of intraoperative fluorescence navigation technology (FNT) and intraoperative ultrasound (IOUS) in primary liver cancer surgery. MATERIAL AND METHODS Fifty consecutive patients with primary liver cancer scheduled to receive surgical treatment were divided into FNT group and IOUS group. FNT and IOUS were separately used to guide tumor resection and detect new cancerous lesions in the 2 groups. The complete tumor resection rate (R0) resection rate, length of the tumor distance from cutting edge, the diagnostic efficacy of cancerous nodules and the fluorescence imaging characteristics of different types tumors were recorded. RESULTS The R0 resection rate was 100% (25 out of 25 patients) in the FNT group and 96% (24 out of 25 patients) in the IOUS group. In the FNT group, 1 case (4%, 1 out of 25 patients) had cancer tissue that was less than 1 cm from the cutting edge, compared to 7 cases (28%, 7 out of 25 patients) in the IOUS group (P=0.049), which was a significant difference. In the remaining livers of 50 consecutive patients, FNT found 5 new cancerous nodules with a sensitivity of 71.4%, a specificity of 11.1%, and a false-positive rate of 88.9%; for IOUS the results were 42.9%, 88.9%, 11.1%. The fluorescence imaging characteristics of all well-differentiated hepatocellular carcinomas were tumor tissue imaging, but all other types of tumors were ring imaging around the tumor. CONCLUSIONS FNT can improve the R0 resection rate, ensure a safe distance between tumor and cutting edge and can identify more new cancerous nodules compared to IOUS. Thus, FNT could improve the surgical treatment effect for primary liver cancer and hopefully further improve the prognosis of patients.

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes.

Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance.

Magnitude and Pathways of Increased Nitrous Oxide Emissions from Uplands Following Permafrost Thaw.

Permafrost thawing may release nitrous oxide (N2O) due to large N storage in cold environments. However, N2O emissions from permafrost regions have received little attention to date, particularly with respect to the underlying microbial mechanisms. We examined the magnitude of N2O fluxes following upland thermokarst formation along a 20-year thaw sequence within a thermo-erosion gully in a Tibetan swamp meadow. We also determined the importance of environmental factors and the related microbial functional gene abundance. Our results showed that permafrost thawing led to a mass release of N2O in recently collapsed sites (3 years ago), particularly in exposed soil patches, which presented post-thaw emission rates equivalent to those from agricultural and tropical soils. In addition to abiotic factors, soil microorganisms exerted significant effects on the variability in the N2O emissions along the thaw sequence and between vegetated and exposed patches. Overall, our results demonstrate that upland thermokarst formation can lead to enhanced N2O emissions, and that the global warming potential (GWP) of N2O at the thermokarst sites can reach 60% of the GWP of CH4 (vs ∼6% in control sites), highlighting the potentially strong noncarbon (C) feedback to climate warming in permafrost regions.