Spatial spillover effects of manufacturing agglomeration on China's total factor carbon productivity: evidence from the regulatory role of fiscal decentralization.

Based on the theory of new economic geography, this paper used panel data from 284 cities in China from 2006 to 2019 to determine the effects of spatial spillover and heterogeneity of manufacturing agglomeration (MA) on urban total factor carbon productivity (TFCP) and the regulatory effect of fiscal decentralization on the outcome. The results showed that (1) MA shifted from the eastern region of China to the central and western regions, with the center of gravity moving towards the south. The spatial pattern of urban TFCP displayed the solidifying characteristics of "low-level agglomeration and high-level dispersion," with technological progress being the primary driver. (2) The MA had a significant U-shaped effect on the TFCP of local and nearby cities, promoting the improvement of urban TFCP through Jacobs' and Porter's externalities but not MAR externalities. (3) Regarding regional differences, MA had a significant U-shaped impact on urban TFCP in the eastern and central regions. At different levels of manufacturing development, there was an inverted U-shaped relationship in both manufacturing and non-manufacturing metropolitan areas. For varying degrees of manufacturing industry agglomeration, increasing the level of MA improved urban TFCP in low agglomeration areas, but inhibited it in high agglomeration areas. (4) The implementation of fiscal decentralization nationwide and in the eastern and central regions significantly weakened the impact of MA on TFCP. Furthermore, fiscal decentralization significantly enhanced the influence of MA on TFCP in cities exhibiting high levels of economic development, advanced industrial structure and strict environmental regulations. Therefore, based on the unique developmental characteristics of the manufacturing industry in various cities, fiscal policies ought to be tailored to local circumstances to support key areas. This strategy should facilitate the high-quality development of manufacturing industry and low-carbon development of cities.

Anti-virulence and bactericidal activities of Stattic against Shigella sonnei.

IMPORTANCE: Shigella sonnei is a major human enteric pathogen that causes bacillary dysentery. The increasing spread of drug-resistant S. sonnei strains has caused an emergent need for the development of new antimicrobial agents against this pathogenic bacterium. In this study, we demonstrate that Stattic employs two antibacterial mechanisms against S. sonnei. It exerted both anti-virulence activity and bactericidal activity against S. sonnei, suggesting that it shows advantages over traditional antibiotics. Moreover, Stattic showed excellent synergistic effects with kanamycin, ampicillin, chloramphenicol, and gentamicin against S. sonnei. Our findings suggest that Stattic has promising potential for development as a new antibiotic or as an adjuvant to antibiotics for infections caused by S. sonnei.

Impact of low-carbon city pilot policies on urban green innovation from the perspective of spatial and temporal heterogeneity.

The low-carbon city pilot policy (LCPP) in China is an active response to climate change, with cities serving as the main agents of action. Enhancing green innovation at a city-wide level can effectively support the promotion of pilot cities' efforts towards sustainable growth. Using panel data from 204 prefectures collected from 2005 to 2019, we adopted the time-varying difference-in-differences (DID) model and the spatial Durbin model combined with time-varying DID (SDM-DID) to determine the impact of the LCPP on urban green innovation and its temporal and spatial heterogeneity. Empirical findings showed that (1) LCPP had a significant positive impact on urban green innovation, and green invention patents had a greater green innovation effect than green utility model patents. (2) Heterogeneity analysis revealed that in terms of geographical location, the pilot policy was more effective in promoting urban green innovation in the eastern and central regions in comparison to the western region. At the city level, the pilot policy had a greater impact on green innovation in first- and second-tier cities. With regard to city scale, large-scale cities showed a greater impact on green innovation than small- and medium-sized cities. (3) Mechanistic testing revealed that LCPPs stimulated urban green innovation by talent aggregation, increasing government support for innovation, and public participation; but the mechanism for alleviating financing constraints has yet to be effectively validated. (4) The LCPP showed a spatial spillover effect, whereby one city's low-carbon governance yielded institutional dividends for neighboring cities both geographically and economically, and the impact was more pronounced in those cities that were not resource-based. This study presents empirical evidence at the urban and spatial levels, supporting the comprehensive promotion of low-carbon city construction and development in China.

Qualitative and Quantitative Changes of Oligosaccharides in Human and Animal Milk over Lactation.

The aim of this study was to investigate the changes in human and animal milk oligosaccharides over lactation. In total, 89, 97, 115, and 71 oligosaccharides were identified in human, bovine, goat, and camel milk. The number of common oligosaccharides between camel and human milk was the highest (16 and 17 in transitional and mature milk). With respect to the absolute concentration of eight oligosaccharides (2'-FL, 3-FL, α3'-GL, LNT, LNnT, 3'-SL, 6'-SL, and DSL), 2'-FL, 3'-FL, LNT, and LNnT were much higher in human than three animal species. 3'-SL had a similar concentration in bovine colostrum (322.2 µg/mL) and human colostrum (321.0 µg/mL), followed by goat colostrum (105.1 µg/mL); however, it had the highest concentration in camel mature milk (304.5 µg/mL). The ratio of 6'-SL and 3'-SL (1.77) in goat colostrum was similar to that in human colostrum (1.68), followed by bovine colostrum (0.13). In terms of changes of eight oligosaccharides over lactation, they all decreased with the increase of lactation in bovine and goat milk; however, α3'-GL, 2'-FL, and 3-FL increased in camel species, and LNT increased first and then decreased over lactation in human milk. This study provides a better understanding of the variation of milk oligosaccharides related to lactation and species.

Total synthesis of chondroitin sulfate E oligosaccharides and biological study.

A total synthesis approach of CS-E oligosaccharides was established and a series of derivatives were synthesized. These oligosaccharides were evaluated for a glycosaminoglycan (GAG)-binding protein interaction against cytokines, midkine, and pleiotrophin, by surface-plasmon resonance (SPR) assay. The binding epitopes of oligosaccharides to midkine were mapped using a saturation transfer difference (STD) NMR technique. The groups on the reducing end contributed to binding affinity, and should not be ignored in biological assays. These findings contribute to the structure and activity relationship research and a foundation of understanding that will underpin potential future optimization of this class of oligosaccharides as pharmaceutical agents.

Fiber coupling efficiency of a Bessel-Gaussian beam received by a Cassegrain antenna under atmospheric turbulence.

A coupling efficiency calculation method for a Bessel-Gaussian (BG) beam in a free space optical communication system received by a parabolic Cassegrain antenna and coupled into a few-mode fiber is proposed. The system of the antenna and the coupling lens is approximate to a ring-shaped lens. The effect of the antenna in the coupling system is analyzed, and maximum coupling efficiency is increased by 76.25% on average by applying the antenna. With the application of the antenna, the configurations to generate the maximum point of coupling efficiency among BG beams of different topological charges are restricted to being almost the same, which is useful for the simultaneous propagation of multiple BG beams. The effects of radial displacement and atmospheric turbulence on coupling efficiency are researched as well. Coupling efficiency becomes more sensitive to radial displacement, while the influence of turbulence on coupling efficiency remains almost the same after applying the antenna. Our calculation method has an average absolute error of only 0.6625% while increasing the calculation speed greatly, which is practical for further studies of vortex beams.

Identification of nucleoside monophosphates and their epigenetic modifications using an engineered nanopore.

RNA modifications play critical roles in the regulation of various biological processes and are associated with many human diseases. Direct identification of RNA modifications by sequencing remains challenging, however. Nanopore sequencing is promising, but the current strategy is complicated by sequence decoding. Sequential nanopore identification of enzymatically cleaved nucleoside monophosphates may simultaneously provide accurate sequence and modification information. Here we show a phenylboronic acid-modified hetero-octameric Mycobacterium smegmatis porin A nanopore, with which direct distinguishing between monophosphates of canonical nucleosides, 5-methylcytidine, N6-methyladenosine, N7-methylguanosine, N1-methyladenosine, inosine, pseudouridine and dihydrouridine was achieved. A custom machine learning algorithm, which reports an accuracy of 0.996, was also applied to the quantitative analysis of modifications in microRNA and natural transfer RNA. It is generally suitable for sensing of a variety of other nucleoside or nucleotide derivatives and may bring new insights to epigenetic RNA sequencing.

Discrimination between Different DNA Lesions by Monitoring Single-Molecule Polymerase Stalling Kinetics during Nanopore Sequencing.

O6-Carboxymethylguanosine (O6-CMG), O6-methylguanosine (O6-MeG), and abasic site (AP site) are DNA lesions induced by alkylating agents. Identification of these lesions in DNA may aid in understanding their relevance to carcinogenesis and may be used for diagnosis. Nanopore sequencing (NPS) may directly report nucleotide modifications solely from the nanopore readout. However, the conventional NPS strategy still suffers from interferences from neighboring sequences. Instead, by observation of the enzymatic stalling kinetics caused by the O6-CMG, O6-MeG, or AP site, discrimination between different DNA lesions is directly achieved. This strategy is not interfered with by the sequence context around the lesion. The lesion, which retards the movement of the DNA through the pore, efficiently prohibits misreading of the DNA lesion. These results suggest a new strategy in the identification of DNA lesions or DNA modifications. It also provides a high-resolution biophysical tool to investigate enzymatic kinetics caused by DNA lesions and the corresponding enzymes.

Evaluation of Behavior and Affective State of Different-Parity Sows with Strong/Weak Pupil Light Reflex.

The stall-housing system is commonly used in the modern swine industry in many countries; however, long-term space restrictions can cause affective and physiological abnormalities in sows. The pupil light reflex (PLR) can reflect the psychological and neurological changes in animals, and confined sows show higher pupillary rigidity. However, the PLR differs between same-parity sows, suggesting differences in behaviors and affective states between parity groups. We subjected confined Yorkshire × Landrace sows of parity 0, 2, and 5 to a PLR test and accordingly assigned them to the weak PLR (WR) group (n = 20) or the strong PLR (SR) group (n = 22). We then observed the sows' behaviors and performed a sucrose/quinine response test and novel object test (NOT) to assess the differences in their affective states. The standing and lateral lying behaviors of the sows were less frequent in WR than in SR (p < 0.05), whereas ventral lying and sitting behaviors was more frequent in WR than in SR (p < 0.05). No changes in chewing behaviors and sucrose/quinine responses were observed (p > 0.05); however, the numbers and duration of novel object contact were lower and the novel object response latency time was longer in WR than in SR (p < 0.05). Regarding parity, standing and lateral lying behaviors were less frequent and ventral lying and sitting behaviors were more frequent at parity 5 than at parity 0 (p < 0.05). Bar-biting, rooting, trough-biting, and sucrose response score were lower at parity 5 than at parity 0 (p < 0.05), and vacuum chewing behavior and quinine response score were higher in sows of parity 5 than in those of parity 0 (p < 0.05). NOT showed that the number of contacts and contact duration in sows decreased with increasing parity (p < 0.05), and the response latency time was longer in sows of parity 5 than in those of lower parity (p < 0.05). In conclusion, the behavioral expression and responses of confined sows to novel objects differed between PLRs. The evaluation of the affective state of sows also revealed marked differences with increasing parity. Thus, confined sows with WR and high parity apparently suffer from more severe psychological problems, and PLR may be a potent indicator for evaluating the affective state of confined sows.

Can reduced-input direct seeding improve resource use efficiencies and profitability of hybrid rice in China?

The mechanization of rice production in China has been accompanied by a rapid reduction in agricultural labor forces and increase in machinery purchase subsidies; however, the comprehensive performance of several major mechanized production modes regarding output, environmental protection, and profit remains uncertain to the Chinese government and farmers alike. Here, a five-year (2015-2019) field experiment was conducted to analyze the performance of farmers' mechanized seedling transplanting (FMST), farmers' mechanized direct seeding (FMDS), and reduced-input direct seeding (RIDS) concerning grain yield, energy use, greenhouse gas emissions, and economic benefits. RIDS used an unmanned aerial vehicle for sowing, fertilizing, and spraying, while adopting no-tillage, bed-furrow irrigation technology. The quantity and stability of RIDS-produced grain were similar to those of FMST and higher than those of FMDS. Furthermore, RIDS yields required significantly less machinery, human labor, fuel, and water, with 34.72% and 24.03% decreases in total energy input compared to that for FMST and FMDS, corresponding to 1.45- and 1.34-fold increases in energy productivity, respectively. The resulting CO2-eq emissions from agricultural inputs for RIDS were 71.26% and 71.32% of those for FMST and FMDS, while CH4 emissions were 32.60% and 29.24% of those for FMST and FMDS, respectively. Despite the high N2O emissions and decomposing trend of soil organic carbon in RIDS, the net global warming potential still decreased by 48.84-58.36%, and the carbon sustainability index and carbon efficiency ratio increased by 87.67-142.14% and 105.32-188.22%, respectively, compared with those of FMST and FMDS. RIDS had the lowest cost, its net return was USD 298.81 ha-1 higher than that of FMDS (similar to FMST), and its benefit-cost ratio was 10-36.19% higher than that of FMST and FMDS. Generally, RIDS offered a higher-yielding, cleaner, more sustainable rice production technology for meeting the needs of the Chinese government and farmers.

[Unsupervised deep learning for identifying the O 6-carboxymethyl guanine by nanopore sequencing].

O 6-carboxymethyl guanine(O 6-CMG) is a highly mutagenic alkylation product of DNA that causes gastrointestinal cancer in organisms. Existing studies used mutant Mycobacterium smegmatis porin A (MspA) nanopore assisted by Phi29 DNA polymerase to localize it. Recently, machine learning technology has been widely used in the analysis of nanopore sequencing data. But the machine learning always need a large number of data labels that have brought extra work burden to researchers, which greatly affects its practicability. Accordingly, this paper proposes a nano-Unsupervised-Deep-Learning method (nano-UDL) based on an unsupervised clustering algorithm to identify methylation events in nanopore data automatically. Specially, nano-UDL first uses the deep AutoEncoder to extract features from the nanopore dataset and then applies the MeanShift clustering algorithm to classify data. Besides, nano-UDL can extract the optimal features for clustering by joint optimizing the clustering loss and reconstruction loss. Experimental results demonstrate that nano-UDL has relatively accurate recognition accuracy on the O 6-CMG dataset and can accurately identify all sequence segments containing O 6-CMG. In order to further verify the robustness of nano-UDL, hyperparameter sensitivity verification and ablation experiments were carried out in this paper. Using machine learning to analyze nanopore data can effectively reduce the additional cost of manual data analysis, which is significant for many biological studies, including genome sequencing.

Gestational Diabetes Mellitus-Induced Changes in Proteomes and Glycated/Glycosylated Proteomes of Human Colostrum.

Gestational diabetes mellitus (GDM) not only has a bad effect on the development of infants but also causes variations in breastmilk composition. This study aims to investigate the changes in the protein profile of colostrum between mothers with GDM and healthy mothers (H) by sequential windowed acquisition of all theoretical fragment ion proteomics techniques. A total of 1295 proteins were detected, with 192 proteins being significantly different between GDM and H. These significantly different proteins were enriched with the carbohydrate and lipid metabolism pathway as well as immunity. Some proteins had an AOC value of 1, such as apolipoprotein E and lipoprotein lipase. In addition, we identified 42 glycated and 93 glycosylated peptides in colostrum without any enrichment, with glycated peptides being upregulated and glycosylated peptides being downregulated in colostrum with GDM. These results help us to better understand the GDM-induced changes in proteomes and glycated and glycosylated level and provide guidance on infant formula adjustment for infants from mothers with GDM.

Rapid and multiplex preparation of engineered Mycobacterium smegmatis porin A (MspA) nanopores for single molecule sensing and sequencing.

Acknowledging its unique conical lumen structure, Mycobacterium smegmatis porin A (MspA) was the first type of nanopore that has successfully sequenced DNA. Recent developments of nanopore single molecule chemistry have also suggested MspA to be an optimum single molecule reactor. However, further investigations with this approach require heavy mutagenesis which is labor intensive and requires high end instruments for purifications. We here demonstrate an efficient and economic protocol which performs rapid and multiplex preparation of a variety of MspA mutants. The prepared MspA mutants were demonstrated in operations such as nanopore insertion, sequencing, optical single channel recording (oSCR), nanopore single molecule chemistry and nanopore rectification. The performance is no different from that of pores however prepared by other means. The time of all human operations and the cost for a single batch of preparation have been minimized to 40 min and 0.4$, respectively. This method is extremely useful in the screening of new MspA mutants, which has an urgent requirement in further investigations of new MspA nanoreactors. Its low cost and simplicity also enable efficient preparations of MspA nanopores for both industrial manufacturing and academic research.

Corrigendum: Proteome Analysis of USP7 Substrates Revealed Its Role in Melanoma Through PI3K/Akt/FOXO and AMPK Pathways.

[This corrects the article DOI: 10.3389/fonc.2021.650165.].

Nanopore Sequencing Accurately Identifies the Cisplatin Adduct on DNA.

Cisplatin, which selectively binds to N7 atoms of purines to inhibit normal replication and transcription, is a widely applied chemotherapeutic drug in the treatment of cancer. Though direct identification of cisplatin lesions on DNA is of great significance, existing sequencing methods have issues such as complications of preamplification or enrichment-induced false-positive reports. Direct identification of cisplatin lesions by nanopore sequencing (NPS) is in principle feasible. However, relevant investigations have never been reported. By constructing model sequences (83 nucleotides in length) containing a sole cisplatin lesion, identification of corresponding lesions by NPS is achieved with <10 ng of input sequencing library. Moreover, characteristic high-frequency noises caused by cisplatin lesions are consistently observed during NPS, clearly identifiable in corresponding high-pass filtered traces. This feature is, however, never observed in any other combinations of natural DNA bases and could be taken as a reference to identify cisplatin lesions on DNA. Further investigations demonstrate that cisplatin stalls the replication of phi29 DNA polymerase, which appears as a ∼5 pA level fluctuation in the single-molecule resolution. These results have confirmed the feasibility of NPS to identify cisplatin lesions at the genomic level and may provide new insights into understanding the molecular mechanism of platinum-based drugs.

Single Molecule Ratcheting Motion of Peptides in a Mycobacterium smegmatis Porin A (MspA) Nanopore.

Diverse functions of proteins, including synthesis, catalysis, and signaling, result from their highly variable amino acid sequences. The technology allowing for direct analysis of protein sequences, however, is still unsatisfactory. Recent developments of nanopore sequencing of DNA or RNA have motivated attempts to realize nanopore sequencing of peptides in a similar manner. The core challenge has been to achieve a controlled ratcheting motion of the target peptide, which is currently restricted to a limited choice of compatible enzymes. By constructing peptide-oligonucleotide conjugates (POCs) and measurements with nanopore-induced phase-shift sequencing (NIPSS), direct observation of the ratcheting motion of peptides has been successfully achieved. The generated events show a clear sequence dependence on the peptide that is being tested. The method is compatible with peptides with either a conjugated N- or C-terminus. The demonstrated results suggest a proof of concept of nanopore sequencing of peptide and can be useful for peptide fingerprinting.

Mapping Potential Engineering Sites of Mycobacterium smegmatis porin A (MspA) to Form a Nanoreactor.

Protein nanopores can be engineered as nanoreactors to investigate single-molecule chemical reactions. Recent studies have demonstrated that Mycobacterium smegmatis porin A (MspA) nanopore is a superior engineering template acknowledging its geometrical advantages. However, reported engineering of MspA to form a nanoreactor has focused only on site 91 and mapping of other engineering sites have never been performed before. By taking tetrachloraurate(III) ([AuCl4]-) as a model reactant, potential engineering sites within the pore constriction of MspA have been thoroughly investigated. It is discovered that the produced event amplitude is inversely correlated to the cross-sectional diameter of the pore constriction size at the engineering site, providing evidence that site 91 is actually already the optimum place to introduce the chemical reactivity. Other unavailable engineering sites, which either significantly interfere with the pore assembly or produce reactive sites facing to the pore's exterior instead of to the pore lumen, were also spotted and discussed. All results demonstrated above have provided a complete map of engineering sites within the constriction area of MspA and may be beneficial as a reference in future engineering of corresponding nanoreactors.

Hydrogen sulfide alleviates the anxiety-like and depressive-like behaviors of type 1 diabetic mice via inhibiting inflammation and ferroptosis.

Studies reported that sodium hydrosulfide (NaHS) can remit the depressive-like and anxiety-like behaviors induced by type 1 diabetes mellitus (T1DM). However, the mechanism is still unclear. In this study, we aimed to investigate the mechanism of NaHS on T1DM. Mice were randomly divided into four groups, including the control group (CON group), DM group, DM + 5.6 mg/kg NaHS group, and CON + 5.6 mg/kg NaHS group. Data showed that NaHS did attenuate the depressive-like and anxiety-like behaviors by OFT, EPM test, FST, and TST. Results suggest that NaHS markedly alleviated the ferroptosis in the prefrontal cortex (PFC) of diabetic mice by reducing iron deposition and oxidative stress, increasing the expression of GPX4 and SLC7A11. Moreover, NaHS could dampen the activation of microglias and the release of pro-inflammatory cytokines, enhance the protein expression of sirtuin 6 (Sirt6) and the interaction between Sirt6 and the acetylation of histoneH3 lysine9 (H3K9ac), and decrease the protein expressions of the Notch1 receptor and H3K9ac. In vitro experiment, NaHS ameliorated the ferroptosis via increasing the protein expressions of SLC7A11, glutathione peroxidase 4 (GPX4), and cystathionine ß-synthase (CBS), reducing the pro-inflammatory cytokines, decreasing the levels of Fe2+, MDA, ROS, and lipid ROS. In conclusion, our results suggested that NaHS did alleviate anxiety-like and depressive-like behaviors. It can inhibit inflammation via modulating Sirt6 and was able to decrease the ferroptosis in the PFC of type 1 diabetic mice and the BV2 cells.