Experimental study on the effect of different cement content on the improvement of dynamic characteristics of seismic-prone poor soil

The improvement of sandy soils with poor seismic properties to modify their dynamic characteristics is of great importance in seismic design for engineering sites. In this study, a series of dynamic tests on sandy soils sandy soils with poor seismic conditions were conducted using the GCTS resonant column system to investigate the improvements effects of different cement contents on dynamic characteristic parameters. The research findings are as follows: The cement content has certain influences on the dynamic shear modulus, dynamic shear modulus ratio, the maximum dynamic shear modulus, and the damping ratio of sandy soils with poor seismic properties. Among them, the influence on dynamic shear modulus is limited, while the damping ratio is significantly affected. The addition of cement to seismic-poor sandy soils significantly enhances their dynamic characteristics. The most noticeable improvement is observed when the cement content is 8%. Through curve fitting analysis, a relationship equation is established between the maximum dynamic shear modulus and the cement content, and the relevant parameters are provided. A comparative test between the improved soils and the remolded soils reveals that the addition of cement significantly improves the seismic performance of the poor soils. The recommended values for the range of variation of the dynamic shear modulus ratio and damping ratio are provided, considering the effect of improvement. These research findings provide reference guidelines for seismic design and engineering sites.

Transcriptomic Profiles of Long Noncoding RNAs and Their Target Protein-Coding Genes Reveals Speciation Adaptation on the Qinghai-Xizang (Tibet) Plateau in Orinus

Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation.

Metabolomic and transcriptomic reveal flavonoid biosynthesis and regulation mechanism in Phlomoides rotata from different habitats

Phlomoides rotata is a traditional medical plant at 3100-5200 m altitude in the Tibet Plateau. In this study, flavonoid metabolites were investigated in P. rotata from Henan County (HN), Guoluo County (GL), Yushu County (YS), and Chengduo County (CD) habitats in Qinghai. The level of kaempferol 3-neohesperidoside, sakuranetin, and biochanin A was high in HN. The content of limocitrin and isoquercetin was high in YS. The levels of ikarisoside A and chrysosplenol D in GL were high. Schaftoside, miquelianin, malvidin chloride, and glabrene in CD exhibited high levels. The results showed a significant correlation between 59 flavonoids and 29 DEGs. Eleven flavonoids increased with altitude. PAL2, UFGT6, COMT1, HCT2, 4CL4, and HCT3 genes were crucial in regulating flavonoid biosynthesis. Three enzymes CHS, 4CL, and UFGT, were crucial in regulating flavonoid biosynthesis. This study provided biological and chemical evidence for the different uses of various regional plants of P. rotata.

The incidence of surgical site infections in China

Surgical site infections (SSIs) are a common type of healthcare-associated infection. We performed a literature review to demonstrate the incidence of SSIs in mainland China based on studies since 2010. We included 231 eligible studies with ≥30 postoperative patients, comprising 14 providing overall SSI data regardless of surgical sites and 217 reporting SSIs for a specific site. We found that the overall SSI incidence was 2.91% (median; interquartile range: 1.05%, 4.57%) or 3.18% (pooled; 95% confidence interval: 1.85%, 4.51%) and the SSI incidence varied remarkably according to the surgical site between the lowest (median, 1.00%; pooled, 1.69%) in thyroid surgeries and the highest (median, 14.89%; pooled, 12.54%) in colorectal procedures. We uncovered that Enterobacterales and staphylococci were the most common types of micro-organisms associated with SSIs after various abdominal surgeries and cardiac or neurological procedures, respectively. We identified two, nine, and five studies addressing the impact of SSIs on mortality, the length of stay (LOS) in hospital, and additional healthcare-related economic burden, respectively, all of which demonstrated increased mortality, prolonged LOS, and elevated medical costs associated with SSIs among affected patients. Our findings illustrate that SSIs remain a relatively common, serious threat to patient safety in China, requiring more action. To tackle SSIs, we propose to establish a nationwide network for SSI surveillance using unified criteria with the aid of informatic techniques and to tailor and implement countermeasures based on local data and observation. We highlight that the impact of SSIs in China warrants further study.

Coordination of histone chaperones for parental histone segregation and epigenetic inheritance

Chromatin-based epigenetic memory relies on the accurate distribution of parental histone H3-H4 tetramers to newly replicated DNA strands. Mcm2, a subunit of the replicative helicase, and Dpb3/4, subunits of DNA polymerase ε, govern parental histone H3-H4 deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. Here, using fission yeast heterochromatin inheritance systems that eliminate interference from initiation pathways, we show that a Mcm2 histone binding mutation severely disrupts heterochromatin inheritance, while mutations in Dpb3/4 cause only moderate defects. Surprisingly, simultaneous mutations of Mcm2 and Dpb3/4 stabilize heterochromatin inheritance. eSPAN (enrichment and sequencing of protein-associated nascent DNA) analyses confirmed the conservation of Mcm2 and Dpb3/4 functions in parental histone H3-H4 segregation, with their combined absence showing a more symmetric distribution of parental histone H3-H4 than either single mutation alone. Furthermore, the FACT histone chaperone regulates parental histone transfer to both strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone H3-H4 density and faithful heterochromatin inheritance. These results underscore the importance of both symmetric distribution of parental histones and their density at daughter strands for epigenetic inheritance and unveil distinctive properties of parental histone chaperones during DNA replication.

Hypoxia-induced miR-5100 promotes exosome-mediated activation of cancer-associated fibroblasts and metastasis of head and neck squamous cell carcinoma

The invasion-metastasis cascade in head and neck squamous cell carcinoma (HNSCC) is predominantly caused by the interaction between tumor cells and tumor microenvironment, including hypoxia as well as stromal cells. However, the mechanism of hypoxia-activated tumor-stroma crosstalk in HNSCC metastasis remains to be deciphered. Here, we demonstrated that HIF1α was upregulated in HNSCC specimens compared with adjacent normal tissues, whose overexpression was associated with lymph node metastasis and predicted unfavorable prognosis. HIF1α expression correlated positively with the levels of miR-5100 as well as α-SMA, the marker of CAFs. Hypoxia/HIF1α regulated transcriptionally miR-5100 to promote the degradation of its target gene QKI, which acts as a tumor suppressor in HNSCC. Hypoxic HNSCC-derived exosomal miR-5100 promoted the activation of CAFs by orchestrating QKI/AKT/STAT3 axis, which further facilitated HNSCC metastasis. Additionally, miR-5100 derived from plasma exosomes indicated HNSCC malignant progression. In conclusion, our findings illuminate a novel HIF1α/miR-5100/QKI pathway in HNSCC metastasis, and suggest that miR-5100 might be a potential biomarker and therapeutic target for HNSCC.

Association Between Number of Missing Teeth and Hyperlipidemia: The TCLSIH Cohort Study

Background

To explore the association between the number of missing teeth and the prevalence of hyperlipidemia in a Chinese adult population.

Methods

13,932 adults were investigated in the TCLSIH cohort study. The number of missing teeth was determined at baseline through a self-reported questionnaire, and then classified into three categories: 0, 1-2, and ≥3. We defined hyperlipidemia as total cholesterol (TC) ≥ 5.17 mmol/L or triglycerides (TG) ≥ 1.7 mmol/L or low-density lipoprotein (LDL) cholesterol ≥ 3.37 mmol/L or a self-report of physician-diagnosed hyperlipidemia during follow-up visits. Cox proportional-hazards regression models were employed to assess the relationship between the number of missing teeth and incident hyperlipidemia.

Results

A total of 6756 first-incident cases of hyperlipidemia occurred during 42,048 person-years of follow-up (median follow-up, 4.2 years). After adjusted confounders, multivariable HRs and 95% CI for incident of hyperlipidemia across the categories of missing teeth were as follows: in male participants, 1.00 (reference), 1.10 (0.98, 1.22), and 1.03 (0.91, 1.16) (P for trend = 0.30); in female participants, 1.00 (reference), 1.09 (0.99, 1.19), and 1.18 (1.04, 1.33) (P for trend < 0.01).

Conclusion

The number of missing teeth is associated with an increased risk of hyperlipidemia in female participants but not in male participants. Systemic chronic inflammation may potentially mediate this association.

The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery

JTE-607 is an anticancer and anti-inflammatory compound and its active form, compound 2, directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-messenger RNA (pre-mRNA) 3' processing. Surprisingly, compound 2-mediated inhibition of pre-mRNA cleavage is sequence specific and the drug sensitivity is predominantly determined by sequences flanking the cleavage site (CS). Using massively parallel in vitro assays, we identified key sequence features that determine drug sensitivity. We trained a machine learning model that can predict poly(A) site (PAS) relative sensitivity to compound 2 and provide the molecular basis for understanding the impact of JTE-607 on PAS selection and transcription termination genome wide. We propose that CPSF73 and associated factors bind to the CS region in a sequence-dependent manner and the interaction affinity determines compound 2 sensitivity. These results have not only elucidated the mechanism of action of JTE-607, but also unveiled an evolutionarily conserved sequence specificity of the mRNA 3' processing machinery.

Surgical excision of a giant solitary keratoacanthoma in the cheek: a case report and literature review

Background

Giant keratoacanthoma, a rare variant solitary of keratoacanthoma is characterized by a diameter exceeding 20 mm, rapid growth, and destruction of underlying tissue. Traditionally, it has been considered to be a self-resolving or low-grade squamous proliferation. Due to their atypical appearance, Giant keratoacanthomas may present a diagnostic challenge. Histopathological examination remains the reference standard for distinguishing squamous cell carcinoma (SCC) from keratoacanthoma. Surgical management is still the standard treatment for solitary keratoacanthoma.

Case Description

We present the case of a 75-year-old man with a giant keratoacanthoma of the cheek, with a transverse length of 25 mm and a longitudinal length of 30 mm located 30 mm below the earlobe that was surgically excised with no obvious recurrence during follow-up. We used the Intraoperative frozen-section examination, which played a crucial role in ensuring clear margins and complete tumor removal.

Conclusions

This case demonstrates that keratoacanthoma can be considered surgically curable and should be distinguished from SCC and other crateriform tumors. After surgical resection of giant isolated keratoacanthoma on the face, the high risk of cosmetic problems should be considered. We suggest free-flap transplantation be performed for functional repair, when the invasion range of the tumor is large and a perforation defect is formed.

[Bioinformatics analysis of primary biliary cholangitis key genes and molecular mechanisms]

Objective: To extract the differentially expressed key genes of primary biliary cholangitis (PBC) using bioinformatics methods, so as to provide information for further study into the mechanism. Methods: The GSE119600 dataset was downloaded from the GEO database to obtain differentially expressed genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for differentially expressed genes. Protein-protein interaction (PPI) network reconstruction, Cytoscape software visualization, and core gene screening were performed. The area under the receiver operating characteristic curve (ROC AUC) was used to assess the diagnostic effectiveness of genes and plot the pROC software package. The x-Cell software was used to calculate the enrichment score of 34 immune cells in each sample. Finally, four key genes (PSMA4, PSMA1, PSMB1, and PSMA3) were selected. Blood samples were analyzed using the qPCR method. Results:: A total of 373 immune-related differentially expressed genes were identified. Eight genes (PSMC6, PSMB2, PSMB1, PSMA3, PSMA4, PSMA1, PSMD7, and PSMB5) were screened from the 178 nodes and 596 edges as hub genes of the PPI network, which were significantly related to amino acid metabolism, hematopoietic stem cell differentiation, cell cycle, and immune processes. PSMA4, PSMA1, PSMB1, and PSMA3 were defined as immunological biomarkers for PBC with an AUC value of the ROC curve > 0.7. Immunoinfiltrating cell analysis showed that the proportion of eosinophils was significantly higher in PBC patients compared to the control group, whereas the proportion of CD4+ memory T cells, plasma cells, Th2 cells, and cDC cells was significantly lower in PBC patients than the control group. Plasma cells were associated with all four immunological biomarkers. Seven PBC patients and seven healthy subjects were selected for peripheral blood qPCR validation, which demonstrates that PSMB1, PSMA3, PSMA1, and PSMA4 levels were significantly lower in PBC patients than healthy subjects, with a statistically significant difference. Conclusion:: Bioinformatics screened eight key genes, of which four were key immunological markers and may serve as a basis for clinical diagnosis and mechanism exploration.

Periodontitis and NAFLD-related diseases: A bidirectional two-sample Mendelian randomization study

BACKGROUND

Epidemiological studies have shown an association between periodontitis and nonalcoholic fatty liver disease (NAFLD)-related diseases. However, a causal relationship between these two diseases remains unclear. To examine the causal relationship between these two diseases, we conducted a bidirectional two-sample Mendelian randomization (MR) analysis using genetic markers as proxies.

METHODS

Statistical summary was obtained from a large genome-wide association study (GWAS) on NAFLD (N = 342,499), nonalcoholic steatohepatitis (NASH, N = 342,499), fibrosis (N = 339,081), cirrhosis (N = 342,499), fibrosis/cirrhosis (N = 334,553), and periodontitis (N = 34,615) in the European ancestry. The inverse variance weighted (IVW) method was used as the main method to estimate the bidirectional association. Sensitivity analysis was performed to evaluate the rigidity of the results.

RESULTS

Limited evidence indicated positive causal associations between genetically predicted NAFLD and periodontitis (IVW odds ratio [OR], 1.094; 95% confidence interval [CI], 1.006-1.189; p = 0.036) and between cirrhosis and periodontitis (IVW OR, 1.138; 95% CI, 1.001-1.294; p = 0.048). However, the opposite trend did not indicate a causative effect of periodontitis on NAFLD-related diseases. The sensitivity analysis revealed no obvious pleiotropy or heterogeneity.

CONCLUSIONS

Our MR analysis provides new evidence in favor of the moderate causal impact of NAFLD on periodontitis. The causal effects of periodontitis on NAFLD-related diseases warrant further investigation.

Fit accuracy in the rest region of RPDs fabricated by digital technologies and conventional lost-wax casting: a systematic review and meta-analysis

BACKGROUND

Digital technologies have recently been introduced into the fabrication of removable partial dentures (RPDs). However, it is still unclear whether the digitally fabricated RPDs fit better than conventionally cast ones in the rest region. The aim of this study was to evaluate the fit accuracy in the rest region of RPDs fabricated by digital technologies and compare it to those made by conventional lost-wax (CLW) technique.

METHODS

A comprehensive search was conducted in Cochrane Library, PubMed, EMbase, Web of Science and SpringerLink. Studies published up to August 2022 were collected. Two authors analyzed the studies independently and assessed the risk of bias on the modified methodological index for non-randomized studies (MINORS) scale. The mean values of gap distance between rests and corresponding rest seats of each study were extracted as outcome. A random-effects model at a significance level of P < 0.05 was used in the global comparison and subgroup analysis was carried out.

RESULTS

Overall, 11 articles out of 1214 complied with the inclusion criteria and were selected, including 2 randomized controlled trials (RCTs), 1 non-randomized clinical trial and 8 in vitro studies. Quantitative data from Meta-analysis revealed that fit accuracy in the rest region of RPDs fabricated with CLW showed no statistically significant difference with digital techniques (SMD = 0.33, 95%CI (-0.18, 0.83), P = 0.21). Subgroup analysis revealed a significantly better fit accuracy of CLW-fabricated RPDs in the rest region than either additive manufacturing (AM) groups or indirect groups (P = 0.03, P = 0.00), in which wax or resin patterns are milled or printed before conventional casting. While milled RPDs fit significantly better than cast ones in the rest region (P = 0.00). With digital relief and heat treatment, hybrid manufactured (HM) clasps obtained better fit accuracy in the rest region (P < 0.05). In addition, finishing and polishing procedure had no significant influence in the fit accuracy in all groups (P = 0.83).

CONCLUSIONS

RPDs fabricated by digital technologies exhibit comparable fit accuracy in rest region with those made by CLW. Digital technologies may be a promising alternative to CLW for the fabrication of RPDs and additional studies are recommended to provide stronger evidence.

TRIAL REGISTRATION

CRD42020201313.

Flavonoid synthesis in Lamiophlomis rotata from Qinghai-Tibet Plateau is influenced by soil properties, microbial community, and gene expression

Lamiophlomis rotata is a medicinal plant in Qinghai-Tibet Plateau, in which flavonoid compounds are the major medicinal components. However, it remains unclear how flavonoid metabolism of L. rotata is influenced by soil properties and microbial community. In this study, we collected L. rotata seedlings and rhizosphere soils from five habitats ranging from 3750 to 4270 m of altitude and analyzed the effects of habitat conditions on flavonoid metabolism. The activities of peroxidase, cellulase, and urease were increased with altitude, while those of alkaline phosphatase, alkaline protease, and sucrase were decreased with altitude. Analysis of OTUs showed that the total number of bacterial genera was higher than that of fungal genera. The highest number of fungal genera was 132, and that of bacterial genera was 33 in Batang (BT) town in Yushu County at an altitude of 3880 m, suggesting that the fungal communities may play a critical role in L. rotata rhizosphere soils. Flavonoids in leaves and roots of L. rotata shared a similar pattern, with a trend of increasing levels with altitude. The highest flavonoid content measured, 12.94 mg/g in leaves and 11.43 mg/g in roots, was from Zaduo (ZD) County at an altitude of 4208 m. Soil peroxidases affected quercetin content in leaves of L. rotata, while the fungus Sebacina affected flavonoid content in leaves and roots of L. rotata. The expression of PAL, F3'H, FLS, and FNS genes showed a declining trend in leaves with altitude, while F3H showed an increasing trend in both leaves and roots. Overall, soil physicochemical properties and microbial community affect flavonoid metabolism in L. rotata in Qinghai-Tibet Plateau. The variations in flavonoid content and gene expression as well as their associations with soil factors revealed the complexity of the growth conditions and genetic makeup in L. rotata habitats of Qinghai-Tibet Plateau.

SARS-CoV-2 and male infertility: from short- to long-term impacts

PURPOSE

The coronavirus 2019 (COVID-19) pandemic-caused by a new type of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-has posed severe impacts on public health worldwide and has resulted in a total of > 6 million deaths. Notably, male patients developed more complications and had mortality rates ~ 77% higher than those of female patients. The extensive expression of the SARS-CoV-2 receptor and related proteins in the male reproductive tract and the association of serum testosterone levels with viral entry and infection have brought attention to COVID-19's effects on male fertility.

METHODS

The peer-reviewed articles and reviews were obtained by searching for the keywords SARS-CoV-2, COVID-19, endocrine, spermatogenesis, epididymis, prostate, and vaccine in the databases of PubMed, Web of Science and Google Scholar from 2020-2022.

RESULTS

This review summarizes the effects of COVID-19 on the male reproductive system and investigates the impact of various types of SARS-CoV-2 vaccines on male reproductive health. We also present the underlying mechanisms by which SARS-CoV-2 affects male reproduction and discuss the potentially harmful effects of asymptomatic infections, as well as the long-term impact of COVID-19 on male reproductive health.

CONCLUSION

COVID-19 disrupted the HPG axis, which had negative impacts on spermatogenesis and the epididymis, albeit further investigations need to be performed. The development of vaccines against various SARS-CoV-2 variations is important to lower infection rates and long-term COVID risks.

The influence of seismic frequency spectrum on the instability of loess slope

The input of seismic wave with different frequency has a significant impact on loess slope instability. On the basis of field investigation and experiments, the particle flow software PFC^2D was used to explore the effect of seismic frequency spectrum on slope instability through the process of calibrating soil microscopic parameters, model establishment, seismic wave input and other processes. The results show that: 1. The low-frequency component of the input wave is the main frequency band that causes the slope instability, the slope has amplifying effect on the low-frequency input wave, and the slope has a "filtering" effect on the high-frequency input wave; 2. The instability of the slope will cause an increase in frequency components above 10 Hz; 3. The special structure of the slope is one of the main reasons for the instability of the slope. This result has theoretical and practical significance for earthquake landslide prevention and monitoring and early warning.

Transcriptome Screening of Long Noncoding RNAs and Their Target Protein-Coding Genes Unmasks a Dynamic Portrait of Seed Coat Coloration Associated with Anthocyanins in Tibetan Hulless Barley

Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding genes (PCGs). Here, we conducted a comprehensive bioinformatics analysis to identify a total of 9414 long noncoding RNAs (lncRNAs) in the seed coats of purple and white hulless barley along a developmental gradient. Transcriptome-wide profiles of lncRNAs documented several properties, including GC content fluctuation, uneven length, a diverse range of exon numbers, and a wide variety of transcript classifications. We found that certain lncRNAs in hulless barley possess detectable sequence conservation with Hordeum vulgare and other monocots. Furthermore, both differentially expressed lncRNAs (DElncRNAs) and PCGs (DEPCGs) were concentrated in the later seed development stages. On the one hand, DElncRNAs could potentially cis-regulate DEPCGs associated with multiple metabolic pathways, including flavonoid and anthocyanin biosynthesis in the late milk and soft dough stages. On the other hand, there was an opportunity for trans-regulated lncRNAs in the color-forming module to affect seed coat color by upregulating PCGs in the anthocyanin pathway. In addition, the interweaving of hulless barley lncRNAs and diverse TFs may function in seed coat coloration. Notably, we depicted a dynamic portrait of the anthocyanin synthesis pathway containing hulless barley lncRNAs. Therefore, this work provides valuable gene resources and more insights into the molecular mechanisms underlying anthocyanin accumulation in hulless barley from the perspective of lncRNAs, which facilitate the development of molecular design breeding in crops.

AI-Assisted Disease Monitoring Using Stretchable Polymer-Based Sensors

Flexible sensors have attracted significant attention for medical applications. Herein, an AI-assisted stretchable polymer-based (AISP) sensor has been developed based on the Beer-Lambert law for disease monitoring and telenursing. Benefiting from the use of superior polymer materials, the AISP sensor features a high tensile strain of up to 100%, durability of >10,000 tests, excellent waterproofness, and no effect of temperature (1.6-60.9 °C). Such advantages support the capability that the AISP can be flexibly pasted on the skin surface as a wearable device for real-time monitoring of multiple physiological parameters. An AISP sensor-based swallowing recognition technique has been proposed with a high accuracy of up to 88.89%. Likewise, it has been expanded to a remote nursing assistance system to meet critical patients' physiological requirements and daily care. The hands-free communication experiment and robot control applications have also been successfully conducted based on the constructed system. Such merits demonstrate its potential as a medical toolkit and indicate promise for intelligent healthcare.

Complex genetic architecture underlying the plasticity of maize agronomic traits

Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude-related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compensation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental variation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9%, 2.2%, and 2.6% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by-environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture.

Novel Method to Achieve Temperature-Stable Microwave Dielectric Ceramics: A Case in the Fergusonite-Structured NdNbO4 System

Microwave dielectric ceramics with permittivity (ε_r) ∼ 20 play an important role in massive multiple-input multiple-output (MIMO) technology in 5G. Although fergusonite-structured materials with low dielectric loss are good candidates for 5G application, tuning the temperature coefficient of resonant frequency (TCF) remains a problem. In the present work, smaller V⁵⁺ ions (r_V = 0.355 Å, with coordination number (CN) = 4) were substituted for Nb⁵⁺ (r_Nb = 0.48 Å with CN = 4) in the Nd(Nb_1-xV_x)O₄ ceramics, which, according to in situ X-ray diffraction data, lowered the fergusonite-to-scheelite phase transition (T_F-S) to 400 °C for x = 0.2. The thermal expansion coefficient (α_L) of the high-temperature scheelite phase was +11 ppm/°C, whereas for the low-temperature fergusonite phase, it was + 14 < α_L < + 15 ppm/°C. The abrupt change in α_L, the associated negative temperature coefficient of permittivity (τ_ε), and the minimum value of ε_r at T_F-S resulted in a near-zero TCF ∼ (+7.8 ppm/°C) for Nd(Nb_0.8V_0.2)O₄ (ε_r ∼ 18.6 and Qf ∼ 70,100 GHz). A method to design near-zero TCF compositions based on modulation of τ_ε and α_L at T_F-S is thus demonstrated that may also be extended to other fergusonite systems.

The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery

JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3' processing. Although CPSF73 is universally required for mRNA 3' end formation, we have unexpectedly found that Compound 2- mediated inhibition of pre-mRNA 3' processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity. A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3' processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. As the Compound 2-resistant CS sequences, characterized by U/A-rich motifs, are prevalent in PASs from yeast to human, the CS region sequence may have more fundamental functions beyond determining drug resistance. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown and evolutionarily conserved sequence-specificity of the mRNA 3' processing machinery.

The Radiological Evaluation of the Anatomy of the Alveolar Antral Artery and the Lateral Wall Thickness Using Cone-Beam Computed Tomography: A Retrospective Study

The objectives study aims to assess the position and route of the alveolar antral artery and the lateral wall thickness of the maxillary sinus using cone-beam computed tomography (CBCT), reducing the risk of complications and improving the success rate of surgery.

MATERIALS AND METHODS

This study included CBCT scans from 238 patients. The detection diameter of AAA and distance of the lower border of AAA to the maxillary sinus floor at the first premolar, second premolar, first molar, and second molar locations were evaluated. The route of AAA was observed with novel classification. Furthermore, the distance from the maxillary sinus floor to the alveolar crest at four posterior tooth locations was measured respectively. Moreover, the lateral wall thickness at four locations was assessed. Data were subjected to statistical analysis.

RESULTS

AAA was observed in 62.18% of all sinuses. The mean diameter was 0.99±0.21 mm, with significant differences within gender. Half of the route of AAA was intrasinus intraosseous type. The mean distance between the maxillary sinus floor and AAA was 8.00±2.68 mm, with a significant difference between dentate and edentulous status at the first molar location. Distance from the sinus floor to the alveolar ridge crest in edentulous status negatively correlated with the distance from the sinus floor to AAA at the first molar location. The mean thickness of the lateral wall was 2.03±0.91 mm, and the difference in thickness between males and females at the four locations was statistically significant.

CONCLUSION

intrasinus-intraosseous type, is the most common route. Special care should be taken at the first molar location during a lateral window sinus floor elevation. CBCT is highly recommended to before lateral wall maxillary sinus floor elevation.

Portable nanopore-sequencing technology: Trends in development and applications

Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.

Combination of external fixation using digital six-axis fixator and internal fixation to treat severe complex knee deformity

BACKGROUND

Severe knee valgus/varus or complex multiplanar deformities are common in clinic. If not corrected in time, cartilage wear will be aggravated and initiate the osteoarthritis due to lower limb malalignment. Internal fixation is unable to correct severe complex deformities, especially when combined with lower limb discrepancy (LLD). Based on the self-designed digital six-axis external fixator Q spatial fixator (QSF), which can correct complex multiplanar deformities without changing structures, accuracy of correction can be improved significantly.

METHODS

This retrospective study included 24 patients who suffered from complex knee deformity with LLD treated by QSF and internal fixation at our institution from January 2018 to February 2021. All patients had a closing wedge distal femoral osteotomy with internal fixation for immediate correction and high tibia osteotomy with QSF fixation for postoperative progressive correction. Data of correction prescriptions were computed by software from postoperative CT scans.

RESULTS

Mean discrepancy length of operative side was 2.39 ± 1.04 cm (range 0.9-4.4 cm) preoperatively. The mean difference of lower limb was 0.32 ± 0.13 cm (range 0.11-0.58 cm) postoperatively. The length of limb correction had significant difference (p < 0.05). The mean MAD and HKA decreased significantly (p < 0.05), and the mean MPTA and LDFA increased significantly (p < 0.05). There were significant increase (p < 0.05) in the AKSS-O, AKSS-F and Tegner Activity Score. The lower limb alignment was corrected (p < 0.05). The mean time of removing external fixator was 112.8 ± 17.9 days (range 83-147 days).

CONCLUSIONS

Complex knee deformity with LLD can be treated by six-axis external fixator with internal fixation without total knee arthroplasty. Lower limb malalignment and discrepancy can be corrected precisely and effectively by this approach.

LDMD: A database of microbes in human lung disease

Background

Lungs were initially thought to be sterile. However, with the development of sequencing technologies, various commensal microorganisms, especially bacteria, have been observed in the lungs of healthy humans. Several studies have also linked lung microbes to infectious lung diseases. However, few databases have focused on the metagenomics of lungs to provide microbial compositions and corresponding metadata information. Such a database would be handy for researching and treating lung diseases.

Methods

To provide researchers with a preliminary understanding of lung microbes and their research methods, the LDMD collated nearly 10,000 studies in the literature covering over 30 diseases, gathered basic information such as the sources of lung microbe samples, sequencing methods, and processing software, as well as analyzed the metagenomic sequencing characteristics of lung microbes. Besides, the LDMD also contained data collected in our laboratory.

Results

In this study, we established the Lung Disease Microorganisms Database (LDMD), a comprehensive database of microbes involved in lung disease. The LDMD offered sequence analysis capabilities, allowing users to upload their sequencing results, align them with the data collated in the database, and visually analyze the results.

Conclusion

In conclusion, the LDMD possesses various functionalities that provide a convenient and comprehensive resource to study the lung metagenome and treat lung diseases.

Application of SolidWorks software in preoperative planning of high tibial osteotomy

Purpose

Open-wedge high tibial osteotomy (HTO) is a common surgical treatment for medial osteoarthritis in young and active patients. The accuracy of osteotomy is closely associated with postoperative efficacy. The accuracy of digital preoperative planning is higher than that of the preoperative manual measurement and several computer software with varying accuracy and convenience are used for digital preoperative planning. This study aimed to use the SolidWorks software for HTO preoperative planning and to determine its accuracy and reliability in HTO preoperative planning.

Methods

We reviewed the data of 28 patients with 54 with medial compartment knee arthritis who underwent open-wedge HTO preoperative planning using SolidWorks between June 2019 and March 2021. The standard anteroposterior standing whole-leg radiographs were assessed before and 6 weeks after the surgery. The correction angle, weight-bearing line (WBL) ratio, mechanical femorotibial angle (mFTA), and medial proximal tibial angle (MPTA) before and after the surgery were compared. The clinical results were evaluated using the Knee Society score.

Results

At 6 weeks after the surgery, the WBL ratio was corrected from 16.8% to 50.5%, mFTA was corrected from 6.4° varus to 1.2° valgus, and MPTA was corrected from 83.4° to 89.3°. No significant difference was observed between the predicted correction angle before the surgery and the correction angle measured 6 weeks after the surgery (t = -1.745, p = 0.087). The knee score and function score of Knee Society increased from 76.4 and 80.7 before surgery to 95.0 and 95.7, respectively.

Conclusions

The SolidWorks software showed high accuracy and reliability in preoperative planning of open-wedge HTO in patients with medial compartment knee arthritis.

Prediction of accessory canals on the apical third of mandibular second molar based on micro-computed tomography

OBJECTIVE

The aim of this study was to investigate the anatomical factors influencing the incidence of accessory canals (ACs) in the apical third of the mandibular second molar in Chinese population.

METHODS

Micro-CT was performed on 86 root canals. The five possible factors influencing the incidence of ACs in the apical third were named X1 to X5. These factors were the canal length of the apical third, fused roots, location of apical foramen, curvature of the root canals, and complexity of the canals. Statistical analysis was performed by the least absolute shrinkage and selection operator, receiver operating characteristic curve, and the χ2 test (α = 0.05).

RESULTS

The selected variables in the least absolute shrinkage and selection operator regression model were fused roots and complex root canals. The area under the curve was 0.737, indicating that the model had a certain predictive ability. ACs were mainly distributed in the buccal wall and mesial wall of root canals in the apical third of molars (p < 0.05).

CONCLUSIONS

For Chinese population, fused roots and complex root canals are anatomical factors influencing ACs in the apical one-third of mandibular second molars, and the ACs mainly occur in the buccal wall and mesial wall of the root canal.

Analysis of flavonoid metabolism during fruit development of Lycium chinense

Lycium chinense is an important medicinal plant in the northwest of China. Flavonoids are the major pharmacological components of L. chinense fruits. However, flavonoid metabolism during fruit development of L. chinense remains to be studied. Here, we analyzed the change of flavonoid contents, enzyme activity, and gene expression during fruit development of L. chinense. We found that flavonoids, anthocyanins, and catechins are the most important components of L. chinense fruits. Flavonoid content was increased with fruit development and was high at the late developmental stage. PAL, CHS, and F3H enzymes played a significant role in flavonoid accumulation in fruits. Transcriptomic analysis showed that anthocyanin pathway, flavonol pathway, flavonoid biosynthesis, and phenylpropanoid synthesis pathway were the major pathways involved in flavonoid metabolism in L. chinense. Gene expression analysis indicated that PAL1 and CHS2 genes were critical for flavonoid metabolism in L. chinense fruits. These discoveries help us understand the dynamic changes in flavonoids during fruit development and enhance the use of L. chinense fruits.

Progresses of CRISPR/Cas9 genome editing in forage crops

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated-genome editing has evolved into a powerful tool that is widely used in plant species to induce editing in the genome for analyzing gene function and crop improvement. CRISPR/Cas9 is an RNA-guided genome editing tool consisting of a Cas9 nuclease and a single-guide RNA (sgRNA). The CRISPR/Cas9 system enables more accurate and efficient genome editing in crops. In this review, we summarized the advances of the CRISPR/Cas9 technology in plant genome editing and its applications in forage crops. We described briefly about the development of CRISPR/Cas9 technology in plant genome editing. We assessed the progress of CRISPR/Cas9-mediated targeted-mutagenesis in various forage crops, including alfalfa, Medicago truncatula, Hordeum vulgare, Sorghum bicolor, Setaria italica and Panicum virgatum. The potentials and challenges of CRISPR/Cas9 in forage breeding were discussed.

Defb19 regulates the migration of germ cell and is involved in male fertility

β-defensins are small antimicrobial peptides that play essential roles in male fertility. Although several members of the β-defensin family are preferentially expressed in the testis, their involvement in spermatogenesis remains elusive. In this study, we have characterized the expression and function of Defb19 in mouse testis. Our results showed that Defb19 is expressed in both Sertoli cells and germ cells. Overexpression of Defb19 in the 15P-1 Sertoli cell line decreases the expression of cell junction molecules and promotes the matrix adhesion and migration of Sertoli cells. Recombinant DEFB19 and conditioned medium of Defb19-overexpressed 15P-1 cells promote the migration of GC2-spd spermatocyte cell line. Knockout of Defb19 in mouse by CRISPR/Cas9 resulted in male subfertility with testicular and epididymal atrophy. A marked increase in apoptosis and a significant decrease in the sperm count were observed in the KO mice. Together, our study has uncovered an important role of Defb19 in male fertility by regulating the migration of both the Sertoli cells and the germ cells. Our study has shed new light on the functions of β-defensins in the testis.

Correction of severe lower extremity deformity with digital hexapod external fixator based on CT data

Purpose

Our goal was to examine the therapeutic effect of a self-designed digital six-axis external fixator technique for the correction of severe lower extremity deformities.

Patients and methods

Between January 2017 and December 2020, our institution employed self-developed digital hexapod external fixator technology (QSF), based on CT data, to gradually correct 28 severe tibial deformities, and 15 femurs underwent osteotomy and internal fixation. The mean patient age was 32.6 ± 14.3 years, and the mean follow-up duration was 27.4 ± 16.1 months. We also recoded and analyzed the values of preoperative and final follow-up MAD, mFTA, MPTA, LLD, mLDFA, LEFS, KSS, and functional score.

Results

The QSF adjustment duration was 21.4 ± 10.8 days, and the healing duration of the tibial osteotomy site was 17.6 ± 7.0 weeks. The preoperative MAD, mFTA, and MPTA were 54.1 ± 26.2 mm, 167.7 ± 15.7°, and 75.2 ± 12.0°, respectively. At the last follow-up, the MAD was 8.2 ± 9.9 mm, mFTA was 177.6 ± 3.4°, and MPTA was 87.6 ± 2.4°. Based on these data, we achieved significant improvement post operation. The preoperative LLD and mLDFA values were 13.8 ± 18 mm and 83.7 ± 10.8°, respectively, and the values were 7.6 ± 7.6 mm and 87.8 ± 2.6°, respectively, at the last follow-up. This indicated no significant difference in these values before and after the operation. Finally, the LEFS, KSS, and functional scores improved from preoperative 51.6 ± 11.2, 68.5 ± 11.7, and 67.8 ± 11.2 to postoperative 72.3 ± 6.1, 92.9 ± 3.4, and 94.2 ± 6.3, respectively.

Conclusions

Based on our analyses, the QSF technique accurately corrected severe multiplanar tibial deformities in adults. When combined with femoral osteotomy, satisfactory lower extremity alignment was obtained while correcting for femoral deformity. This technology has the advantages of simple operation, reliable fixation, less trauma, and less complications.

Design and Fabrication of a C-Band Dielectric Resonator Antenna with Novel Temperature-Stable Ce(Nb1-xVx)NbO4 (x = 0-0.4) Microwave Ceramics

Vanadium(V)-substituted cerium niobate [Ce(Nb1-xVx)O4, CNVx] ceramics were prepared to explore their structure-microwave (MW) property relations and application in C-band dielectric resonator antennas (DRAs). X-ray diffraction and Raman spectroscopy revealed that CNVx (0.0 ≤ x ≤ 0.4) ceramics exhibited a ferroelastic phase transition at a critical content of V (xc = 0.3) from a monoclinic fergusonite structure to a tetragonal scheelite structure (TF-S), which decreased in temperature as a function of x according to thermal expansion analysis. Optimum microwave dielectric performance was obtained for CNV0.3 with permittivity (εr) of ∼16.81, microwave quality factor (Qf) of ∼41 300 GHz (at ∼8.7 GHz), and temperature coefficient of the resonant frequency (TCF) of ∼ -3.5 ppm/°C. εr is dominated by Ce-O phonon absorption in the microwave band; Qf is mainly determined by the porosity, grain size, and proximity of TF-S; and TCF is controlled by the structural distortions associated with TF-S. Terahertz (THz) (0.20-2.00 THz, εr ∼ 12.52 ± 0.70, and tan δ ∼ 0.39 ± 0.17) and infrared measurements are consistent, demonstrating that CNVx (0.0 ≤ x ≤ 0.4) ceramics are effective in the sub-millimeter as well as MW regime. A cylindrical DRA prototype antenna fabricated from CNV0.3 resonated at 7.02 GHz (|S11| = -28.8 dB), matching simulations, with >90% radiation efficiency and 3.34-5.93 dB gain.

AutoNanopore: An Automated Adaptive and Robust Method to Locate Translocation Events in Solid-State Nanopore Current Traces

Solid-state nanopore sequencing has shown impressive performances in several research scenarios but is still challenging, mainly due to the ultrafast speed of DNA translocation and significant noises embedded in raw signals. Hence, event detection, aiming to locate precisely these translocation events, is the fundamental step of data analysis. However, existing event detection methods use either a user-defined global threshold or an adaptive threshold determined by the data, assuming the baseline current to be stable over time. These disadvantages limit their applications in real-world application scenarios, especially considering that the results of different methods are often inconsistent. In this study, we develop an automated adaptive method called AutoNanopore, for fast and accurate event detection in current traces. The method consists of three consecutive steps: current trace segmentation, current amplitude outlier identification by straightforward statistical analyses, and event characterization. Then we propose ideas/metrics on how to quantitatively evaluate the performance of an event detection method, followed by comparing the performance of AutoNanopore against two state-of-the-art methods, OpenNanopore and EventPro. Finally, we examine if one method can detect the overlapping events detected by the other two, demonstrating that AutoNanopore has the highest coverage ratio. Moreover, AutoNanopore also performs well in detecting challenging events: e.g., those with significantly varying baselines.

Discovery of compounds that reactivate p53 mutants in vitro and in vivo

The tumor suppressor p53 is the most frequently mutated protein in human cancer. The majority of these mutations are missense mutations in the DNA binding domain of p53. Restoring p53 tumor suppressor function could have a major impact on the therapy for a wide range of cancers. Here we report a virtual screening approach that identified several small molecules with p53 reactivation activities. The UCI-LC0023 compound series was studied in detail and was shown to bind p53, induce a conformational change in mutant p53, restore the ability of p53 hotspot mutants to associate with chromatin, reestablish sequence-specific DNA binding of a p53 mutant in a reconstituted in vitro system, induce p53-dependent transcription programs, and prevent progression of tumors carrying mutant p53, but not p53null or p53WT alleles. Our study demonstrates feasibility of a computation-guided approach to identify small molecule corrector drugs for p53 hotspot mutations.

A Novel Low-Cost 3D Printed Brace Design Method for Early Onset Scoliosis

Early onset scoliosis (EOS) is a type of spine deformity that presents before 10 years of age. The biomechanical properties in scoliosis have been found to be di?erent, especially in the case of the concave and convex paraverte-bral muscles. Based on this fact, a novel 3d printed patient-specific asymmetric stiffness brace design method is proposed in this paper, aiming to provide asymmetric stiffness to match "imbalanced" biomechanical properties of the concave and convex paravertebral muscles, respectively, and treat EOS by applying the block-structure brace.A 3d CAD draft model of the brace contour was implemented from 3D scanning. The asymmetric stiffness block-structure brace was designed in Rhinoceros and the Finite Ele-ment (FE) model was imported into ABAQUS. FE simulation was employed to study the mechanical characteristics of the brace, which provided a quan-titative index for the "imbalanced" property of brace stiffness. The results of the FE simulation showed that the stiffnesses of the concave and convex sides were 145.88 N/mm and 35.95 N/mm, respectively. The block-structure brace was fabricated using 3d printing. Asymmetric stiffness was evaluated by corrective force measurements, which were obtained from a thin-film pressure sensor equipped on the brace. The patient-specific asymmetric stiffness brace was applied to clinical practice in a one-year old EOS patient. A novel low-cost 3D printed brace design method for EOS was proposed in this study that could potentially be useful in patient treatment acceptance.

[Clinical study of digital six-axis external fixation frame based on CT data for tibiofibular fractures]

Objective: To investigate the clinical effect of applying the digital six-axis external fixation frame based on CT data in the treatment of tibiofibular fractures. Methods: The clinical data of 43 patients with tibiofibular fractures treated by the self-developed digital six-axis external fixation frame based on CT data at Integrated Orthopedic Department of Traditional Chinese Medicine (TCM) and Western Medicine,HongHui Hospital from January 2018 to January 2021 were retrospective analysis.There were 27 males and 16 females,aged (36.0±9.4) years(range:25 to 50 years).AO classification:15 cases of 42A,11 cases of 42B, and 17 cases of 42C.There were 7 open fractures and Gustilo fracture classification:2 cases of type Ⅰ,4 cases of type Ⅱ,and 1 case of type Ⅲ.The two or three plane rings were connected with six connecting rods to form a complete six-axis external fixation frame,and the distal and proximal fracture blocks were connected to the distal and proximal rings by fixation pins,and the lengths of the six connecting rods needed to be adjusted were calculated by using the supporting software according to the CT data after surgery,and then the lengths of the connecting rods were adjusted one by one to complete the reduction of the fracture. The reduction accuracy of this six-axis external fixation brace was evaluated by measuring postoperative radiographs; postoperative recovery and complications were collected,the time of brace removal was recorded,and the function of the affected limb was evaluated according to the Johner-Wruhs score at the final follow-up. Results: Postoperative radiographs showed that all patients achieved satisfactory reduction with lateral displacement(M(IQR)) of 2.3(2.5) mm (range:0.3 to 7.3 mm),anteroposterior displacement of 2.1 (2.4) mm (range:0.3 to 5.7 mm),anteroposterior angulation of 2.5(2.4)°(range:0 to 5°),internal and external angulation of 2.1(1.5)°(range:0 to 4°), and no significant internal or external rotational deformity was detected on the exterior.On the second postoperative day,all patients were able to walk with partial weight-bearing on crutches. All 43 patients were followed up for more than 6 months,with a follow-up period of (33.3±7.3) weeks (range:24 to 42 weeks).The external fixation frame was removed after the fracture healed.The external frame was removed at 20(3)weeks (range:18 to 25 weeks) postoperatively. Up to the final follow up, no secondary fracture occurred in any of them.The Johner-Wruhs score of the affected limb at the last follow-up was excellent in 39 cases and good in 4 cases. Conclusion: The digital six-axis external fixator based on CT data for tibiofibular fractures has the advantages of precise reduction,firm fixation,simple operation,rapid fracture healing,and minimal trauma, which is a minimally invasive method for treating tibiofibular fractures,especially suitable for patients with poor skin and soft tissue conditions such as open injuries.

RNA binding protein POP7 regulates ILF3 mRNA stability and expression to promote breast cancer progression

RNA Binding Proteins(RBPs)play pivotal roles in breast cancer (BC) development. As a RBP, Processing of precursor 7 (POP7) is one of the subunits of RNase P and RNase MRP, however, its exact function and mechanism in BC remain unknown. Here, we showed that expression of POP7 was frequently increased in breast cancer cells and in primary breast tumors. Up-regulated POP7 significantly promoted BC cell proliferation in vitro and primary tumor growth in vivo. POP7 also increased cell migration, invasion in vitro and lung metastasis in vivo. Through RNA-immunoprecipitation coupled with sequencing (RIP-seq), we found that POP7 bound preferentially to intron regions and POP7-binding peak associated genes were mainly enriched in cancer-related pathways. Further, POP7 regulated Interleukin Enhancer Binding Factor 3 (ILF3) expression through influencing its mRNA stability. Knockdown of ILF3 significantly impaired the increased malignant potential of POP7 over-expressing cells, suggesting that POP7 enhances BC progression through regulating ILF3 expression. Collectively, our findings provide the first evidence for the important role of POP7 and its regulation of ILF3 in promoting breast cancer progression.

Epididymis cell atlas in a patient with a sex development disorder and a novel NR5A1 gene mutation

This study aims to characterize the cell atlas of the epididymis derived from a 46,XY disorders of sex development (DSD) patient with a novel heterozygous mutation of the nuclear receptor subfamily 5 group A member 1 (NR5A1) gene. Next-generation sequencing found a heterozygous c.124C>G mutation in NR5A1 that resulted in a p.Q42E missense mutation in the conserved DNA-binding domain of NR5A1. The patient demonstrated feminization of external genitalia and Tanner stage 1 breast development. The surgical procedure revealed a morphologically normal epididymis and vas deferens but a dysplastic testis. Microfluidic-based single-cell RNA sequencing (scRNA-seq) analysis found that the fibroblast cells were significantly increased (approximately 46.5%), whereas the number of main epididymal epithelial cells (approximately 9.2%), such as principal cells and basal cells, was dramatically decreased. Bioinformatics analysis of cell-cell communications and gene regulatory networks at the single-cell level inferred that epididymal epithelial cell loss and fibroblast occupation are associated with the epithelial-to-mesenchymal transition (EMT) process. The present study provides a cell atlas of the epididymis of a patient with 46,XY DSD and serves as an important resource for understanding the pathophysiology of DSD.

New technique for detecting cracked teeth and evaluating the crack depth by contrast-enhanced cone beam computed tomography: an in vitro study

Background

Cracked teeth may cause various clinical symptoms depending on the extension depth of the crack and the subsequent bacterial infections. However, techniques to reliably determine the extension depths of cracks in teeth before treatment are lacking. The aim of this study was to develop a new technique based on contrast-enhanced cone beam computed tomography (CBCT) to improve the accuracy of crack depth evaluation in vitro.

Methods

We developed an in vitro artificial simulation model of cracked teeth. Pre-experimental CBCT (pre-CBCT), and micro-computed tomography (micro-CT) were first performed for all cracked teeth (n = 31). Contrast-enhanced CBCT was then performed by infiltrating the crack with ioversol under vacuum conditions. The sensitivities of pre-CBCT and contrast-enhanced CBCT for the diagnosis of cracked teeth were calculated. According to the K-means clusters, crack depths measured by micro-CT were changed into categorical variables. Bland–Altman plot and the intraclass correlation coefficient (ICC) were used to analyze the consistency of the crack depths between the pre-CBCT and contrast-enhanced CBCT, as well as the ICC between the contrast-enhanced CBCT and micro-CT. Receiver operating characteristic (ROC) curves were generated to assess the ability for predicting crack depth in the differential diagnosis using pre-CBCT and contrast-enhanced CBCT. Restricted cubic splines were also used to model the non-linear relationship between the crack depths of contrast-enhanced CBCT and micro-CT.

Results

The sensitivities of pre-CBCT and contrast-enhanced CBCT were 48.4%, and 67.7%, respectively. The ICC value of crack depth as measured by pre-CBCT and contrast-enhanced CBCT was 0.847 (95% confidence interval [CI] 0.380–0.960; P < 0.001). The areas under ROC curves (AUC) of pre-CBCT and contrast-enhanced CBCT were different: the AUC of pre-CBCT was 0.958 (P = 0.000, 95% CI 0.843–1.074), and the AUC of contrast-enhanced CBCT was 0.979 (P = 0.000, 95% CI 0.921–1.037), and the difference was not statistically significant (Z = − 0.707, P = 0.480). The ICC value of crack depth as measured by contrast-enhanced CBCT and micro-CT was 0.753 (95% CI 0.248–0.911; P < 0.001).

Conclusion

Contrast-enhanced CBCT under vacuum conditions with a contrast medium can significantly improve the crack detection rate of cracked teeth; however, it cannot measure the crack depths accurately.

Dental anxiety is related to postoperative symptoms in third molar surgery

PURPOSE

To examine the association of preoperative dental anxiety with the severity of postoperative symptoms among patients undergoing lower third molar (LM3) extraction surgery.

MATERIALS AND METHODS

We conducted a hospital-based prospective study with a sample size of 213 patients. All the patients underwent LM3 extraction surgery at the Stomatology Hospital of Tianjin Medical University. Preoperative dental anxiety was measured using the Dental Anxiety Scale for Third Molar Surgery (DAS-TMS) and classified into four categories: No anxiety, Some unease, Anxious, and Very anxious. The primary outcome was defined using the postoperative symptom severity scale on the seventh day after surgery. The patients' clinical characteristics, radiologic features, and surgery-related variables were used as control variables. Bivariate analysis involved Fisher's exact test and Kruskal-Wallis test. Multivariable logistic analysis was used to assess preoperative dental anxiety in relation to the severity of postoperative symptoms. We applied a two-piecewise regression model to examine the potential non-linear associations.

RESULTS

The mean (SD) dental anxiety score was 10.56 (3.84). The proportion of dental anxiety was as follows: No anxiety, 7.5%; Some unease, 46.9%; Anxious, 31.0%; Very anxious, 14.6%. The multivariable-adjusted ORs with 95% CIs of postoperative symptoms were 1.00 for No anxiety, 3.63 (0.90-14.68) for Some unease, 5.29 (1.25-22.33) for Anxious, and 4.75 (1.02-22.18) for Very anxious (P for trend = 0.047). The risk of serious postoperative symptoms increased with the dental anxiety level up to 7 points (adjusted OR 1.94, 95% CI 1.12-3.74; P = 0.012). When the dental anxiety level exceeded 7 points, the level of DAS-TMS was not associated with the risk of serious postoperative symptoms (OR 0.98, 95% CI 0.88-1.08; P = 0.756).

CONCLUSIONS

Findings suggest that dental anxiety is associated with a risk of serious postoperative symptoms following LM3 removal. The degree of dental anxiety in patients before LM3 extraction surgery should be of concern to clinicians.

AMDBNorm: an approach based on distribution adjustment to eliminate batch effects of gene expression data

Batch effects explain a large part of the noise when merging gene expression data. Removing irrelevant variations introduced by batch effects plays an important role in gene expression studies. To obtain reliable differential analysis results, it is necessary to remove the variation caused by technical conditions between different batches while preserving biological variation. Usually, merging data directly with batch effects leads to a sharp rise in false positives. Although some methods of batch correction have been developed, they have some drawbacks. In this study, we develop a new algorithm, adjustment mean distribution-based normalization (AMDBNorm), which is based on a probability distribution to correct batch effects while preserving biological variation. AMDBNorm solves the defects of the existing batch correction methods. We compared several popular methods of batch correction with AMDBNorm using two real gene expression datasets with batch effects and analyzed the results of batch correction from the visual and quantitative perspectives. To ensure the biological variation was well protected, the effects of the batch correction methods were verified by hierarchical cluster analysis. The results showed that the AMDBNorm algorithm could remove batch effects of gene expression data effectively and retain more biological variation than other methods. Our approach provides the researchers with reliable data support in the study of differential gene expression analysis and prognostic biomarker selection.

Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma

Background:

Endometrial carcinoma (EC) is one of the most common malignancies in women worldwide. For EC patients discovered at an early stage, the prognosis is good. However, the advanced EC patients (stage III-IV) have very poor prognoses. The competitive endogenous RNAs (ceRNA) regulatory network in EC remains unclear, and the relationship between hub RNAs and important clinical characters (clinical stage) has not been strictly studied yet.

Objective:

In order to study the development of endometrial carcinoma and the identification of early diagnostic markers, the relationship between hub RNAs and important clinical traits (clinical stage) was strictly studied.

Methods:

The co-expression networks of mRNA, lncRNA, and miRNA were constructed by weighted gene co-expression network analysis. Gene ontology (GO) biological process terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out for DEmRNA. AceRNA regulated network was constructed based on miRcode, miRDB, TargetScan, and miRTarBase. Furthermore, survival analysis, regression analysis of mRNA-lncRNA pairs, and gene set enrichment analysis were carried out.

Results:

A ceRNA network containing 11 mRNAs, 4 miRNAs, and 18 lncRNAs was constructed based on aberrantly expressed RNAs in the co-expression modules. In this network, 7 mRNAs, 4 lncRNAs, and 1 miRNA were found closely related to the overall survival of EC. The positive correlations of 35 pairs of mRNA and lncRNA in the ceRNA network were obtained. Notably, 5 mRNAs, 3 lncRNAs, and 1 miRNA were identified as potential prognostic biomarkers for EC. Single gene GSEA analysis revealed that the signal pathways related to cell cycle and cancer were highly enriched.

Conclusion:

Identification of five mRNAs (CBX6, PIM1, RIMS3, SOX11, and XKR7), three lncRNA (WT1-AS, LINC00494, and LINC00501), and one miRNA (miR-195) as potential prognostic biomarkers for EC was helpful for the early diagnosis, prognosis, and development of new treatment strategies of EC patients.

Comparing the Traditional Versus Conservative Endodontic Access Cavities Design of the Maxillary First Molar: Using Cone-Beam Computed Tomography

Background

This study aimed to compare the size and location of the traditional and conservative endodontic access cavities of the right maxillary first molar teeth, projected on the occlusal surface using cone-beam computed tomography (CBCT), to obtain an ideal access cavity.

Material/Methods

Five hundred CBCT images of the right maxillary first molars, including 198 males and 302 females, were retrospectively evaluated using KaVo eXam Vision software. First, a rectangular coordinate system was established. The coordinates of 4 pulp horns and 3 root canal orifices, which projected on the occlusal surface, were marked on it. Two different access cavities were then created by connecting these points: (1) traditional endodontic access cavity (TEC) required removal of the entire roof of the pulp chamber to establish a straight-line access to the root canal system; (2) conservative endodontic access cavity (CEC) was formed by connecting the projection of each root canal orifice on the occlusal. Data were analyzed using Kruskal-Wallis and Pearson’s correlation tests at a 5% significance level.

Results

The area of TEC was approximately 9.61 mm² for males and 8.91 mm² for females. The area of CEC was approximately 3.4 mm² for males and 3.16 mm² for females. The projections of all pulp horns and root canal orifices were in or near the central area of nine-rectangle-grid.

Conclusions

Compared with the traditional access cavity, creating a conservative access cavity was less invasive. Meanwhile, the access cavity should be limited to the central or near the central area of nine-rectangle-grid.

Comprehensive evaluation of genetic variants using chromosomal microarray analysis and exome sequencing in fetuses with congenital heart defect

OBJECTIVE

To evaluate comprehensively, using chromosomal microarray analysis (CMA) and exome sequencing (ES), the prevalence of chromosomal abnormalities and sequence variants in unselected fetuses with congenital heart defect (CHD) and to evaluate the potential diagnostic yields of CMA and ES for different CHD subgroups.

METHODS

This was a study of 360 unselected singleton fetuses with CHD detected by echocardiography, referred to our department for genetic testing between February 2018 and December 2019. We performed CMA, as a routine test for aneuploidy and copy number variations (CNV), and then, in cases without aneuploidy or pathogenic CNV on CMA, we performed ES.

RESULTS

Overall, positive genetic diagnoses were made in 84 (23.3%) fetuses: chromosomal abnormalities were detected by CMA in 60 (16.7%) and sequence variants were detected by ES in a further 24 (6.7%) cases. The detection rate of pathogenic and likely pathogenic genetic variants in fetuses with non-isolated CHD (32/83, 38.6%) was significantly higher than that in fetuses with isolated CHD (52/277, 18.8%) (P < 0.001), this difference being due mainly to the difference in frequency of aneuploidy between the two groups. The prevalence of a genetic defect was highest in fetuses with an atrioventricular septal defect (36.8%), ventricular septal defect with or without atrial septal defect (28.4%), conotruncal defect (22.2%) or right ventricular outflow tract obstruction (20.0%). We also identified two novel missense mutations (c.2447G>C, p.Arg816Pro; c.1171C>T, p.Arg391Cys) and a new phenotype caused by variants in PLD1.

CONCLUSIONS

Chromosomal abnormalities were identified in 16.7% and sequence variants in a further 6.7% of fetuses with CHD. ES should be offered to all pregnant women with a CHD fetus without chromosomal abnormality or pathogenic CNV identified by CMA, regardless of whether the CHD is isolated. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.

[Early reduction of serum RANTES can predict HBsAg clearance in patients with chronic hepatitis B treated with nucleos(t)ide analogues combined with peginterferon alpha]

Objective: To observe the dynamic changes of serum RANTES during the treatment with nucleos(t)ide analogues combined with pegylated interferon alpha (peginterferon-α), and further analyze the predictive effect of RANTES on HBsAg clearance in patients with chronic hepatitis B. Methods: 98 cases of chronic hepatitis B with quantitative HBsAg < 3 000 IU/ml and HBV DNA < 20 IU/ml after≥1 year NAs treatment were enrolled. Among them, 26 cases continued to receive NAs monotherapy, 72 cases received NAs combined with pegylated interferon alpha therapy. The changes in RANTES during treatment were observed. The receiver operating characteristic curve was used to analyze the early changes of RANTES to predict the HBsAg clearance during 48 weeks. Results: During 48 weeks, 15 cases (20.83%) had achieved HBsAg clearance in combination group, while no patient had achieved HBsAg clearance in NAs group. The overall serum RANTES level had decreased from baseline in NAs and combination group. At week 48, in the combination group, the serum RANTES level was decreased more significantly in patients with HBsAg clearance than patients without. Further analysis showed that, in combination group, HBsAg clearance rate of patients with serum RANTES decreased at week 12 and 24 was higher than patients with elevated (29.17% vs. 4.17%, P = 0.014; 28.00% vs. 4.55%, P = 0.052), and quantitative HBsAg reduction was larger significantly [(1.49 ± 1.26) log(10)IU/ml vs. (0.73 ± 0.81) log(10)IU/ml, P = 0.017; (1.54 ± 1.27) log(10)IU/ml vs. (0.57 ± 0.56) log(10)IU/ml, P = 0.004]. Receiver operating characteristic curve analysis showed that the baseline quantitative HBsAg and the reduction in quantitative HBsAg and serum RANTES during the early period were predictors of HBsAg clearance after 48-week combination therapy. Furthermore, the combination of baseline quantitative HBsAg and 12 - or 24-week reduction of serum RANTES were better predictors of HBsAg clearance than that of baseline quantitative HBsAg combined with HBsAg decrease at week 12 or 24. The area under the receiver operating characteristic curve of the former was 0.925 and 0.939, while that of the latter was 0.909 and 0.929, respectively. Conclusion: Early reduction of serum RANTES at week 12 and 24 can predict HBsAg loss in CHB patients receiving addition of peginterferon-α to ongoing NAs Therapy, so serum RANTES could be one of the key immunological markers for predicting HBsAg clearance.

Clustering of genes from microarray data using hierarchical projective adaptive resonance theory: a case study of tuberculosis

We propose the hierarchical Projective Adaptive Resonance Theory (PART) algorithm for classification of gene expression data. This algorithm is realized by combing transposed quasi-supervised PART and unsupervised PART. We develop the corresponding validation statistics for each process and compare it with other clustering algorithms in a case study of tuberculosis (TB). First, we use sample-based transposed quasi-supervised PART to obtain optimal clustering results of samples distinguished by time post-infection and the representative genes for each cluster including up-regulated, down-regulated and stable genes. The up- and down-regulated genes show more than 90% similarity to the result derived from Linear Models for Microarray Data and are verified by weighted k-nearest neighbor model on TB projection. Second, we use gene-based unsupervised PART algorithm to cluster these representative genes where functional enrichment analysis is conducted in each cluster. We further confirm the main immune response of human macrophage-like THP-1 cells against TB within 2 days is type I interferon-mediated innate immunity. This study demonstrates how hierarchical PART algorithm analyzes microarray data. The sample-based quasi-supervised PART extracts representative genes and narrows down the shortlist of disease-relevant genes and gene-based unsupervised PART classifies representative genes that help to interpret immune response against TB.

Ketogenesis impact on liver metabolism revealed by proteomics of lysine β-hydroxybutyrylation

Ketone bodies are bioactive metabolites that function as energy substrates, signaling molecules, and regulators of histone modifications. β-hydroxybutyrate (β-OHB) is utilized in lysine β-hydroxybutyrylation (Kbhb) of histones, and associates with starvation-responsive genes, effectively coupling ketogenic metabolism with gene expression. The emerging diversity of the lysine acylation landscape prompted us to investigate the full proteomic impact of Kbhb. Global protein Kbhb is induced in a tissue-specific manner by a variety of interventions that evoke β-OHB. Mass spectrometry analysis of the β-hydroxybutyrylome in mouse liver revealed 891 sites of Kbhb within 267 proteins enriched for fatty acid, amino acid, detoxification, and one-carbon metabolic pathways. Kbhb inhibits S-adenosyl-L-homocysteine hydrolase (AHCY), a rate-limiting enzyme of the methionine cycle, in parallel with altered metabolite levels. Our results illuminate the role of Kbhb in hepatic metabolism under ketogenic conditions and demonstrate a functional consequence of this modification on a central metabolic enzyme.