[Statistical methods of unmeasured confounder control based on negative control theory]

Controlling unmeasured confounders in non-randomized controlled studies is challenging. Negative control theory is based on the theoretical concept that the test result of negative controls must be negative. Setting appropriate negative control incorporates the specificity of association into population studies for the identification and control of unmeasured confounders. This paper explains the principles to control unmeasured confounders using negative control theory from a statistical perspective. A detailed introduction of derived methods based on negative control theory is also introduced, including adjusted standardized mortality ratio method, calibrating P-value method, generalized difference-in-difference model and double negative control method. The reasonable application of those derived methods is also comprehensively summarized based on representative case studies. Negative control is an important statistical design to identify, revise and control unmeasured confounders and a valuable method for comparative effectiveness research based on real-world data.

[HbA1c comparison and diagnostic efficacy analysis of multi center different glycosylated hemoglobin detection systems]

Objective: Compare and analyze the results of the domestic Lanyi AH600 glycated hemoglobin analyzer and other different detection systems to understand the comparability of the detection results of different detectors, and establish the best cut point of Lanyi AH600 determination of haemoglobin A1c (HbA1c) in the diagnosis of diabetes. Methods: Multi center cohort study was adopted. The clinical laboratory departments of 18 medical institutions independently collected test samples from their respective hospitals from March to April 2022, and independently completed comparative analysis of the evaluated instrument (Lanyi AH600) and the reference instrument HbA1c. The reference instruments include four different brands of glycosylated hemoglobin meters, including Arkray, Bio-Rad, DOSOH, and Huizhong. Scatter plot was used to calculate the correlation between the results of different detection systems, and the regression equation was calculated. The consistency analysis between the results of different detection systems was evaluated by Bland Altman method. Consistency judgment principles: (1) When the 95% limits of agreement (95% LoA) of the measurement difference was within 0.4% HbA1c and the measurement score was≥80 points, the comparison consistency was good; (2) When the measurement difference of 95% LoA exceeded 0.4% HbA1c, and the measurement score was≥80 points, the comparison consistency was relatively good; (3) The measurement score was less than 80 points, the comparison consistency was poor. The difference between the results of different detection systems was tested by paired sample T test or Wilcoxon paired sign rank sum test; The best cut-off point of diabetes was analyzed by receiver operating characteristic curve (ROC). Results: The correlation coefficient R² of results between Lanyi AH600 and the reference instrument in 16 hospitals is≥0.99; The Bland Altman consistency analysis showed that the difference of 95% LoA in Nanjing Maternity and Child Health Care Hospital in Jiangsu Province (reference instrument: Arkray HA8180) was -0.486%-0.325%, and the measurement score was 94.6 points (473/500); The difference of 95% LoA in the Tibetan Traditional Medical Hospital of TAR (reference instrument: Bio-Rad Variant II) was -0.727%-0.612%, and the measurement score was 89.8 points; The difference of 95% LoA in the People's Hospital of Chongqing Liang Jiang New Area (reference instrument: Huizhong MQ-2000PT) was -0.231%-0.461%, and the measurement score was 96.6 points; The difference of 95% LoA in the Taihe Hospital of traditional Chinese Medicine in Anhui Province (reference instrument: Huizhong MQ-2000PT) was -0.469%-0.479%, and the measurement score was 91.9 points. The other 14 hospitals, Lanyi AH600, were compared with 4 reference instrument brands, the difference of 95% LoA was less than 0.4% HbA1c, and the scores were all greater than 95 points. The results of paired sample T test or Wilcoxon paired sign rank sum test showed that there was no statistically significant difference between Lanyi AH600 and the reference instrument Arkray HA8180 (Z=1.665,P=0.096), with no statistical difference. The mean difference between the measured values of the two instruments was 0.004%. The comparison data of Lanyi AH600 and the reference instrument of all other institutions had significant differences (all P<0.001), however, it was necessary to consider whether it was within the clinical acceptable range in combination with the results of the Bland-Altman consistency analysis. The ROC curve of HbA1c detected by Lanyi AH600 in 985 patients with diabetes and 3 423 patients with non-diabetes was analyzed, the area under curve (AUC) was 0.877, the standard error was 0.007, and the 95% confidence interval 95%CI was (0.864, 0.891), which was statistically significant (P<0.001). The maximum value of Youden index was 0.634, and the corresponding HbA1c cut point was 6.235%. The sensitivity and specificity of diabetes diagnosis were 76.2% and 87.2%, respectively. Conclusion: Among the hospitals and instruments currently included in this study, among these four hospitals included Nanjing Maternity and Child Health Care Hospital in Jiangsu Province (reference instrument: Arkray HA8180), Tibetan Traditional Medical Hospital of TAR (reference instrument: Bio-Rad Variant Ⅱ), the People's Hospital of Chongqing Liang Jiang New Area (reference instrument: Huizhong MQ-2000PT), and the Taihe Hospital of traditional Chinese Medicine in Anhui Province (reference instrument: Huizhong MQ-2000PT), the comparison between Lanyi AH600 and the reference instruments showed relatively good consistency, while the other 14 hospitals involved four different brands of reference instruments: Arkray, Bio-Rad, DOSOH, and Huizhong, Lanyi AH600 had good consistency with its comparison. The best cut point of the domestic Lanyi AH600 for detecting HbA1c in the diagnosis of diabetes is 6.235%.

Association of rs35006907 Polymorphism with Risk of Dilated Cardiomyopathy in Han Chinese Population

Background

Several investigations have demonstrated the association of MTSS1 with left ventricular (LV) structure and function. A recently published study has even revealed that rs35006907 was associated with both MTSS1 expression and the risk of dilated cardiomyopathy (DCM).

Objective

Our study intended to investigate the relationship between rs35006907 and the risk of DCM in the Han Chinese population.

Methods

A total of 529 DCM and 600 healthy controls were recruited. We conducted genotyping for rs35006907 in all participants. Gene association studies were performed to assess the association between rs35006907 and the risk of DCM. A series of functional assays including western blot, realtime PCR and firefly luciferase reporter gene assays were conducted to illuminate the underlying mechanism.

Results

We found that rs35006907-A allele was significantly associated with reduced risk of DCM in additive (p= 0.004; OR=0.78; 95% CI=0.66-0.93) and recessive models (p= 0.0005; OR=0.56; 95%CI=0.41-0.78) when compared with the rs35006907-C allele. There were significant differences in the left ventricular end-diastolic diameter (LVEDD) and left ventricular ejection fraction (LVEF) between rs35006907-CC/AC and AA genotypes. Furthermore, the variant rs35006907-A allele presented lower reporter gene activity, reduced mRNA and protein expression levels when compared with the C allele.

Conclusions

Our findings demonstrated that rs35006907-C allele increased the risk of DCM in Han Chinese population. Besides, rs35006907-C displayed higher reporter gene activity and increased MTSS1 expression in human samples.

[Feasibility and safety of transseptal transcatheter mitral valve replacement for severe mitral regurgitation]

A prospective, single-center, single-arm, and open-design study was performed to evaluate the feasibility and safety of transseptal transcatheter mitral valve replacement in the treatment of severe mitral regurgitation. Patients with symptomatic moderate-severe or severe mitral regurgitation at high-surgical risk and anatomically appropriate for the HighLife transseptal mitral valve replacement (TSMVR) system in West China Hospital, Sichuan University from December 2021 to August 2022 were enrolled. Four patients (1 male and 3 females) with severe mitral regurgitation were included, with a median age of 68.5 (64.0-77.0) years and a median Society of Thoracic Surgeons (STS) score of 8.1% (6.4%-8.9%). Technical success was achieved in all the patients. There was no residual mitral regurgitation, paravalvular leakage, or left ventricular outflow tract obstruction. Three major cardiovascular and cerebrovascular adverse events occurred within 30 days after the procedure, including ventricular tachycardia, iatrogenic atrial septal defect closure, and heart failure readmission. The current study preliminarily demonstrates that transcatheter mitral valve replacement using the HighLife system via the transseptal approach for severe mitral regurgitation is feasible and relatively safe.

Quality of long standing radiographs assessment of the patella position

BACKGROUND

The gold standard for evaluating leg alignment is a long leg standing radiograph (LSR). The research states that a correct LSR should have a patella that is centered and facing forward as well as a fibula head superimposition (FHS) with a tibia that is 1/3 larger than the fibula. The purpose of this study was to determine levels of quality for LSR by quantifying and correlating the patella position and fibular head superimposition.

METHOD

741 lower limbs were included using two distinct measurement techniques, we calculated the patella position's (PD) departure from the center of the knee joint (M1 and M2). To measure the inter-rater dependability in assessing PD and FHS, intraclass correlation coefficients were determined. The Bland-Altman approach was used to compare M1 with M2's performance. We created three quality groups based on the average quantity of PD.

RESULTS

The mean PD was 3.5 mm for M1 and 4.1 mm for M2, respectively. Three quality categories were created: group A for PD ≤ 5 mm, group B for PD 5-10 mm, and group C for PD of ≥10 mm. Group A takes up 70.9% of the LSR. Interestingly, group A's FHS was 21.3% than the typical value of 1/3.

CONCLUSIONS

The patella's center should be centered within a 5 mm range and the fibular head should be 1/5 covered from the tibia. This study is the first to define quantitative metrics based on LSR analysis.

LEVEL OF EVIDENCE

Level IV (diagnostic retrospective case series).

[Allogeneic hematopoietic stem cell transplantation in acute leukemia patients with the SET-NUP214 fusion gene: Efficacy and survival analysis]

Objective: To investigate the clinical efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for patients with acute leukemia who are positive for the SET-NUP214 fusion gene (SET-NUP214⁺AL). Methods: This was a retrospective case series study. Clinical data of 18 patients with SET-NUP214⁺AL who received allo-HSCT in the First Affiliated Hospital of Soochow University and Soochow Hongci Hematology Hospital from December 2014 to October 2021 were retrospectively analyzed to investigate treatment efficacy and prognosis. The Kaplan-Meier method was used for survival analysis. Results: Of the 18 patients, 12 were male and 6 were female, and the median age was 29 years (range, 13-55 years). There were six cases of mixed phenotype acute leukemia (three cases of myeloid/T, two cases of B/T, one case of myeloid/B/T), nine cases of acute lymphoblastic leukemia (ALL) (one case of B-ALL and eight cases of T-ALL), and three cases of acute myeloid leukemia. All patients received induction chemotherapy after diagnosis, and 17 patients achieved complete remission (CR) after chemotherapy. All patients subsequently received allo-HSCT. Pre-transplantation status: 15 patients were in the first CR, 1 patient was in the second CR, 1 was in partial remission, and 1 patient did not reach CR. All patients were successfully implanted with stem cells. The median time of granulocyte and platelet reconstitution was +12 and +13 days, respectively. With a median follow-up of 23 (4-80) months, 15 patients survived, while 3 patients died. The cause of death was recurrence of SET-NUP214⁺AL after transplantation. After allo-HSCT, 5 patients relapsed. The estimated 3-year overall survival (OS) and relapse-free survival (RFS) rates were 83.3%±15.2% and 55.4%±20.7%, respectively. Among the 15 patients who achieved CR before transplantation, there was no significant difference in OS and RFS between haploidentical HSCT and matched sibling donor HSCT (all P>0.05). Conclusions: Allo-HSCT can improve the prognosis and long-term survival rate of patients with SET-NUP214⁺AL. Disease recurrence is the most important factor affecting long-term survival.

Using deep learning for pruning region detection and plant organ segmentation in dormant spur-pruned grapevines

Even though mechanization has dramatically decreased labor requirements, vineyard management costs are still affected by selective operations such as winter pruning. Robotic solutions are becoming more common in agriculture, however, few studies have focused on grapevines. This work aims at fine-tuning and testing two different deep neural networks for: (i) detecting pruning regions (PRs), and (ii) performing organ segmentation of spur-pruned dormant grapevines. The Faster R-CNN network was fine-tuned using 1215 RGB images collected in different vineyards and annotated through bounding boxes. The network was tested on 232 RGB images, PRs were categorized by wood type (W), orientation (Or) and visibility (V), and performance metrics were calculated. PR detection was dramatically affected by visibility. Highest detection was associated with visible intermediate complex spurs in Merlot (0.97), while most represented coplanar simple spurs allowed a 74% detection rate. The Mask R-CNN network was trained for grapevine organs (GOs) segmentation by using 119 RGB images annotated by distinguishing 5 classes (cordon, arm, spur, cane and node). The network was tested on 60 RGB images of light pruned (LP), shoot-thinned (ST) and unthinned control (C) grapevines. Nodes were the best segmented GOs (0.88) and general recall was higher for ST (0.85) compared to C (0.80) confirming the role of canopy management in improving performances of hi-tech solutions based on artificial intelligence. The two fine-tuned and tested networks are part of a larger control framework that is under development for autonomous winter pruning of grapevines.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11119-023-10006-y.

Genome-wide identification and expression analysis of SlRR genes in response to abiotic stress in tomato

The cytokinin two-component signal transduction system (TCS) is involved in many biological processes, including hormone signal transduction and plant growth regulation. Although cytokinin TCS has been well characterized in Arabidopsis thaliana, its role in tomato remains elusive. In this study, we characterized the diversity and function of response regulator (RR) genes, a critical component of TCS, in tomato. In total, we identified 31 RR genes in the tomato genome. These SlRR genes were classified into three subgroups (type-A, type-B and type-C). Various stress-responsive cis-elements were present in the tomato RR gene promoters. Their expression responses under pesticide treatment were evaluated by transcriptome analysis. Their expression under heat, cold, ABA, salinity and NaHCO₃ treatments was further investigated by qRT-PCR and complemented with the available transcription data under these treatments. Specifically, SlRR13 expression was significantly upregulated under salinity, drought, cold and pesticide stress and was downregulated under ABA treatment. SlRR23 expression was induced under salt treatment, while the transcription level of SlRR1 was increased under cold and decreased under salt stress. We also found that GATA transcription factors played a significant role in the regulation of SlRR genes. Based on our results, tomato SlRR genes are involved in responses to abiotic stress in tomato and could be implemented in molecular breeding approaches to increase resistance of tomato to environmental stresses.

Single-Cell Analyses of the Oral Mucosa Reveal Immune Cell Signatures

Inflammatory bowel disease (IBD) is a common immune-related disease of the gastrointestinal tract that affects many people around the world. Extraintestinal manifestations of IBD have been frequently observed in recent years; one of these, periodontitis, has gained increasing attention. Periodontitis is a chronic inflammatory disease characterized by inflammation and destruction of periodontal tissues due to the disruption of host immune homeostasis. Clinical studies have revealed that periodontal inflammation is associated with IBD. However, the detailed heterogeneity of immune cells and their developmental relationships remain poorly understood at the single-cell level. In this study, we performed single-cell RNA (scRNA) sequencing to assess the transcriptome heterogeneity in periodontal tissues. We found the cellular composition and subclusters with specific gene expression profiles by uniform manifold approximation and projection. Pseudo-time analysis combined with gene enrichment analysis was performed to reveal cell states and key pathways. Ligand-receptor pairs revealed cell-cell communication among the immune cell types in periodontal tissues. Based on our analysis, we identified an essential role for Tcr⁺ macrophage, Prdx1⁺ neutrophil, and Mif⁺ T subpopulations with proinflammatory phenotype infiltration. Moreover, we examined the heterogeneity of monocytic cells and B cells. Collectively, the mapping of scRNA revealed the complex cellular landscape of oral mucosa immune cells and highlighted these immune cells as a previously unrecognized factor that may aggravate inflammation. Our analysis proves that periodontitis could exacerbate colitis and provides novel ideas for controlling and preventing IBD exacerbations.

Reference intervals of systemic immune-inflammation index, neutrophil-to-lymphocyte ratio, lymphocyte-to-monocyte ratio, and platelet-to-lymphocyte ratio during normal pregnancy in China

OBJECTIVE

To observe the changes in systemic immune-inflammation index (SII), neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), and platelet-to-lymphocyte ratio (PLR) during normal pregnancy and establish appropriate reference intervals (RIs) for healthy pregnant women.

PATIENTS AND METHODS

This retrospective study was conducted from March 2018 to February 2019. Blood samples were collected from healthy pregnant and nonpregnant women. The complete blood count (CBC) parameters were measured, and SII, NLR, LMR, and PLR were calculated. RIs were established using the 2.5th and 97.5th percentile of the distribution. Besides, the differences in CBC parameters between three pregnant trimesters and maternal ages were also compared to assess their influences on each indicator.

RESULTS

SII and NLR in three pregnant trimesters increased in pregnant women, and the upper limit of SII and NLR in trimester 2 showed the highest value. On the contrary, LMR decreased in all three pregnant trimesters compared with nonpregnant women, and the values of LMR and PLR showed a gradual downward trend along with the trimesters. Besides, RIs of SII, NLR, LMR, and PLR during different trimesters in different age partitions showed that the values of SII, NLR, and PLR increased with age in a general trend, while LMR showed the opposite trend (p < 0.05).

CONCLUSIONS

The SII, NLR, LMR, and PLR showed dynamic changes during pregnant trimesters. RIs of SII, NLR, LMR, and PLR for healthy pregnant women according to pregnant trimesters and maternal age were established and validated in this study, which will promote the standardization of clinical application.

Establishment of a novel experimental system for studying the photoperiodic response of short-day dicots using soybean 'cotyledon-only plant' as material

Soybean is an important model crop for photoperiodic response studies in plants and contributes significantly to the study of plant development and physiology in the past century. Because soybean plant is much bigger in size and longer in life cycle than Arabidopsis, it needs much more space for growth and time for investigation, which significantly hamper the efficiency of research. In the current study, we tested the photoperiodic response of a distinctive artificially-made cotyledon-only plant (COP) using a photoperiod-sensitive soybean variety Zigongdongdou (ZGDD) and other varieties with diverse sensitivity to photoperiod. ZGDD COPs flowered 39.4 ± 2.5 d after emergence under short-day conditions but maintained vegetative growth under long-day and night break conditions, which is similar to the case in the intact ZGDD plants. The COPs of early-maturing and medium-maturing soybean varieties also grew and flowered normally under natural day-length conditions. At the molecular level, the key genes in the photoperiodic pathway such as E1, GmFT1a, GmFT2a, and GmFT5a in the COPs also showed the same photoperiod sensitivity as in the intact plants. In addition, a simpler material of COP with only one cotyledon and root was generated and found to be sensitive to photoperiod as well. Notably, the COPs are only one-fifth the height of intact plants and one-third the maximum diameter of the intact plants grown in chambers 30 d after emergence. Based on COPs, we established a novel experimental system characterized by an entire photoperiodic response and longer longevity of cotyledons in addition to small plant size, ensuring the consistency, reliability, and stability of plant materials. COPs have the potential to be a novel model material for studies of the developmental biology of soybean and other dicots.

[Specification of statistical graphics in medical research]

Statistical graphics has a long history and is an important mean to present study design, analysis results and conclusions of medical research. A survey of statistical graphs of recent publications in Chinese and English academic journals shows that scientific and technical specifications of statistical graphics are still lacking. Based on the requirements of statistical graphics in prestigious medical journals (NEJM, Lancet, JAMA and The BMJ), this paper summarizes the technical requirements, key points of design of statistical graphs and practical conditions of common statistical graphs to provide reference for clinical researchers.

RADIOMICS BASED ON TWO-DIMENSIONAL AND THREE-DIMENSIONAL ULTRASOUND FOR EXTRATHYROIDAL EXTENSION FEATURE PREDICTION IN PAPILLARY THYROID CARCINOMA

Aim

To evaluate the diagnostic performance of radiomics features of two-dimensional (2D) and three-dimensional (3D) ultrasound (US) in predicting extrathyroidal extension (ETE) status in papillary thyroid carcinoma (PTC).

Patients and Methods

2D and 3D thyroid ultrasound images of 72 PTC patients confirmed by pathology were retrospectively analyzed. The patients were assigned to ETE and non-ETE. The regions of interest (ROIs) were obtained manually. From these images, a larger number of radiomic features were automatically extracted. Lastly, the diagnostic abilities of the radiomics models and a radiologist were evaluated using receiver operating characteristic (ROC) analysis. We extracted 1693 texture features firstly.

Results

The area under the ROC curve (AUC) of the radiologist was 0.65. For 2D US, the mean AUC of the three classifiers separately were: 0.744 for logistic regression (LR), 0.694 for multilayer perceptron (MLP), 0.733 for support vector machines (SVM). For 3D US they were 0.876 for LR, 0.825 for MLP, 0.867 for SVM. The diagnostic efficiency of the radiomics was better than radiologist. The LR model had favorable discriminate performance with higher area under the curve.

Conclusion

Radiomics based on US image had the potential to preoperatively predict ETE. Radiomics based on 3D US images presented more advantages over radiomics based on 2D US images and radiologist.

[Altered dynamics of brain spontaneous activity in betel quid dependence chewers]

Objective: To investigate the dynamic characteristics of brain spontaneous activity in betel quid dependence (BQD) chewers and its relationship with clinical indexes. Method: This study was conducted in Hainan General Hospital from April to December 2019 and the data of 53 BQD chewers (37 males and 16 females, aged 20 to 58(38±11) years) and 37 healthy controls (HC) (24 males and 13 females, aged 23-57(42±12) years) were collected. All these subjects underwent resting-state functional magnetic resonance imaging (rs-fMRI) scan. The dynamic characteristics of resting fMRI indexes, including dynamic amplitude of low-frequency fluctuations (ALFF), regional homogeneity (ReHo) and degree centrality (DC) of these subjects were calculated using the sliding time window method, parameters such as age and dynamic local consistency were analyzed and compared between the two groups. Pearson correlation was used to analyze the relationship between dynamic indexes, betel quid dependence score (BQDS) and disease duration in BQD group. Results: BQD chewers showed decreased dynamic ALFF in the left orbital prefrontal cortex (0.138±0.041 vs 0.171±0.070), the right temporal pole superior temporal gyrus (0.277±0.070 vs 0.319±0.086) and the right inferior parietal lobule (0.223±0.052 vs 0.259±0.088) than HC (all P<0.05). For regional homogeneity, BQD chewers showed a decrease dynamic ReHo in the right inferior temporal gyrus (0.055±0.008 vs 0.061±0.009), the orbital prefrontal cortex (0.058±0.005 vs 0.063±0.008), the right inferior frontal gyrus (0.081±0.006 vs 0.087±0.011), the right superior occipital gyrus (0.056±0.007 vs 0.062±0.008), the left precentral gyrus (0.068±0.008 vs 0.074±0.008), and the left superior frontal gyrus (0.058±0.008 vs 0.064±0.009) than HC (all P<0.05). BQD chewers showed an increase dynamic ReHo in the right precuneus (0.095±0.009 vs 0.089±0.008) (P<0.05). There was no significant difference in DC between the two groups (all P>0.05). The relationships between three dynamic ALFF and BQDS (r=-0.104, -0.015, -0.119), seven dynamic ReHo and BQDS (r=-0.099, -0.141, -0.055, -0.078, -0.027, -0.111, -0.090), three dynamic ALFF and disease duration (r=-0.122, -0.095, -0.171), and seven dynamic ReHo and disease duration (r=0.242, -0.252, 0.035, 0.056, 0.047, 0.081, 0.169) were not statistically significant (all P>0.05). Conclusions: BQD chewers showed a decrease dynamic ReHo and/or ALFF in multiple brain regions dominated by prefrontal cortex, and an increase dynamic ReHo in the right precuneus.

Semen parameters and sex hormones as affected by SARS-CoV-2 infection: A systematic review

Background

Impaired semen quality and reproductive hormone levels were observed in patients during and after recovery from coronavirus disease 2019 (COVID-19), which raised concerns about negative effects on male fertility. Therefore, this study systematically reviews available data on semen parameters and sex hormones in patients with COVID-19.

Methods

Systematic search was performed on PubMed and Google Scholar until July 18th, 2022. We identified relevant articles that discussed the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on male fertility.

Results

A total number of 1,684 articles were identified by using a suitable keyword search strategy. After screening, 26 articles were considered eligible for inclusion in this study. These articles included a total of 1,960 controls and 2,106 patients. When all studies were considered, the results showed that the semen parameters and sex hormone levels of patients infected with SARS-CoV-2 exhibited some significant differences compared with controls. Fortunately, these differences gradually disappear as patients recover from COVID-19.

Conclusion

While present data show the negative effects of SARS-CoV-2 infection on male fertility, this does not appear to be long-term. Semen quality and hormone levels will gradually increase to normal as patients recover.

Genomic Dissection and Diurnal Expression Analysis Reveal the Essential Roles of the PRR Gene Family in Geographical Adaptation of Soybean

Pseudo-response regulator (PRR) family members serve as key components of the core clock of the circadian clock, and play important roles in photoperiodic flowering, stress tolerance, growth, and the development of plants. In this study, 14 soybean PRR genes were identified, and classified into three groups according to phylogenetic analysis and structural characteristics. Real-time quantitative PCR analysis revealed that 13 GmPRRs exhibited obvious rhythmic expression under long-day (LD) and short-day (SD) conditions, and the expression of 12 GmPRRs was higher under LD in leaves. To evaluate the effects of natural variations in GmPRR alleles on soybean adaptation, we examined the sequences of GmPRRs among 207 varieties collected across China and the US, investigated the flowering phenotypes in six environments, and analyzed the geographical distributions of the major haplotypes. The results showed that a majority of non-synonymous mutations in the coding region were associated with flowering time, and we found that the nonsense mutations resulting in deletion of the CCT domain were related to early flowering. Haplotype analysis demonstrated that the haplotypes associated with early flowering were mostly distributed in Northeast China, while the haplotypes associated with late flowering were mostly cultivated in the lower latitudes of China. Our study of PRR family genes in soybean provides not only an important guide for characterizing the circadian clock-controlled flowering pathway but also a theoretical basis and opportunities to breed varieties with adaptation to specific regions and farming systems.

[A deep learning segmentation model for detecting caries in molar teeth]

This study aimed to build a home use deep learning segmentation model to identify the scope of caries lesions. A total of 494 caries photographs of molars and premolars collected via endoscopy were selected. Subsequently, these photographs were labeled by physicians and underwent segmentation training by using DeepLabv3+, and then verification and evaluation were performed. The mean accuracy was 0.993, the sensitivity was 0.661, the specificity was 0.997, the Dice coefficient was 0.685, and the intersection over union (IoU) was 0.529. Therefore, the present deep learning segmentation model can identify and segment the scope of caries.