Scale-invariant topology and bursty branching of evolutionary trees emerge from niche construction.

Phylogenetic trees describe both the evolutionary process and community diversity. Recent work has established that they exhibit scale-invariant topology, which quantifies the fact that their branching lies in between the two extreme cases of balanced binary trees and maximally unbalanced ones. In addition, the backbones of phylogenetic trees exhibit bursts of diversification on all timescales. Here, we present a simple, coarse-grained statistical model of niche construction coupled to speciation. Finite-size scaling analysis of the dynamics shows that the resultant phylogenetic tree topology is scale-invariant due to a singularity arising from large niche construction fluctuations that follow extinction events. The same model recapitulates the bursty pattern of diversification in time. These results show how dynamical scaling laws of phylogenetic trees on long timescales can reflect the indelible imprint of the interplay between ecological and evolutionary processes.

Efficacy and safety of anti-PD-1/PD-L1 therapy in the treatment of advanced colorectal cancer: a meta-analysis.

BACKGROUND: Immune checkpoint inhibitors have shown promise in microsatellite instability-high/mismatch repair deficient (MSI-H/dMMR) advanced colorectal cancer (CRC) immunotherapy, and many clinical trials have been conducted. OBJECTIVE: To evaluate the efficacy and safety of PD-1/PD-L1 inhibitors in advanced CRC. METHOD: PubMed, Web of Science, Embase, and The Cochrane Library were searched for relevant studies up to September 2021. A retrospective cross-sectional data analysis was performed and Stata 16 software was used for analyses. RESULTS: Sixteen studies including 1503 patients were analyzed. The objective response rate (ORR) of anti-PD-1/PD-L1 was 23% (95% CI 0.14, 0.31); the overall 1-year survival rate (OSR) was 57% (95% CI 0.42, 0.73). The ORR of MSI-H/dMMR advanced CRC was 37% (95% CI 0.25, 0.48) and that of microsatellite stable/mismatch repair proficient (MSS/pMMR) disease was 11% (95% CI 0.06, 0.16). The ORR was 42% in the BRAF mutant subgroup and 19% in the RAS mutant group. The ORR was 14% in the PD-L1 ( +) subgroup and 32% in the PD-L1(-) subgroup. The rate of adverse effects was 85% (95% CI 0.80, 0.91). CONCLUSION: Anti-PD-1/PD-L1 therapy in MSI-H/dMMR advanced CRC was associated with improved survival. Anti PD-1/PD-L1 combined with antiangiogenic drugs, targeted agents, or chemotherapy might be effective in MSS mCRC. Immunotherapy was effective for the BRAF mutant and KRAS/NRAS(RAS) mutant CRC. Low expression of PD-L1 was a potential predictive marker for positive response and outcome. The high incidence of adverse events at 85% was worthy of further investigation. Further analysis with a higher number of high-quality studies is needed to verify the conclusions.

Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell.

Phylogenetic evidence suggests that the invasion and proliferation of retroelements, selfish mobile genetic elements that copy and paste themselves within a host genome, was one of the early evolutionary events in the emergence of eukaryotes. Here we test the effects of this event by determining the pressures retroelements exert on simple genomes. We transferred two retroelements, human LINE-1 and the bacterial group II intron Ll.LtrB, into bacteria, and find that both are functional and detrimental to growth. We find, surprisingly, that retroelement lethality and proliferation are enhanced by the ability to perform eukaryotic-like nonhomologous end-joining (NHEJ) DNA repair. We show that the only stable evolutionary consequence in simple cells is maintenance of retroelements in low numbers, suggesting how retrotransposition rates and costs in early eukaryotes could have been constrained to allow proliferation. Our results suggest that the interplay between NHEJ and retroelements may have played a fundamental and previously unappreciated role in facilitating the proliferation of retroelements, elements of which became the ancestors of the spliceosome components in eukaryotes.

Coevolution Maintains Diversity in the Stochastic "Kill the Winner" Model.

The "kill the winner" hypothesis is an attempt to address the problem of diversity in biology. It argues that host-specific predators control the population of each prey, preventing a winner from emerging and thus maintaining the coexistence of all species in the system. We develop a stochastic model for the kill the winner paradigm and show that the stable coexistence state of the deterministic kill the winner model is destroyed by demographic stochasticity, through a cascade of extinction events. We formulate an individual-level stochastic model in which predator-prey coevolution promotes the high diversity of the ecosystem by generating a persistent population flux of species.

Silica Wastes to High-Performance Lithium Storage Materials: A Rational Designed Al2 O3 Coating Assisted Magnesiothermic Process.

Si/C yolk-shell structures have been developed to deal with the major issues associated with Si anodes: the huge volume changes and the low electrical conductivity. However, the fabrication process often involves expensive starting materials and/or simultaneously generates insulated SiC, which is harmful for Si anodes. Here, silica wastes from the optical fibers industry are used as starting materials to prepare high performance Si/C materials with Si@void@C yolk-shell structure via a rational designed Al2 O3 coating assisted magnesiothermic process. The obtained yolk-shell Si@void@C materials have a capacity of more than 1450 mA h g-1 after 100 cycles at 0.4 A g-1 . Thanks to the easily coated and removed Al2 O3 layer, the general formation of SiC can be avoided which is beneficial for improving the rate performances, and a capacity of ≈800 mA h g-1 is still kept after 200 cycles at a high rate of 10 A g-1 with a low capacity loss of 0.08% per cycle.

Stochastic Predator-Prey Dynamics of Transposons in the Human Genome.

Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic, relying on the enzymes produced by the regular transposons. In this case, we show that a stochastic model, which takes into account the small copy numbers of the active transposons in a cell, predicts noise-induced predator-prey oscillations with a characteristic time scale that is much longer than the cell replication time, indicating that the state of the predator-prey oscillator is stored in the genome and transmitted to successive generations. Our work demonstrates the important role of the number fluctuations in the expression of mobile genetic elements, and shows explicitly how ecological concepts can be applied to the dynamics and fluctuations of living genomes.

[Driving Forces and Mitigation Potential of CO2 Emissions for Ship Transportation in Guangdong Province, China].

Ships are important sources of carbon dioxide (CO2) emissions in Guangdong Province. The study of historical evolutions, drivers, and projected pathways of CO2 emissions can provide scientific support for the development of carbon peaking and carbon neutral strategies in Guangdong Province. The emission factor method, log-average index (LMDI) method, and scenario analysis method were adopted to estimate CO2 emissions, identify the drivers, and explore the mitigation potential from ships in Guangdong Province, separately. The results showed that:① CO2 emissions from ships in Guangdong Province increased from 3.319 4 million tons to 6.392 9 million tons from 2006 to 2020, with dry bulk carriers and container ships being the main ship types causing the increase in emissions. ② The positive drivers of CO2 emissions from ships in Guangdong Province from 2006 to 2020 were transport intensity (51%) and economic factors (49%), and the negative drivers were energy intensity (93%) and cargo class structure (7%). ③ Carbon peaking would not be reached by 2030 if Guangdong Province maintains the current policy (baseline scenario) for ship transportation. ④ Simultaneous optimization of the energy structure and promotion of the energy intensity (energy-efficient and low-carbon scenario) had a 56.51% potential to reduce CO2 emissions from ships compared to the baseline scenario. This can provide scientific support for Guangdong Province to develop a carbon peaking and carbon neutral control strategy for the shipping industry.

Efficacy of neoadjuvant immunotherapy in advanced colorectal cancer: a meta-analysis of cross-sectional studies.

BACKGROUND: Although neoadjuvant immunotherapy is being widely studied, there is no consensus on its efficacy in microsatellite-stable (MSS) or mismatch repair proficient (pMMR) colorectal cancer (CRC). This meta-analysis aimed to evaluate studies on neoadjuvant immunotherapy for advanced CRC to assess its efficacy and provide new clinical guidelines. METHODS: We searched literature databases to identify studies that assessed the efficacy of neoadjuvant immunotherapy in advanced CRC. The outcomes evaluated were pathological complete response (pCR), major pathological response (MPR), R0 resection, and anal preservation rates. Heterogeneity among the included studies was assessed by sensitivity analysis, and publication bias was evaluated using Begg and Egger tests. RESULTS: Eleven articles were included in the analysis. The pCR, MPR, R0 resection, and anal preservation rates reported in these studies were 39 and 49, 97, and 76%, respectively. The MSI-H and MSS groups had pooled pCR rates of 70 and 24%, respectively. The pCR rates for the induction, consolidation, and concurrent immuno-chemoradiotherapy (CRT) subgroups were 43, 33, and 27%, respectively, and those for the single and double immunotherapy subgroups were 34 and 40%, respectively. CONCLUSION: Neoadjuvant immunotherapy combined with CRT is effective in treating MSI-H/dMMR advanced CRC. It could also be a new first-line therapeutic option for MSS/pMMR advanced CRC.

circDYRK1A tethers biological behaviors of gastric carcinoma using novel bioinformatics analysis and experimental validations.

Gastric cancer has been one of the wide public health burdens with its high morbidity and mortality over several decades. As the unconventional modules among RNA families, circular RNAs present their blazing biological effects during gastric carcinogenesis. Though diverse hypothetical mechanisms were reported, further tests were necessitated for authentication. Herein, this study pinpointed a representative circDYRK1A which screened from vast amounts of public data sets using surprisingly novel bioinformatics approaches together with validations from the in vitro findings and then concluded that circDYRK1A tethered the biological behavior and swayed the clinicopathological features with gastric cancer patients thus providing an in-depth awareness for gastric carcinoma.

[Evolution Characteristics and Driving Forces of Carbon Dioxide Emissions and Sinks in the Pearl River Delta Region, China].

With the rapid economic and population growth, the Pearl River Delta(PRD) Region is one of the regions in China under the greatest pressure to be carbon neutral. This study analyzed the historical evolution characteristics of the carbon dioxide(CO2) emissions and sinks from 2006-2020 and identified the key drivers of the CO2 emissions and sinks based on the exponential decomposition method. The results showed that:① from 2006 to 2020, the total carbon emissions in the PRD Region increased from 218.22 million tons to 366.30 million tons, showing a fluctuating and rising evolution characteristic, with an overall increase of 67.86%. The carbon emission had not yet reached a peak. ② From 2006 to 2020, the total carbon sinks in the PRD Region decreased from 15.67 million tons to 15.53 million tons, showing a trend of fluctuation and decline, with an overall decrease of 0.94%. The carbon sinks were far lower than the carbon emissions, and there was still a large gap between carbon neutrality. ③ The main carbon emission sectors in the PRD Region were the energy sector(40.38%) and industrial sector(26.33%), and the carbon sinks mainly came from forestland(67.92%) and farmland(18.09%). ④ During the period from the "11th Five-Year Plan" to the "13th Five-Year Plan," the main positive driving factors for carbon emissions were economic growth and population size, whereas the main negative driving factor was energy intensity(energy use per unit GDP). However, since the "13th Five-Year Plan," the CO2 emission reduction potential released by reducing energy intensity has been weakening. In the future, the PRD Region needs to address the negative driving potential of the structural adjustment in energy, industry, transportation, and land use. ⑤ During the period from the "11th Five-Year Plan" to the "13th Five-Year Plan," the main positive driving factor for the carbon sink was the green scale, which was conducted by the increase in urban green space during the "11th Five-Year Plan." The main negative driving factor for the carbon sink was the carbon sink coefficient, which was caused by the natural disaster-induced yield reductions in crops with a high carbon sink coefficient, such as rice. Green space structure adjustment should be emphasized in the future. This study can provide scientific support for developing robust carbon-neutral policies in the PRD Region.

[Evolution Characteristics of Atmospheric Formaldehyde Emissions in Guangdong Province from 2006 to 2020].

Atmospheric formaldehyde, a key precursor for ozone (O3) and secondary PM2.5, is carcinogenic and plays an important role in atmospheric photochemistry and the formation of secondary pollution. However, the lack of understanding of the emission sources of atmospheric formaldehyde limits the study on the formation mechanism of secondary pollution and the formulation of pollution control strategies. This study used the emission factor and source profile methods to establish the emission inventories of formaldehyde in Guangdong Province from 2006 to 2020 and identified the main emission sources of formaldehyde and spatial and temporal evolution characteristics. The results showed that the formaldehyde emissions in Guangdong Province fluctuated in the range of 39000-56000 tons during 2006 to 2020, exhibiting a very weak downward trend. Biomass combustion is an important source of formaldehyde emission in Guangdong Province, of which the contribution decreased from 58% in 2006 to 27% in 2020 owing to effective control measures implemented in Guangdong Province. The solvent use source became the predominant emission source of formaldehyde in 2020 by contributing up to 28%, primarily through plastic products and asphalt paving sources. The construction machinery and trucks fueled by diesel were important contributors of formaldehyde emissions from mobile sources. Although the formaldehyde emissions in the Pearl River Delta and the non-Pearl River Delta were equivalent, the spatial distributions showed that formaldehyde emission hotspots were concentrated in the center of the Pearl River Delta and the eastern and western areas of the non-Pearl River Delta. This was primarily because the solvent use and mobile sources were the main sources of formaldehyde emissions in the Pearl River Delta, whereas the biomass combustion source was the dominant source in the non-Pearl River Delta. Therefore, the formaldehyde emission mitigations of the industrial and mobile sources in the central region of the Pearl River Delta and the biomass combustion source in the western area of Guangdong should be further strengthened in the future.

Tumor budding as a predictor for prognosis and therapeutic response in gastric cancer: A mini review.

In recent years, the role of tumor budding in gastric cancer has received increased attention across a number of disciplines. Several studies have found associations between tumor budding and the prediction of lymph node metastasis in early gastric cancer, prognosis of advanced gastric cancer, predictors of therapeutic response to immune checkpoint inhibitors, such as microsatellite instability (MSI), and therapeutic targets of molecular targeted therapy, such as human epidermal growth factor receptor 2 (HER-2). Therefore, tumor budding is a major element in the formulation of risk stratification and precision medicine strategies for patients with gastric cancer.

[Volatile Organic Compound Emission Characteristics and Influences Assessment of a Petrochemical Industrial Park in the Pearl River Delta Region].

The petrochemical industry is one of the major emission sources of volatile organic compounds (VOCs). However, the current studies have mostly focused on the identification of the chemical characteristics of non-methane hydrocarbon (NMHC) VOCs species from the petroleum refining sub-sector. Research on the characteristics of VOCs components in oxygenated VOCs (OVOCs) species and other important sub-sectors is still lacking. Therefore, eight enterprises at a petrochemical industrial park in the Pearl River Delta region were carefully selected to represent three major subsectors, namely petroleum refining, synthetic materials, and organic chemicals, for the petrochemical industry. The VOCs (including 22 OVOCs species) from stack emissions and fugitive emissions, as well as nearby sensitive sites, were sampled, and the source reactivity (SR), the thresholds of malodor, and the carcinogenic and non-carcinogenic risks were assessed. The main results were as follows:① the VOCs concentrations of the stack emissions from the petrochemical industrial park were between 0.2-46.3 mg·m-3. The VOCs species were greatly affected by the type of after-treatment technology. A major VOC species emitted from the combustion-based after treatments was formaldehyde, whereas the species emitted from the non-combustion-based equipment were acetone, 1,3-butadiene, acrylic, and isobutane. ② The fugitive VOCs emissions from the petroleum storage tank area were dominated by alkanes, whereas the other fugitive emission sites and the sensitive sites were dominated by OVOCs such as acetone, formaldehyde, and ethyl acetate. ③ The SRs were mainly contributed by OVOCs, aromatics, and olefins, with average proportions of 43.1%, 24.2%, and 21.1%, respectively, with the major species being formaldehyde, acetaldehyde, m/p-xylene, ethylene, and toluene. ④ The malodor appeared both in fugitive emission areas and the sensitive sites. The main odor components were OVOCs such as n-butyraldehyde, propionaldehyde, hexanal, and valeraldehyde. ⑤ The non-carcinogenic risks occurred in the fugitive emission areas and the sensitive sites of resin, alcohol, and aldehyde production, which were mainly caused by OVOCs such as free acetaldehyde, acrolein, and propionaldehyde. No carcinogenic risk was found in any of the sampled sites. This research can provide scientific support for the formulation of priority VOCs species-based precise control strategies in petrochemical industrial parks.

[Effect of Soil Moisture and Temperature on the Soil Inorganic Carbon Release of Brown Limestone Soil in the Karst Region of Southwestern China].

In order to understand the influence of environmental factors on the carbonate conversion of the Karst soil, typical brown limestone and red soil samples were collected from the Karst ecosystem, and a 100-day incubation experiment was conducted. The characteristics of inorganic carbon release from the soil under three temperature gradients (15, 25, and 35℃) and water contents (30%, 65%, and 100% WHC) were studied by adding 14C-CaCO3 for 100 d. The results showed that under the different soil moisture and temperature conditions, the maximum rate and the cumulative amount of inorganic carbon release from the soil over 100 days varied between 0.7-16.8 mg·(kg·d)-1and 5.9-29.4 mg·kg-1, respectively, in the brown limestone soil, and varied between 39.7-103.3 mg·(kg·d)-1 and 83.3-135.1 mg·kg-1, respectively in the red soil. Under drought conditions (30% WHC), the cumulative amount of inorganic carbon release was the highest for the two soils and increased with increasing temperature. At 65% WHC and 100% WHC, increasing temperature can still promote inorganic carbon release from the soil. The temperature sensitivity of the soil inorganic carbon release in the brown limestone soil is greater than that of the red soil, which is significantly affected by soil moisture. The soil pH and MBC content were remarkably increased after adding CaCO3, and the difference between the two soils was significant. The variance partition showed that temperature and soil moisture can explain 7.6% and 2.0% of the soil inorganic carbon release variability, respectively. In conclusion, warming and drought aggravate inorganic carbon release from brown limestone soil in the southwestern Karst region. Therefore, in the context of global warming and more frequent extreme precipitation events, the effects of soil moisture and temperature on inorganic carbon conversion in soil should be fully considered when studying the soil carbon cycle and its dynamic changes in southwestern Karst. This research can provide a scientific basis for further understanding the influence of climate change on the global carbon cycle.

[Straw Returning Plus Nitrogen Fertilizer Affects the Soil Microbial Community and Organic Carbon Mineralization in Karst Farmland].

The use of straw returning plus nitrogen fertilizer on farmland is one of the important agronomic practices for adjusting soil organic carbon (SOC) transformations. To explore the mechanisms of straw and nitrogen fertilizer application on straw and SOC mineralization in long-term fertilized soils, an incubation experiment with the 13C isotope tracing technique was conducted, which involved three long-term fertilized models in typical karst soils (no fertilization, inorganic fertilization, and a combination of inorganic fertilization and straw). To study the mechanisms of 13C-labeled straw and SOC mineralization, four treatments were designed as follows:no straw and nitrogen (control), and straw combined with three levels of nitrogen fertilizer (0, 214.0, and 571.0 mg·kg-1 soil). The results showed that cumulative mineralization amounts of straw-derived organic carbon in long-term fertilized soils were markedly higher than those in non-fertilized soil. Straw-derived organic carbon mineralization was significantly affected by nitrogen fertilizer levels. The positive priming effects (PE) in long-term fertilized soils were much lower than those in non-fertilized soil. The PE was decreased at the low nitrogen fertilizer level but increased at the high nitrogen fertilizer level. The principal component analysis (PCA) of phospholipid fatty acids (PLFAs) indicated that the soil microbial community structure was greatly affected by the long-term fertilization models and combined straw and nitrogen fertilizer application. Moreover, the content of PLFAs in soil microorganisms, namely, bacteria and fungi, were remarkably increased by the straw plus nitrogen fertilizer (values increased by 40.3%-53.0%, 41.1%-62.6%, and 60.5%-148.6% compared with control), but levels were not significantly affected by nitrogen fertilizer levels alone. The ratios between PLFAs of soil gram-positive and gram-negative bacteria (G+/G-) decreased and were stable at around 0.8. The structure equation models (SEM) demonstrated that the combination of straw and nitrogen affected the soil gram-positive and gram-negative bacteria structure and increased the soil DOC content, which promoted the decomposition of straw and affected the mineralization of SOC. These results indicate that straw returning plus low nitrogen fertilizer can improve the SOC sequestration capacity in karst farmland.

Functional bacterial and archaeal diversity revealed by 16S rRNA gene pyrosequencing during potato starch processing wastewater treatment in an UASB.

Microbial community structure of sludge sampled from an UASB treating potato starch processing wastewater (PSPW) was investigated. Operational taxonomic units revealed at 97% sequence identity tolerance was 2922, 2869 and 3919 for bottom, middle and top sections of the reactor, respectively. Overall abundant phylum observed within the UASB was low-G+C-Gram-positive bacteria affiliated to Firmicutes (26.01%) followed by Chloroflexi (16.70%), Proteobacteria (12.71%), Cloacimonetes (10.72%), Bacteroidetes (7.87%), Synergistetes (9.02%) and Euryarchaeota (8.82%). Whiles Firmicutes had dominated the bottom and top section by 34.01% and 28.64%, respectively, middle section was predominantly Euryarchaeota (24.32%) with major dominance in methanogens affiliated to genus Methanosaeta. The results demonstrated substantial stratification of the microbial community structure along the reactor height with various functional bacterial groups which subsequently allowed degradation of organics in PSPW in sequential mode. The findings herein would provide guidance for optimizing the anaerobic process and operation of the UASB.

[Identification of the source and types of cells of Schistosoma japonicum by histochemical staining].

OBJECTIVE: To study the possibility on in vitro identifying the source or kinds of cells from Schistosoma japonicum (S.j). METHODS: The cells from digested tissues of 18 days old schistosomula were smeared on slides. The adult worms of S.j were used for making paraffin sections. The cell smears and tissue sections were stained with 6 different methods of histochemical staining including Periodic Acid-Schiff (PAS), Argyrophil reaction (by Grimeliu's), Picric acid-acid Fuchsin (by Van Gieson, VG), Thionin, Toluidine blue (TB) and Hematoxylin-Eosin (HE) staining parallelly. The results were judged through inspecting the specific color of the cells on smears referring to location of corresponding staining of paraffin sections of adult worm tissues under light microscopy. RESULTS: Vitelline gland cells, mother germ cells, nerve cells, digestive epithelial cells, muscular cells and mast cells were shown clearly. The stainings of VG, PAS and Thionin demonstrated cell types coinciding to histological location. The TB staining did not find red-purple mast cell in tissue sections but one in cell smears. The Grimeliu's argyrophil reaction displayed that intestine wall of tissure sections and stained cells of cell smears were in black clearly. CONCLUSION: HE staining together with histochemical staining can reliably and rapidly distinguish the cell types of Schistosoma japonicum.