Structural and electronic properties of clathrate-like hydride: MH6 and MH9 (M = Sc, Y, La).

CONTEXT: The addition of central metal atoms to hydrogen clathrate structures is thought to provide a certain amount of "internal chemical pressure" to offset some of the external physical pressure required for compound stability. The size and valence of the central atoms significantly affect the minimum pressure required for the stabilization of hydrogen-rich compounds and their superconducting transition temperature. In recent years, many studies have calculated the minimum stable pressure and superconducting transition temperature of compounds with H24, H29, and H32 hydrogen clathrates, with centrally occupied metal atoms. In order to investigate the stability and physical properties of compounds with H cages in which the central atoms change in the same third group B, herein, based on first-principles calculations, we systematically investigated the lattice parameters, crystal volume, band structures, density of states, Mulliken analysis, charge density, charge density difference, and electronic localization function in I m 3 ¯ m -MH6 and P63/mmc-MH9 systems with different centered rare earth atoms M (M = Sc, Y, La) under a series of pressures. We find that for MH9, the pressure mainly changes the crystal lattice parameters along the c-axis, and the contributions of the different H atoms in MH9 to the Fermi level are H3 > H1 > H2. The density of states at the Fermi level of MH6 is mainly provided by H 1 s. Moreover, the size of the central atom M is particularly important for the stability of the crystal. By observing a series of properties of the structures with H24 and H29 cages wrapping the same family of central atoms under a series of pressures, our theoretical study is helpful for further understanding the formation mechanism of high-temperature superconductors and provides a reference for future research and design of high-temperature superconductors. METHODS: The first principles based on the density functional theory and density functional perturbation theory were employed to execute all calculations by using the CASTEP code in this work.

Structural, elastic, mechanical, electronic, and optical properties of cubic K2Pb2O3 from first-principle study.

CONTEXT: Based on first principles, the structure, elasticity, mechanics, electronics, and optical properties of cubic K2Pb2O3 were studied. The structural parameters calculated by this method are close to the previous theoretical results. The elastic constant, bulk modulus, shear modulus, Young's modulus, Poisson's ratio, and mechanical stability are studied, and it is shown that cubic K2Pb2O3 is mechanically stable, isotropic, and brittleness. The electrical conductivity and chemical bonding of cubic K2Pb2O3 were analyzed based on the calculated band structure, density of states (DOS), and bond populations. The dispersion of optical functions, including the dielectric function, refractive index, extinction coefficient, reflectivity, absorption coefficient, and loss function, is displayed and analyzed. METHODS: All computations have been carried out based on density functional theory (DFT) as implemented in the CASTEP code. The norm conservation pseudopotential method is used to exchange correlation functionals within the generalized gradient approximation (GGA).

Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

INTRODUCTION: The clinical presentations of dry eye disease (DED) and depression (DEP) often comanifest. However, the robustness and the mechanisms underlying this association were undetermined. OBJECTIVES: To this end, we set up a three-segment study that employed multimodality results (meta-analysis, genome-wide association study [GWAS] and Mendelian randomization [MR]) to elucidate the association, common pathways and causality between DED and DEP. METHODS: A meta-analysis comprising 26 case-control studies was first conducted to confirm the DED-DEP association. Next, we performed a linkage disequilibrium (LD)-adjusted GWAS and targeted phenotype association study (PheWAS) in East Asian TW Biobank (TWB) and European UK Biobank (UKB) populations. Single-nucleotide polymorphisms (SNPs) were further screened for molecular interactions and common pathways at the functional gene level. To further elucidate the activated pathways in DED and DEP, a systemic transcriptome review was conducted on RNA sequencing samples from the Gene Expression Omnibus. Finally, 48 MR experiments were implemented to examine the bidirectional causation between DED and DEP. RESULTS: Our meta-analysis showed that DED patients are associated with an increased DEP prevalence (OR = 1.83), while DEP patients have a concurrent higher risk of DED (OR = 2.34). Notably, cross-disease GWAS analysis revealed that similar genetic architecture (rG = 0.19) and pleiotropic functional genes contributed to phenotypes in both diseases. Through protein-protein interaction and ontology convergence, we summarized the pleiotropic functional genes under the ontology of immune activation, which was further validated by a transcriptome systemic review. Importantly, the inverse variance-weighted (IVW)-MR experiments in both TWB and UKB populations (p value <0.001) supported the bidirectional exposure-outcome causation for DED-to-DEP and DEP-to-DED. Despite stringent LD-corrected instrumental variable re-selection, the bidirectional causation between DED and DEP remained. CONCLUSION: With the multi-modal evidence combined, we consolidated the association and causation between DED and DEP.

De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis.

Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F1 hybrids, we found strong positive correlations between better-parent heterosis of the F1 hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.

Symmetric subgenomes and balanced homoeolog expression stabilize the establishment of allopolyploidy in cyprinid fish.

BACKGROUND: Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. RESULTS: We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. CONCLUSIONS: Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution.

The structural, mechanical and electronic properties of Ti-Al-based compounds by first-principles calculations.

The first-principles calculations with density functional theory were performed to investigate the effects of transition metal elements (Mo, Cu, Fe, Ni and Nb) on the physical properties of the Ti-Al-based compounds. Our optimized crystal parameters are in good agreement with the previous theoretical and experimental values. The mechanical stability is verified by the independent elastic constants. The B/G and Poisson's ratio ν both show that Al6TiMo is brittle, while other compounds exhibit ductility. The values of compression anisotropy of the compounds are small, but the shear anisotropy of AlCu2Ti and AlNi2Ti is much more intense than that of other compounds. The anisotropy in elastic properties of AlFe2Ti and AlNbTi2 is smaller than that of the others. It can be seen that the capacity to compress along c-axis is smaller than that along a-axis and b-axis for AlNbTi2. For AlNbTi2, the anisotropy of the bulk modulus along a-axis relative to b-axis is more insignificant than that along c-axis relative to b-axis. The hardness and Debye temperature verify that AlFe2Ti has the greatest resistance to the plastic deformation and more intense inter-atomic bonding force, respectively. Band structures and DOS are used to investigate the electronic properties. The band structures without band gaps show that these ternary Ti-Al-based compounds are conductors. DOS shows the interactions between elements and gives the bond properties. Density of states and charge density both show the strong covalent properties of AlFe2Ti by the hybridization between Fe-3d and Ti-3d states.

Genetics behind Cerebral Disease with Ocular Comorbidity: Finding Parallels between the Brain and Eye Molecular Pathology.

Cerebral visual impairments (CVIs) is an umbrella term that categorizes miscellaneous visual defects with parallel genetic brain disorders. While the manifestations of CVIs are diverse and ambiguous, molecular diagnostics stand out as a powerful approach for understanding pathomechanisms in CVIs. Nevertheless, the characterization of CVI disease cohorts has been fragmented and lacks integration. By revisiting the genome-wide and phenome-wide association studies (GWAS and PheWAS), we clustered a handful of renowned CVIs into five ontology groups, namely ciliopathies (Joubert syndrome, Bardet-Biedl syndrome, Alstrom syndrome), demyelination diseases (multiple sclerosis, Alexander disease, Pelizaeus-Merzbacher disease), transcriptional deregulation diseases (Mowat-Wilson disease, Pitt-Hopkins disease, Rett syndrome, Cockayne syndrome, X-linked alpha-thalassaemia mental retardation), compromised peroxisome disorders (Zellweger spectrum disorder, Refsum disease), and channelopathies (neuromyelitis optica spectrum disorder), and reviewed several mutation hotspots currently found to be associated with the CVIs. Moreover, we discussed the common manifestations in the brain and the eye, and collated animal study findings to discuss plausible gene editing strategies for future CVI correction.

Synthesis and Anticancer Activity of Rhopaladins' Analog RPDPD Against the HeLa Human Cervical Cancer Cell Line.

Heterocyclic compounds were widely used in many domains; pyrrolidone is a derivative of heterocycles that can be used to synthesize anticancer drugs. A new fluorine-containing rhopaladins' analog(E)-2-(4-bromobenzoyl)-N-(tert-butyl)-4-(4-fluoro benzylidene)-5-oxo-1-propylpyrrolidine-2-carboxamide (RPDPD for short) of 2-aroyl-4-arylidene-5-oxopyrrolidine derivative was synthesized by the one-pot synthesis method and evaluated for its anti-tumor activity in vitro via CCK8 assay and annexin V/propidium iodide (PI) staining of HeLa cells. The results exhibited that compound RPDPD has inhibited the proliferation of HeLa in a dose-dependent manner with an IC50 of 24.23 µmol/L (p < 0.05) and has low hepatotoxicity with an IC50 of 235.6 µmol/L (p < 0.05) to normal hepatocyte LO2 cells. The apoptotic assay demonstrated that compound RPDPD has induced apoptosis in HeLa cells (from 14.26 to 23.4%, p < 0.05). qRT-PCR results showed that the compound RPDPD could inhibit the expression of oncogene E6/E7 mRNA (p < 0.05) of human papillomavirus (HPV). The results of Western blot showed that the compound RPDPD promoted the expression of TIMP3 protein and inhibited the expression of MMP3 (p < 0.05). In conclusion, the compound RPDPD can inhibit the proliferation of cervical cancer cells and induce the apoptosis of cervical cancer cells, and its mechanism may be related to the inhibition of E6 mRNA and E7 mRNA expressions, and the anticancer effect of the compound RPDPD on cervical cancer is closely related to the TIMP3/MMP3 signaling axis.

The genome of low-chill Chinese plum "Sanyueli" (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds.

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum "Sanyueli", which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46 Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in "Sanyueli" revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of "Sanyueli" was significantly lower than that in the dormant flower buds of the high chill requiring "Furongli" plum. In addition, PsDAM6 expression was repressed by chilling treatment. The genome sequence of "Sanyueli" plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity.

Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change. Analysis of a chromosome-level assembly and resequencing of individuals across wide latitude distribution in the estuarine oyster (Crassostrea ariakensis) revealed unexpectedly low genomic diversity and population structures shaped by historical glaciation, geological events and oceanographic forces. Strong selection signals were detected in genes responding to temperature and salinity stress, especially of the expanded solute carrier families, highlighting the importance of gene expansion in environmental adaptation. Genes exhibiting high plasticity showed strong selection in upstream regulatory regions that modulate transcription, indicating selection favoring plasticity. Our findings suggest that genomic variation and population structure in marine bivalves are heavily influenced by climate history and physical forces, and gene expansion and selection may enhance phenotypic plasticity that is critical for the adaptation to rapidly changing environments.

Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome.

Zanthoxylum bungeanum is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites, which create a characteristic aroma and tingling sensation in the mouth. Owing to the high proportion of repetitive sequences, high heterozygosity, and increased chromosome number of Z. bungeanum, the assembly of its chromosomal pseudomolecules is extremely challenging. Here, we present a genome sequence for Z. bungeanum, with a dramatically expanded size of 4.23 Gb, assembled into 68 chromosomes. This genome is approximately tenfold larger than that of its close relative Citrus sinensis. After the divergence of Zanthoxylum and Citrus, the lineage-specific whole-genome duplication event η-WGD approximately 26.8 million years ago (MYA) and the recent transposable element (TE) burst ~6.41 MYA account for the substantial genome expansion in Z. bungeanum. The independent Zanthoxylum-specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture. Integrative genomic and transcriptomic analyses suggested that prominent species-specific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools, terpenoids, and anthocyanins, which contribute to the special flavor and appearance of Z. bungeanum. In summary, the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate Zanthoxylum improvement.

Relationship between lung function impairment, hypertension, and major adverse cardiovascular events: A 10-year follow-up study.

Lung function impairment and hypertension, especially hypertension, are risk factors of major adverse cardiovascular events (MACEs). However, the relationships among lung function impairment, hypertension, and MACEs have not been well-reported. We aimed to investigate the association between lung function and hypertension and MACEs. We studied 6769 people who were a representative sample of the general population in Jiangsu Province using the multi-stage stratified cluster sampling method. The average age was 51.54 years. Cox proportional hazards models were used to analyze the relationships between the blood pressure status and various types of lung function impairment related to MACEs. Over a follow-up of 10 years, 236 MACEs occurred. After adjusting for age, sex, BMI, smoking, drinking, education, physical activity, diabetes mellitus, dyslipidemia, creatine and use of antihypertensive drugs, hypertension [hazard ratio (HR) = 2.154, 95% confidence intervals (CI): 1.565-2.966], and restrictive lung function impairment (RLFI) (HR = 1.398, 95% CI: 1.021-1.879) were independently associated with MACEs. Individuals with hypertension and RFLI had the highest risk for MACEs (HR = 2.930, 95% CI: 1.734-4.953) and stroke (HR = 3.296, 95% CI: 1.862-5.832). Moreover, when combined with hypertension, obstructive lung function impairment (OLFI) (HR = 2.376, 95% CI: 1.391-4.056) and mixed lung function impairment (MLFI) (HR = 2.423, 95% CI: 1.203-4.882) were associated with MACEs. There is a synergistic effect of lung function impairment (especially RLFI) and hypertension on MACEs. Therefore, more attention should be paid to the incidence of MACEs in individuals with impaired lung function, especially those who have hypertension.

The study of spectroscopy and vibrational assignments of high nitrogen material 1,1'-azobis-1,2,3-triazole.

Benefiting from the new strategy of oxidative azo coupling of the N-NH2 moiety, a series of energetic nitrogen-rich molecules with long catenated nitrogen chains have been successfully synthesized. As one of them, the synthesized 1,1'-azobis-1,2,3-triazole shows excellent thermal stability, great explosive performance, and special photochromic properties, which has caused widespread concern. To further characterize its performance, the structural, electronic, vibrational, mechanical, and thermodynamic properties of 1,1'-azobis-1,2,3-triazole were investigated based on the first-principles density functional theory calculations. The obtained structural parameters are consistent with previous results. We used the band structure, density of states, Mulliken charges, bond populations, and electron density to analyze the electronic properties and chemical bonding. The vibrational frequency regions (396.51-3210.12 cm-1) were assigned to the corresponding vibrational modes. Furthermore, mechanical properties of 1,1'-azobis-1,2,3-triazole are also calculated. Finally, the thermodynamic properties of 1,1'-azobis-1,2,3-triazole were calculated, including the specific heat at constant volume Cv, temperature*entropy TS, enthalpy H, Gibbs free energy G, and Debye temperature ΘD.

The genome of Nautilus pompilius illuminates eye evolution and biomineralization.

Nautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.

Estimation of trapezoidal-shaped overlapping nuclear pulse parameters based on a deep learning CNN-LSTM model.

The Long Short-Term Memory neural network (LSTM) has excellent learning ability for the time series of the nuclear pulse signal. It can accurately estimate the parameters (such as amplitude, time constant, etc.) of the digitally shaped nuclear pulse signal (especially the overlapping pulse signal). However, due to the large number of pulse sequences, the direct use of these sequences as samples to train the LSTM increases the complexity of the network, resulting in a lower training efficiency of the model. The convolution neural network (CNN) can effectively extract the sequence samples by using its unique convolution kernel structure, thus greatly reducing the number of sequence samples. Therefore, the CNN-LSTM deep neural network is used to estimate the parameters of overlapping pulse signals after digital trapezoidal shaping of exponential signals. Firstly, the estimation of the trapezoidal overlapping nuclear pulse is considered to be obtained after the superposition of multiple exponential nuclear pulses followed by trapezoidal shaping. Then, a data set containing multiple samples is set up; each sample is composed of the sequence of sampling values of the trapezoidal overlapping nuclear pulse and the set of shaping parameters of the exponential pulse before digital shaping. Secondly, the CNN is used to extract the abstract features of the training set in these samples, and then these abstract features are applied to the training of the LSTM model. In the training process, the pulse parameter set estimated by the present neural network is calculated by forward propagation. Thirdly, the loss function is used to calculate the loss value between the estimated pulse parameter set and the actual pulse parameter set. Finally, a gradient-based optimization algorithm is applied to update the weight by getting back the loss value together with the gradient of the loss function to the network, so as to realize the purpose of training the network. After model training was completed, the sampled values of the trapezoidal overlapping nuclear pulse were used as input to the CNN-LSTM model to obtain the required parameter set from the output of the CNN-LSTM model. The experimental results show that this method can effectively overcome the shortcomings of local convergence of traditional methods and greatly save the time of model training. At the same time, it can accurately estimate multiple trapezoidal overlapping pulses due to the wide width of the flat top, thus realizing the optimal estimation of nuclear pulse parameters in a global sense, which is a good pulse parameter estimation method.

The use of a transolecranon pin joystick technique in the treatment of multidirectionally unstable supracondylar humeral fractures in children.

Multidirectionally unstable supracondylar humeral fractures cause severe instability in both flexion and extension movements. The traditional closed reduction often fails to overcome this lack of stability. The aim of this study is to use a closed reduction technique with a transolecranon pin to achieve temporary stability. From 35 pediatric multidirectionally unstable supracondylar humeral fractures hospitalized between March 2012 and March 2018 at our hospital, 23 fractures (65.7%) were treated with closed reduction and percutaneous pinning (CRPP) (group 1) and the remaining twelve fractures (34.3%) were treated utilizing a transolecranon pin joystick technique of CRPP (group 2). Both groups were followed over 16 weeks. The outcomes of our analysis included surgical time, times of fluoroscopy, Baumann angle, postoperative range of motion and complications. The surgical time and times of fluoroscopy were significantly shorter for patients in group 2 when compared with group 1 (P < 0.05). All cases showed restoration of the normal anterior humeral line-capitellar relationship. However, the quality of reduction on the anteroposterior radiographic view was significantly better for patients in group 2 than that of group 1 (P < 0.05). No immediate postoperative complications were observed. The range of motion was similar in both groups during the last follow-up appointment. A transolecranon pin is a safe and effective method for closed reduction of multidirectionally unstable supracondylar humeral fractures in children. The joystick technique can shorten surgical time and improve quality of reduction with no increasing risk of complications. Level of evidence: level III.

Effects of molecular vacancy and ethylenediamine on structural and electronic properties of CH3NO2 surfaces.

The structural and electronic properties of (100) surface for nitromethane (NM) are studied using density functional theory (DFT) with the generalized gradient approximation and Perdew-Burke-Ernzerhof functional (GGA-PBE). Molecular vacancy and ethylenediamine (C2H8N2) substitution are considered in this work. We find that ethylenediamine substitution significantly decreases the band gap, while molecular vacancy increases the band gap slightly. It indicates that ethylenediamine substitution has a positive effect on the impact sensitivity of NM. Also, the formation energies are calculated and the reasons for the decrease of band gap for ethylenediamine substitution and the increase of band gap for CH3NO2 vacancy are explained.

Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals.

Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.