Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex.

Elucidating the cellular organization of the cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing and spatial transcriptomic analysis of 143 macaque cortical regions, we obtained a comprehensive atlas of 264 transcriptome-defined cortical cell types and mapped their spatial distribution across the entire cortex. We characterized the cortical layer and region preferences of glutamatergic, GABAergic, and non-neuronal cell types, as well as regional differences in cell-type composition and neighborhood complexity. Notably, we discovered a relationship between the regional distribution of various cell types and the region's hierarchical level in the visual and somatosensory systems. Cross-species comparison of transcriptomic data from human, macaque, and mouse cortices further revealed primate-specific cell types that are enriched in layer 4, with their marker genes expressed in a region-dependent manner. Our data provide a cellular and molecular basis for understanding the evolution, development, aging, and pathogenesis of the primate brain.

A de novo variant in RERE causes autistic behavior by disrupting related genes and signaling pathway.

Autism spectrum disorder (ASD) is a highly variable neurodevelopmental disorder that typically manifests childhood, characterized by a triad of symptoms: impaired social interaction, communication difficulties, and restricted interests with repetitive behaviors. De novo variants in related genes can cause ASD. We present the case of a 6-year-old Chinese boy with autistic behavior, including language communication impairments, intellectual disabilities, stunted development, and irritability in social interactions. Using Sanger sequencing, we confirmed a pathogenic in the RERE gene (NM_012102.4) (c.3732delC, p.Tyr1245Thrfs*12; EX21; Het). Subsequently, we generated an RERE point mutation cell line (ReMut) using CRISPR/Cas9 Targeted Genome Editing. Immunofluorescence was conducted to determine the location of the mutant RERE. RNA-sequencing and mass spectrometry analyses were performed to elucidate the ASD-related genes and signaling pathways disrupted by this variant in RERE. We identified 3790 differentially expressed genes and 684 differentially expressed proteins. The SHH signaling pathway was found to be downregulated, and the Hippo pathway was upregulated in ReMut. Genes implicated in autism, such as CNTNAP2, STX1A, FARP2, and GPC1, were significantly downregulated. Simultaneously, we noted alterations in HDAC1 and HDAC2, which are members of the WHHERE complex, suggesting their role in the pathogenesis of this patient. In conclusion, we report a de novo variant in RERE associated with autistic behavior. The finding that ASD is associated with RERE variants underscore the role of genetic factors in ASD and provides insights regarding the mechanisms underlying RERE variants in disease onset.

Epidemiological characteristics of human metapneumovirus among children in Nanjing, China.

PURPOSE: The objective of this study was to examine the molecular epidemiology and clinical characteristics of HMPV infection among children with ARIs in Nanjing. METHODS: The respiratory samples were collected from 2078 children (≤ 14 years) with acute respiratory infections and were tested for HMPV using real-time RT-PCR. Amplification and sequencing of the HMPV G gene were followed by phylogenetic analysis using MEGA 7.0. RESULT: The detection rate of HMPV among children was 4.7% (97/2078), with a concentration in those under 5 years of age. Notably, the peak season for HMPV prevalence was observed in winter. Among the 97 HMPV-positive samples, 51.5% (50/97) were available for characterization of the HMPV G protein gene. Phylogenetic analysis indicated that the sequenced HMPV strains were classified into three sublineages: A2c111nt - dup (84.0%), B1 (2.0%), and B2 (14.0%). CONCLUSION: There was an incidence of HMPV among hospitalized children during 2021-2022 in Nanjing with A2c111nt - dup being the dominant strain. This study demonstrated the molecular epidemiological characteristics of HMPV among children with respiratory infections in Nanjing, China.

Generalized Excess Spectroscopy.

With a clear enhancement of the apparent resolution of experimentally determined spectra, excess spectroscopy has been developed as a powerful tool to study solution structures and molecular interactions. In the standard procedure of the method, excess spectra are calculated based on the ideal spectra constructed using two pure compounds. This limits the applications of the method when the pure compounds are unstable or their physical state is different from that of the mixtures. To overcome the problem or to extend the application, we propose generalized excess spectroscopy in this work, where the ideal spectrum is evaluated from the spectra of reference mixtures. After deducing the working equations, we performed digital simulation and then applied the novel approach to a binary system consisting of tert-butanol and carbon tetrachloride. Both results illustrated the feasibility and universality of the method.

Effects of prenatal exposure to persistent organic pollutants on neonatal Outcomes:A mother-child cohort (Shanghai, China).

Persistent organic pollutants (POPs), known as common environmental pollutants, which have adverse effects on neurobehavioral development, are widely applied in industry and agriculture. However, evidence about neurodevelopmental toxicity of POPs in humans is limited. This study aimed to explore the relationship between prenatal exposure to POPs and birth outcome of the newborn including birth length, weight, and head circumference. In this study, 1522 mother-child pairs were included in this study and cord blood samples were collected, which were detected to determine exposure level of 37 POPs in total. After delivery, the neonatal anthropometric indices detection (birth length, weight, and head circumference) was performed. According to the multivariate linear regression, the newborn with high detection rates (≥75 percentile) of hexachlorobenzene (HCB), beta-hexachlorocyclohexane (ß-HCH), p,p'-dichlorodiphenyl dichloroethylene (p,p'-DDE) in the umbilical cord blood were demonstrated negative relationship with birth head circumference after adjusting for confounding factors, but not related with birth length and weight. After confirming that there was a nonlinear relationship between HCB and birth head circumference based on sex stratification through the generalized additive model (GAM), further two-piecewise linear regression model was conducted to explore the saturation threshold effect between HCB and birth head circumference, which showed cord serum HCB concentration greater than 0.5 µg/L was negatively associated with birth head circumference in girls. Our study provided evidence for the adverse influence of HCB, ß-HCH and p,p'-DDE exposure during pregnancy on the birth head circumference of offspring. Although HCB induced reduction of birth head circumference was found in girls, the mechanism of gender difference remained unclear. Further studies are needed to explore the effect of POPs on the growth and development of offspring based on in vivo or in vitro experimental models.

Abnormalities of the Halogen Bonds in the Complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I).

In this work, the hydrogen bonds and halogen bonds in the complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I) have been studied by quantum chemical calculations. We found three interesting abnormalities regarding the interactions. Firstly, the strength of halogen bonds increases in the order of IF < BrF < ClF < F2. Secondly, the halogen bonds formed by F2 are very strong, with an interaction energy in the range between −199.8 and −233.1 kJ/mol. Thirdly, all the halogen bonds are stronger than the hydrogen bonds in the systems we examined. All these results are against the general understanding of halogen bonds. These apparent abnormal properties are reconciled with the high polarizability of the Te atom and the strong inducing effect of F on the Te atom of Y2CTe. These findings provide a new perspective on halogen bonds. Additionally, we also proposed bonding distance-based methods to compare the strength of halogen/hydrogen bonds formed between different donor atoms and the same acceptor atom.

The role of ADRB2 gene polymorphisms in malignancies.

Beta-2-adrenergic receptor is a member of the G protein-coupled receptor superfamily, which is highly expressed in most malignancies. There is increasing evidence showing that beta-2-adrenergic receptors are associated with carcinogenesis, proliferation, immune regulation, invasion, angiogenesis, clinical prognosis and treatment resistance in malignancies. Polymorphisms of the ADRB2 gene have been confirmed to be associated with transcriptional activity, mRNA translation, and beta-2-adrenergic receptor expression and sensitivity. This review discusses clinically relevant examples of single nucleotide polymorphisms of ADRB2 in malignancies and the effects of these polymorphisms on cancer susceptibility, prognosis and treatment response of cancer patients.

Association between prenatal exposure to persistent organic pollutants and neurodevelopment in early life: A mother-child cohort (Shanghai, China).

As common environmental pollutants, persistent organic pollutants (POPs) that are widely applied in industry and agriculture have adverse effects on neurodevelopment. However, evidence on the neurotoxicity of POPs in neural development of offspring is limited. This study explored the relationship between prenatal exposure to POPs and neurodevelopment of 18-month-old toddlers in a mother-child cohort in Shanghai, China. In this study, we determined exposure levels of 37 POPs in cord blood serum collected at the time of delivery. The detection rate of pollutants HCB, ß-HCH, and p,p'-DDE was higher than 60%, so these will be discussed in the following analysis. From birth to approximately 18 months, we followed up infants to longitudinally explore whether POPs influenced their language, motor, and cognitive development according to a Bayley-Ⅲ assessment . Based on multivariable regression analyses, the ß-HCH concentration in cord serum was negatively related to motor development scores in children at 18 months by adjusting for the covariates, but there was no change in language and cognition. Further piecewise linear regression analysis showed that a cord serum ß-HCH concentration greater than 0.2 µg/L had a significantly negative correlation with the motor development scores. p,p'-DDE was positively associated with language development at 18 months before and after adjusting for covariates. But prenatal HCB levels were not associated with any of the Bayley-Ⅲ subscales at 18 months. We concluded that prenatal exposure to ß-HCH might have adverse effects on infants' motor development. The minimum harmful concentration of ß-HCH was estimated at 0.2 µg/L in cord serum. The unexpected positive association between p,p'-DDT and language development could be due to live birth bias.

Spin-Valley Locking Effect in Defect States of Monolayer MoS2.

Valley pseudospin in two-dimensional (2D) transition-metal dichalcogenides (TMDs) allows optical control of spin-valley polarization and intervalley quantum coherence. Defect states in TMDs give rise to new exciton features and theoretically exhibit spin-valley polarization; however, experimental achievement of this phenomenon remains challenges. Here, we report unambiguous valley pseudospin of defect-bound localized excitons in CVD-grown monolayer MoS2; enhanced valley Zeeman splitting with an effective g-factor of -6.2 is observed. Our results reveal that all five d-orbitals and the increased effective electron mass contribute to the band shift of defect states, demonstrating a new physics of the magnetic responses of defect-bound localized excitons, strikingly different from that of A excitons. Our work paves the way for the manipulation of the spin-valley degrees of freedom through defects toward valleytronic devices.

The Structures of ZnCl2-Ethanol Mixtures, a Spectroscopic and Quantum Chemical Calculation Study.

We report in this article the structural properties, spectral behavior and heterogeneity of ZnCl2-ethanol (EtOH) mixtures in a wide-composition range (1:3 to 1:14 in molar ratios), using ATR-FTIR spectroscopy and quantum chemical calculations. To improve the resolution of the initial IR spectra, excess spectroscopy and two-dimensional correlation spectroscopy were employed. The transformation process was suggested to be from EtOH trimer and EtOH tetramer to EtOH monomer, EtOH dimer and ZnCl2-3EtOH complex upon mixing. The theoretical findings showed that increasing the content of EtOH was accompanied with the flow of negative charge to ZnCl2. This led to reinforcement of the Zn←O coordination bonds, increase of the ionic character of Zn‒Cl bond and weakening and even dissociation of the Zn‒Cl bond. It was found that in some of the ZnCl2-EtOH complexes optimized at the gas phase or under the solvent effect, there existed hydroxyls with a very special interactive array in the form of Cl‒Zn+←O‒H…Cl-, which incredibly red-shifted to wavenumbers <3000 cm-1. This in-depth study shows the physical insights of the respective electrolyte alcoholic solutions, particularly the solvation process of the salt, help to rationalize the reported experimental results, and may shed light on understanding the properties of the deep eutectic solvents formed from ZnCl2 and an alcohol.

Efficacy of mandibular molar distalization by clear aligner treatment. / æ— æ‰˜æ§½éšå½¢çŸ«æ²»å™¨è¿œç§»ä¸‹é¢Œç£¨ç‰™çš„ç–—æ•ˆ.

OBJECTIVES: At present, the research on clear aligner of molar distalization mainly focuses on the upper jaw, while the research on mandibular molars is few.This study aims to evaluate the therapeutic effect of mandibular molars distalization with clear aligner via cone beam CT (CBCT) and Dolphin software. METHODS: Twenty cases of mandibular molars with clear aligner were included according to the inclusion and exclusion criteria. CBCT was taken before treatment (T0) and when the first molar was moved in place (T1). Dolphin software was used to measure the effectiveness of molar distalization. Three-dimensional changes in direction and the impact on the incisors and facial soft and hard tissues were evaluated. RESULTS: The effective rates of crown and root distalization of the second and first mandibular molars were 74%, 49%, and 71%, 47%, respectively. The second and first molars were both the distal buccal cusp with the largest distalization [(2.15 ± 0.91) mm and (1.85±1.09) mm], respectively, with significant difference between the T0 and T1 (P<0.05). The second and first molars were accompanied by depression, distal tilt, and buccal tilt with 1.06 mm, 2.10°, 2.27°, and 0.91 mm, 1.62°, and 1.91°, respectively, with significant differences between the T0 and T1 (all P<0.05). There was no obvious difference between men and women. The mandibular central incisor showed a lip-side movement of 1.02 mm, a depression of 0.82 mm, a mesial incline of 0.66°, and a crown-lip torque of 1.51° after molar distalization, with significant differences between the T0 and T1 (all P<0.001). Only the lower lip thickness increased by 0.1 cm, the length of the lower lip increased by 0.1 cm, and the ANS-ME (distance from anterior nasal spine to submental point) decreased by 0.13 cm, with significant differences between the T0 and T1 (all P<0.05). CONCLUSIONS: Clear aligner can effectively move mandibular molars farther, the crown is more effective than the root, and it is tilted. The second mandibular molar is more effective than the first mandibular molar in its distant displacement and three-dimensional changes. Molar distalization causes minor changes in mandibular incisors and facial soft and hard tissues.

Identification of Essential Sensitive Regions of the Aerolysin Nanopore for Single Oligonucleotide Analysis.

The aerolysin nanopore channel is one of the confined spaces for single molecule analysis which displays high spatial and temporal resolution for the discrimination of single nucleotides, identification of DNA base modification, and analyzing the structural transition of DNAs. However, to overcome the challenge of achieving the ultimate goal of the widespread real analytical application, it is urgent to probe the sensing regions of the aerolysin to further improve the sensitivity. In this paper, we explore the sensing regions of the aerolysin nanopore by a series of well-designed mutant nanopore experiments combined with molecular dynamics simulations-based electrostatic analysis. The positively charged lumen-exposed Lys-238, identified as one of the key sensing sites due to the presence of a deep valley in the electrostatic potentials, was replaced by different charged and sized amino acids. The results show that the translocation time of oligonucleotides through the nanopore can be readily modulated by the choice of the target amino acid at the 238 site. In particular, a 7-fold slower translocation at a voltage bias of +120 mV is observed with respect to the wild-type aerolysin, which provides a high resolution for methylated cytosine discrimination. We further determine that both the electrostatic properties and geometrical structure of the aerolysin nanopore are crucial to its sensing ability. These insights open ways for rationally designing the sensing mechanism of the aerolysin nanopore, thus providing a novel paradigm for nanopore sensing.

Fragment-based quantum mechanical calculation of protein-protein binding affinities.

The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method has been successfully utilized for efficient linear-scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE-GMFCC method for calculation of binding affinity of Endonuclease colicin-immunity protein complex. The binding free energy changes between the wild-type and mutants of the complex calculated by EE-GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6-31G*-D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein-protein binding affinities. Moreover, the self-consistent calculation of PB solvation energy is required for accurate calculations of protein-protein binding free energies. This study demonstrates that the EE-GMFCC method is capable of providing reliable prediction of relative binding affinities for protein-protein complexes. © 2018 Wiley Periodicals, Inc.

Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore.

RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.

Measuring a frequency spectrum for single-molecule interactions with a confined nanopore.

Nanopore analysis is a powerful technique for single molecule analysis by virtue of its electrochemically confined effects. As a single molecule translocates through the nanopore, the featured ionic current pattern on the time scale contains single molecule characteristics including volume, charge, and conformational properties. Although the characteristics of a single molecule in a nanopore have been written to the featured ionic current, extracting the dynamic information from a complex current trace is still a big challenge. Here, we present an applicable nanopore analysis method employing the Hilbert-Huang Transform (HHT) to study the vibrational features and interactions of a single molecule during the dynamic translocation process through the confined space of a nanopore. The HHT method is specially developed for analyzing nonlinear and non-stationary data that is highly compatible with nanopore data with a high frequency resolution. To provide proof-of-concept, we applied HHT to measure the frequency response for the wild-type (WT) aerolysin and mutant K238E aerolysin nanopores with and without the presence of poly(dA)4, respectively. The energy-frequency-time distribution spectra demonstrate that the biological nanopore contributes greatly to the characteristics of the high frequency component (>2 kHz) in the current recording. Our results suggest that poly(dA)4 undergoes relatively more consistent and confined interactions with K238E than WT, leading to a prolonging of the duration time. Therefore, the characteristics in frequency analysis could be regarded as an "single-molecule ionic spectrum" inside the nanopore, which encodes the detailed behaviours of single-molecule weak interactions.

Direct Readout of Single Nucleobase Variations in an Oligonucleotide.

Direct, low-cost, label-free, and enzyme-free identification of single nucleobase is a great challenge for genomic studies. Here, this study reports that wild-type aerolysin can directly identify the difference of four types of single nucleobase (adenine, thymine, cytosine, and guanine) in a free DNA oligomer while avoiding the operations of additional DNA immobilization, adapter incorporation, and the use of the processing enzyme. The nanoconfined space of aerolysin enables DNA molecules to be limited in the narrow pore. Moreover, aerolysin exhibits an unexpected capability of detecting DNA oligomers at the femtomolar concentration. In the future, by virtue of the high sensitivity of aerolysin and its high capture ability for DNA oligomers, aerolysin will play an important role in the studies of single nucleobase variations and open up new avenues for a broad range of nucleic-acid-based sensing and disease diagnosis.

Driven Translocation of Polynucleotides Through an Aerolysin Nanopore.

Aerolysin has been used as a biological nanopore for studying peptides, proteins, and oligosaccharides in the past two decades. Here, we report that wild-type aerolysin could be utilized for polynucleotide analysis. Driven a short polynucleotide of four nucleotides length through aerolysin occludes nearly 50% amplitude of the open pore current. Furthermore, the result of total internal reflection fluorescence measurement provides direct evidence for the driven translocation of single polynucleotide through aerolysin.

Effect of downregulation of ZEB1 on vimentin expression, tumour migration and tumourigenicity of melanoma B16F10 cells and CSCs.

Zinc-finger E-box binding homeobox 1 (ZEB1) is a master regulator of epithelial-mesenchymal transition (EMT) and has been implicated in primary epithelial cancer biological processes, such as invasion and metastasis. However, the role of ZEB1 in progression of melanoma and cancer stem cells (CSCs) remains obscure. In this study, the recombinant plasmids of t3 shRNAs targeting mouse ZEB1 were constructed and transfected into melanoma B16F10 cells. The stable transfected cells were selected and the characteristics of ZEB1 downregulated B16F10 cells was assessed. The tumourigenicity of CD44(+) CD133(+) CSCs isolated from B16F10 cells stably transfected with the ZEB1-shRNA2 recombinant was also assessed. ZEB1-shRNAs B16F10 showed a lower expression of ZEB1 and vimentin, weaker migration, invasiveness, colony forming, and proliferation, and a lower tumourigenicity than the control cells. The tumourigenicity of the ZEB1-shRNA2 CD44(+) CD133(+) CSCs was also inhibited. In conclusion, ZEB1-shRNA2-mediated downregulation of ZEB1 expression in B16F10 cells and CSCs is involved in the inhibition of the EMT process. ZEB1 may be a potential target in melanoma targeted.

Role cognition of assigned nurses supporting Hubei Province in the fight against COVID-19 in China: a hermeneutic phenomenological study.

Aims: During the COVID-19 epidemic, nurses played a crucial role in clinical treatment. As a special group, front-line nurses, especially those assigned to support Hubei Province in the fight against COVID-19 between February and April 2020, brought diverse experiences from different provinces in China in taking care of COVID-19 patients and role cognition. Therefore, our purpose is to explore the real coping experience and role cognition of front-line nurses during the novel coronavirus outbreak to provide relevant experience references for society and managers in the face of such major public health emergencies in the future. Design: This qualitative study was performed using the phenomenological hermeneutics method. Method: This is a qualitative phenomenological study. Semi-structured in-depth interviews were used to collect data. The interviewees were 53 front-line nurses who assisted and supported the fight against COVID-19 in Hubei Province during the COVID-19 epidemic. Data were collected through individual online and telephone interviews using a semi-structured interview during March 2020. The COREQ guidance was used to report this study. Results: The findings revealed that front-line nurses assisting in the fight against COVID-19 developed a context-specific role cognition of their work and contribution to society. The qualitative analysis of the data revealed 15 sub-categories and 5 main categories. These five themes represented the different roles identified by nurses. The roles included expectations, conflicts, adaptation, emotions, and flow of blessing. Belief in getting better, a sense of honor, and training could help them to reduce feelings of conflict in this role and adapt more quickly. Discussion: This article discusses the real coping experience and role cognition of front-line nurses during the novel coronavirus epidemic. It provides relevant experience references for society and managers to face similar major public health emergencies in the future. This study makes a significant contribution to the literature because it demonstrates how non-local nurses sent to Hubei to work perceived their roles as part of a larger narrative of patriotism, duty, solidarity, and hope.

The Impact of Frailty on Chemotherapy Outcomes in Patients With Digestive System Tumors: A Systematic Review and Meta-analysis.

BACKGROUND: The prevalence of patients with digestive system tumors has been high. In recent years, frailty has been considered to be associated with poor prognosis of digestive system tumors, but there are conflicting research results. A better understanding of the relationship between frailty and outcomes after chemotherapy can help advance the development of oncology care. OBJECTIVE: The aim of this study was to evaluate the effects of prechemotherapy frailty on chemotherapy toxicity, overall mortality, unplanned hospitalization, and overall survival in patients with digestive system tumors. METHODS: Up to April 2023, observational studies assessing the impact of frailty on chemotherapy outcomes in patients with digestive system tumors were collected through searching 10 online research databases. Two evaluators independently extracted literature based on the inclusion and exclusion criteria and evaluated the quality of the studies using the Newcastle-Ottawa Scale. RESULTS: Eventually, 11 cohort studies encompassing 2380 patients were included. The meta-analysis revealed that the frail group exhibited an increased risk of overall mortality, with poorer overall survival than the nonfrail group. CONCLUSION: Frailty increases the risk of chemotherapy-induced toxic effects, unplanned hospitalization, and death in patients. However, because of this study's limited number of participants, large-sample, multicenter studies to verify these findings are required. IMPLICATIONS FOR PRACTICE: This study provides theoretical support for incorporating frailty assessment into the nursing evaluation of patients with digestive system tumors before chemotherapy. This integration aids in predicting patients at a high risk of chemotherapy toxicity, mortality, and unplanned hospitalization, therefore providing corresponding interventions in advance to reduce adverse outcomes.