GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases

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The patient-level genotype-phenotype correlations in GPCards accelerated the development of medical genetics.

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The integrated 62 genomic sources provide comprehensive information for interpreting pathogenicity.

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Analysis function in GPCards would help users to decipher their data of genotype-phenotype correlations.

Genotype–phenotype correlations are the basis of precision medicine of human genetic diseases. However, it remains a challenge for clinicians and researchers to conveniently access detailed individual-level clinical phenotypic features of patients with various genetic variants. To address this urgent need, we manually searched for genetic studies in PubMed and catalogued 8,309 genetic variants in 1,288 genes from 17,738 patients with detailed clinical phenotypic features from 1,855 publications. Based on genotype–phenotype correlations in this dataset, we developed an user-friendly online database called GPCards (http://genemed.tech/gpcards/), which not only provided the association between genetic diseases and disease genes, but also the prevalence of various clinical phenotypes related to disease genes and the patient-level mapping between these clinical phenotypes and genetic variants. To accelerate the interpretation of genetic variants, we integrated 62 well-known variant-level and gene-level genomic data sources, including functional predictions, allele frequencies in different populations, and disease-related information. Furthermore, GPCards enables automatic analyses of users’ own genetic data, comprehensive annotation, prioritization of candidate functional variants, and identification of genotype–phenotype correlations using custom parameters. In conclusion, GPCards is expected to accelerate the interpretation of genotype–phenotype correlations, subtype classification, and candidate gene prioritisation in human genetic diseases.

Regional brain network and behavioral alterations in EGR3 gene transfected rat model of schizophrenia

Schizophrenia is a severe psychiatric disease while its etiology and effective treatment are not completely clear. A rat model of schizophrenia was previously established by transfecting EGR3 gene into the hippocampus of rats. This study aimed to investigate the behavioral and cerebral alterations of the schizophrenic model rats and the risperidone effects. Twenty-six rats were divided into 3 groups: schizophrenia model group (E group), risperidone treatment group (T group), and healthy control group (H group). Morris water maze and open field test were used as behavioral tests, resting-state functional magnetic resonance imaging (fMRI) was performed after EGR3 gene transfection and risperidone therapy. Graph analyses were used for examining cerebral alterations of the rats. Behavioral tests demonstrated reduced spatial working memory and exploring unfamiliar space ability in schizophrenic model rats. Graph analyses revealed reduced regional architectures in the olfactory bulb, nucleus accumbens, and pineal gland in group E compared to group H (p < 0.05), while group T showed increased regional architecture in pineal gland compared to group E (p < 0.05). Besides, the regional architectures in the olfactory bulb, nucleus accumbens were lower in group T than group H, while the hippocampus showed increased regional architecture in group T compared to group H (p < 0.05). Schizophrenia induced several regional alterations in the cerebrum while risperidone can reverse part of these alterations. This study lends support for future research on the pathology of schizophrenia and provides new insights on the role of risperidone in schizophrenia.

Predicting the Level of Tumor-Infiltrating Lymphocytes in Patients With Breast Cancer: Usefulness of Mammographic Radiomics Features

Objectives

This study aimed to investigate whether radiomics classifiers from mammography can help predict tumor-infiltrating lymphocyte (TIL) levels in breast cancer.

Methods

Data from 121 consecutive patients with pathologically-proven breast cancer who underwent preoperative mammography from February 2018 to May 2019 were retrospectively analyzed. Patients were randomly divided into a training dataset (n = 85) and a validation dataset (n = 36). A total of 612 quantitative radiomics features were extracted from mammograms using the Pyradiomics software. Radiomics feature selection and radiomics classifier were generated through recursive feature elimination and logistic regression analysis model. The relationship between radiomics features and TIL levels in breast cancer patients was explored. The predictive capacity of the radiomics classifiers for the TIL levels was investigated through receiver operating characteristic curves in the training and validation groups. A radiomics score (Rad score) was generated using a logistic regression analysis method to compute the training and validation datasets, and combining the Mann–Whitney U test to evaluate the level of TILs in the low and high groups.

Results

Among the 121 patients, 32 (26.44%) exhibited high TIL levels, and 89 (73.56%) showed low TIL levels. The ER negativity (p = 0.01) and the Ki-67 negative threshold level (p = 0.03) in the low TIL group was higher than that in the high TIL group. Through the radiomics feature selection, six top-class features [Wavelet GLDM low gray-level emphasis (mediolateral oblique, MLO), GLRLM short-run low gray-level emphasis (craniocaudal, CC), LBP2D GLRLM short-run high gray-level emphasis (CC), LBP2D GLDM dependence entropy (MLO), wavelet interquartile range (MLO), and LBP2D median (MLO)] were selected to constitute the radiomics classifiers. The radiomics classifier had an excellent predictive performance for TIL levels both in the training and validation sets [area under the curve (AUC): 0.83, 95% confidence interval (CI), 0.738–0.917, with positive predictive value (PPV) of 0.913; AUC: 0.79, 95% CI, 0.615–0.964, with PPV of 0.889, respectively]. Moreover, the Rad score in the training dataset was higher than that in the validation dataset (p = 0.007 and p = 0.001, respectively).

Conclusion

Radiomics from digital mammograms not only predicts the TIL levels in breast cancer patients, but can also serve as non-invasive biomarkers in precision medicine, allowing for the development of treatment plans.

[The application of Voriconazole in 76 patients with cirrhosis at Child-Pugh C stage complicated by invasive fungal infection]

Objective: To investigate the safety and efficacy of voriconazole in the patients with cirrhosis at Child-Pugh C stage complicated by invasive fungal infection(IFI). Methods: A retrospective collection of medical records of 76 patients with cirrhosis at Child-Pugh C stage complicated by IFI who were admitted to our hospital, from August 2014 to August 2017 was carried out. All the 76 patients who used voriconazole to treat IFI were divided into recommended dose group for hepatic insufficiency(56 cases) and routine dose group(20cases). The two groups were observed and compared in terms of the voriconazole's plasma concentrations, the outcomes of IFI and the rate of untoward reactions. The liver functional indicators were also compared between before and after treatment each group. We used Student's t test, Z test, chi-square test, or Fisher's exact test, as appropriate, for statistical analysis. Results: Both groups had good performance and low frequencies of side effects in the treatment of IFI, but there were also significant differences in the plasma concentrations of voriconazole and the incidence of untoward reactions between the two groups(P = 0.008 and P = 0.022). There commended dose group for hepatic insufficiency had lower adverse effect rate. The levels of direct bilirubin, alanine aminotransferase and aspartate aminotransferase were significantly lower after treatment of IFI in the recommended dose group for hepatic insufficiency(P < 0.05). Conclusion: In our research, it is relatively safe and effective to use voriconazole to treat IFI in the patients with cirrhosis at Child-Pugh C stage if according to the recommended dose regimen for cirrhosis at Child-Pugh A,B stage.

De novo mutations in folate-related genes associated with common developmental disorders

Folate deficiency is an environmental risk factor for several developmental disorders. De novo mutations (DNMs) also play important etiological roles in various developmental disorders. However, it remains unclear whether DNMs in folate-related genes (FRGs) contribute to developmental disorders. We obtained a list of 1,821 FRGs from folate metabolism pathways and the Comparative Toxicogenomics Database, along with data concerning DNMs in 15,404 cases and 3,391 controls from the Gene4Denovo database. We used a TADA-Denovo model to prioritize candidate disease-associated FRGs, and characterized these genes in terms of genic intolerance, functional networks, and expression patterns. Compared with the controls, FRGs were significantly enriched in likely damaging DNMs (ldDNMs) in patients with developmental disorders (1.54 ≤ odds ratio ≤ 3.39, P_adj ≤ 0.0075). Furthermore, FRGs with ldDNMs rather than with likely non-damaging DNMs (lndDNMs) overlapped significantly among the five developmental disorders included in the datasets. The TADA-Denovo model prioritized 96 candidate disease-associated FRGs, which were intolerant to genetic variants. Their functional networks mainly involved pathways associated with chromatin modification, organ development, and signal transduction pathways. DNMT3A, KMT2B, KMT2C, and YY1 emerged as hub FRGs from the protein–protein interaction network. These candidate disease-associated FRGs are preferentially expressed in the excitatory neurones during embryonic development, and in the cortex, cerebellum, striatum, and amygdala during foetal development. Overall, these findings show that DNMs in FRGs are associated with the risk of developmental disorders. Further research on these DNMs may facilitate the discovery of developmental disorder biomarkers and therapeutic targets, enabling detailed, personalized, and precise folate treatment plan.

Alterations and Associations Between Magnetic Susceptibility of the Basal Ganglia and Diffusion Properties in Alzheimer's Disease

This study adopted diffusion tensor imaging to detect alterations in the diffusion parameters of the white matter fiber in Alzheimer’s disease (AD) and used quantitative susceptibility mapping to detect changes in magnetic susceptibility. However, whether the changes of susceptibility values due to excessive iron in the basal ganglia have correlations with the alterations of the diffusion properties of the white matter in patients with AD are still unknown. We aim to investigate the correlations among magnetic susceptibility values of the basal ganglia, diffusion indexes of the white matter, and cognitive function in patients with AD. Thirty patients with AD and nineteen healthy controls (HCs) were recruited. Diffusion indexes of the whole brain were detected using tract-based spatial statistics. The caudate nucleus, putamen, and globus pallidus were selected as regions of interest, and their magnetic susceptibility values were measured. Compared with HCs, patients with AD showed that there were significantly increased axial diffusivity (AxD) in the internal capsule, superior corona radiata (SCR), and right anterior corona radiata (ACR); increased radial diffusivity (RD) in the right anterior limb of the internal capsule, ACR, and genu of the corpus callosum (GCC); and decreased fractional anisotropy (FA) in the right ACR and GCC. The alterations of RD values, FA values, and susceptibility values of the right caudate nucleus in patients with AD were correlated with cognitive scores. Besides, AxD values in the right internal capsule, ACR, and SCR were positively correlated with the magnetic susceptibility values of the right caudate nucleus in patients with AD. Our findings revealed that the magnetic susceptibility of the caudate nucleus may be an MRI-based biomarker of the cognitive dysfunction of AD and abnormal excessive iron distribution in the basal ganglia had adverse effects on the diffusion properties of the white matter.

Anterior Mediastinal Lesion Segmentation Based on Two-Stage 3D ResUNet With Attention Gates and Lung Segmentation

OBJECTIVES

Anterior mediastinal disease is a common disease in the chest. Computed tomography (CT), as an important imaging technology, is widely used in the diagnosis of mediastinal diseases. Doctors find it difficult to distinguish lesions in CT images because of image artifact, intensity inhomogeneity, and their similarity with other tissues. Direct segmentation of lesions can provide doctors a method to better subtract the features of the lesions, thereby improving the accuracy of diagnosis.

METHOD

As the trend of image processing technology, deep learning is more accurate in image segmentation than traditional methods. We employ a two-stage 3D ResUNet network combined with lung segmentation to segment CT images. Given that the mediastinum is between the two lungs, the original image is clipped through the lung mask to remove some noises that may affect the segmentation of the lesion. To capture the feature of the lesions, we design a two-stage network structure. In the first stage, the features of the lesion are learned from the low-resolution downsampled image, and the segmentation results under a rough scale are obtained. The results are concatenated with the original image and encoded into the second stage to capture more accurate segmentation information from the image. In addition, attention gates are introduced in the upsampling of the network, and these gates can focus on the lesion and play a role in filtering the features. The proposed method has achieved good results in the segmentation of the anterior mediastinal.

RESULTS

The proposed method was verified on 230 patients, and the anterior mediastinal lesions were well segmented. The average Dice coefficient reached 87.73%. Compared with the model without lung segmentation, the model with lung segmentation greatly improved the accuracy of lesion segmentation by approximately 9%. The addition of attention gates slightly improved the segmentation accuracy.

CONCLUSION

The proposed automatic segmentation method has achieved good results in clinical data. In clinical application, automatic segmentation of lesions can assist doctors in the diagnosis of diseases and may facilitate the automated diagnosis of illnesses in the future.

Spatiotemporal Analysis of AIDS Incidence and Its Influencing Factors on the Chinese Mainland, 2005-2017

Acquired Immune Deficiency Syndrome (AIDS) has become one of the most severe public health issues and nowadays around 38 million people are living with the human immunodeficiency virus (HIV). Ensuring healthy lives and promoting well-being is one of 17 United Nations Sustainable Development Goals. Here, we used the Markov chain matrix and geospatial clustering to comprehensively quantify the trends of the AIDS epidemic at the provincial administrate level in the mainland of China from 2005 to 2017. The Geographically Weighted Regression (GWR) model was further adopted to explore four groups of potential influencing factors (i.e., economy, traffic and transportation, medical care, and education) of the AIDS incidence rate in 2017 and their spatially distributed patterns. Results showed that the AIDS prevalence in southeastern China had been dominant and become prevalent in the past decade. The AIDS intensity level had been increasing between 2008 and 2011 but been gradually decreasing afterward. The analysis of the Markov chain matrix indicated that the AIDS epidemic has been generally in control on the Chinese mainland. The economic development was closely related to the rate of AIDS incidence on the Chinese mainland. The GWR result further suggested that medical care and the education effects on AIDS incidence rate can vary with different regions, but significant conclusions cannot be directly demonstrated. Our findings contribute an analytical framework of understanding AIDS epidemic trends and spatial variability of potential underlying factors throughout a complex extent to customize scientific prevention.

Alterations of Iron Level in the Bilateral Basal Ganglia Region in Patients With Middle Cerebral Artery Occlusion

Background and Purpose: The purpose of this study was to explore the changes of iron level using quantitative susceptibility mapping (QSM) in the bilateral basal ganglia region in middle cerebral artery occlusion (MCAO) patients with long-term ischemia.

Methods: Twenty-seven healthy controls and nine patients with MCAO were recruited, and their QSM images were obtained. The bilateral caudate nucleus (Cd), putamen (Pt), and globus pallidus (Gp) were selected as the regions of interest (ROIs). Susceptibility values of bilateral ROIs were calculated and compared between the affected side and unaffected side in patients with MCAO and between patients with MCAO and healthy controls. In addition, receiver operating characteristic (ROC) curves were performed to evaluate the diagnostic capability of susceptibility values in differentiating healthy controls and patients with MCAO by the area under the curve (AUC).

Results: The susceptibility values of bilateral Cd were asymmetric in healthy controls; however, this asymmetry disappeared in patients with MCAO. In addition, compared with healthy controls, the average susceptibility values of the bilateral Pt in patients with MCAO were increased (P < 0.05), and the average susceptibility value of the bilateral Gp was decreased (P < 0.05). ROC curves showed that the susceptibility values of the Pt and Gp had a larger AUC (AUC = 0.700 and 0.889, respectively).

Conclusion: As measured by QSM, the iron levels of the bilateral basal ganglia region were significantly changed in patients with MCAO. Iron dyshomeostasis in the basal ganglia region might be involved in the pathophysiological process of middle cerebral artery stenosis and occlusion. These findings may provide a novel insight to profoundly address the pathophysiological mechanisms of MCAO.

Efficacy and safety of endothelin receptor antagonists in type 2 diabetic kidney disease: A systematic review and meta-analysis of randomized controlled trials

AIM

To analyse the efficacy and safety of endothelin receptor antagonists for people with diabetic kidney disease.

METHODS

Randomized controlled trials comparing endothelin receptor antagonists with placebo in people with diabetic kidney disease were identified through PubMed, Embase and the Cochrane Library. We used a random-effect model to calculate the mean difference or risk ratio with the 95% CI.

RESULTS

Seven studies with a total of 4730 participants were included. Overall, endothelin receptor antagonists significantly reduced albuminuria compared with placebo (standardized mean difference -0.48, 95% CI -0.64 to -0.33). Atrasentan, in particular, effectively reduced albuminuria (standardized mean difference -0.58, 95% CI -1.00 to -0.17) and the risk of composite renal endpoints (risk ratio 0.65; 95% CI 0.49 to 0.88), with insignificant change in the rate of congestive heart failure (risk ratio 1.40, 95% CI 0.76 to 2.56) and mortality (risk ratio 1.11, 95% CI 0.77 to 1.61). In contrast, although avosentan reduced albuminuria (standardized mean difference -0.47, 95% CI -0.57 to -0.36) and the risk of composite renal endpoints (risk ratio 0.63, 95% CI 0.42 to 0.94), it was associated with a significant increase in congestive heart failure risk (risk ratio 2.61, 95% CI 1.36 to 5.00) and an insignificant increase in mortality risk (risk ratio 1.50, 95% CI 0.81, 2.78). No significant change in efficacy or safety outcomes with bosentan was detected. Dose-response analysis indicated that 0.75 mg/day atrasentan is expected to be optimal for renoprotection, with maximal albuminuria reduction and minimal fluid retention events.

CONCLUSIONS

Among the endothelin receptor antagonists, atrasentan and avosentan, but not bosentan, are effective for renoprotection in people with diabetic kidney disease. Compared with other types and doses, atrasentan 0.75 mg/day is the most promising, with maximal albuminuria reduction and minimal fluid retention. Vigilant monitoring of congestive heart failure risk is needed in future clinical practice. (PROSPERO registration no. CRD42020169840).

Genome-Wide Identification of Tannase Genes and Their Function of Wound Response and Astringent Substances Accumulation in Juglandaceae

Tannins are important polyphenol compounds with different component proportions in different plant species. The plants in the Juglandaceae are rich in tannins, including condensed tannins and hydrolyzable tannins. In this study, we identified seven tannase genes (TAs) responsible for the tannin metabolism from walnut, pecan, and Chinese hickory, and three nut tree species in the Juglandaceae, which were divided into two groups. The phylogenetic and sequence analysis showed that TA genes and neighboring clade genes (TA-like genes) had similar sequences compared with other carboxylesterase genes, which may be the origin of TA genes produced by tandem repeat. TA genes also indicated higher expressions in leaf than other tissues and were quickly up-regulated at 3 h after leaf injury. During the development of the seed coat, the expression of the synthesis-related gene GGTs and the hydrolase gene TAs was continuously decreased, resulting in the decrease of tannin content in the dry sample of the seed coat of Chinese hickory. However, due to the reduction in water content during the ripening process, the tannin content in fresh sample increased, so the astringent taste was obvious at the mature stage. In addition, the CcGGTs' expression was higher than CiGGTs in the initiation of development, but CcTAs continued to be down-regulated while CiTA2a and CiTA2b were up-regulated, which may bring about the significant differences in tannin content and astringent taste between Chinese hickory and pecan. These results suggested the crucial role of TAs in wound stress of leaves and astringent ingredient accumulation in seed coats of two nut tree species in the Juglandaceae.

The role of genetics in Parkinson's disease: a large cohort study in Chinese mainland population

This study aimed to determine the mutational spectrum of familial Parkinson's disease and sporadic early-onset Parkinson's disease (sEOPD) in a mainland Chinese population and the clinical features of mutation carriers. We performed multiplex ligation-dependent probe amplification assays and whole-exome sequencing for 1676 unrelated patients with Parkinson's disease in a mainland Chinese population, including 192 probands from families with autosomal-recessive Parkinson's disease, 242 probands from families with autosomal-dominant Parkinson's disease, and 1242 sEOPD patients (age at onset ≤ 50). According to standards and guidelines from the American College of Medical Genetics and Genomics, pathogenic/likely pathogenic variants in 23 known Parkinson's disease-associated genes occurred more frequently in the autosomal-recessive Parkinson's disease cohort (65 of 192, 33.85%) than in the autosomal-dominant Parkinson's disease cohort (10 of 242, 4.13%) and the sEOPD cohort (57 of 1242, 4.59%), which leads to an overall molecular diagnostic yield of 7.88% (132 of 1676). We found that PRKN was the most frequently mutated gene (n = 83, 4.95%) and present the first evidence of an SNCA duplication and LRRK2 p.N1437D variant in mainland China. In addition, several novel pathogenic/likely pathogenic variants including LRRK2 (p.V1447M and p.Y1645S), ATP13A2 (p.R735X and p.A819D), FBXO7 (p.G67E), LRP10 (c.322dupC/p.G109Rfs*51) and TMEM230 (c.429delT/p.P144Qfs*2) were identified in our cohort. Furthermore, the age at onset of the 132 probands with genetic diagnoses (median, 31.5 years) was about 14.5 years earlier than that of patients without molecular diagnoses (i.e. non-carriers, median 46.0 years). Specifically, the age at onset of Parkinson's disease patients with pathogenic/likely pathogenic variants in ATP13A2, PLA2G6, PRKN, or PINK1 was significantly lower than that of non-carriers, while the age at onset of carriers with other gene pathogenic/likely pathogenic variants was similar to that of non-carriers. The clinical spectrum of Parkinson's disease-associated gene carriers in this mainland Chinese population was similar to that of other populations. We also detected 61 probands with GBA possibly pathogenic variants (3.64%) and 59 probands with GBA p.L444P (3.52%). These results shed insight into the genetic spectrum and clinical manifestations of Parkinson's disease in mainland China and expand the existing repertoire of pathogenic or likely pathogenic variants involved in known Parkinson's disease-associated genes. Our data highlight the importance of genetic testing in Parkinson's disease patients with age at onset < 40 years, especially in those from families with a recessive inheritance pattern, who may benefit from early diagnosis and treatment.

Anisotropy of Anomalous Diffusion Improves the Accuracy of Differentiating and Grading Alzheimer's Disease Using Novel Fractional Motion Model

Background and Purpose: Recent evidence shows that the fractional motion (FM) model may be a more appropriate model for describing the complex diffusion process of water in brain tissue and has shown to be beneficial in clinical applications of Alzheimer's disease (AD). However, the FM model averaged the anomalous diffusion parameter values, which omitted the impacts of anisotropy. This study aimed to investigate the potential feasibility of anisotropy of anomalous diffusion using the FM model for distinguishing and grading AD patients. Methods: Twenty-four patients with AD and 11 matched healthy controls were recruited, diffusion MRI was obtained from all participants and analyzed using the FM model. Generalized fractional anisotropy (gFA), an anisotropy metric, was introduced and the gFA values of FM-related parameters, Noah exponent (α) and the Hurst exponent (H), were calculated and compared between the healthy group and AD group and between the mild AD group and moderate AD group. The receiver-operating characteristic (ROC) analysis and the multivariate logistic regression analysis were used to assess the diagnostic performances of the anisotropy values and the directionally averaged values. Results: The gFA(α) and gFA(H) values of the moderate AD group were higher than those of the mild AD group in left hippocampus. The gFA(α) value of the moderate AD group was significantly higher than that of the healthy control group in both the left and right hippocampus. The gFA(ADC) values of the moderate AD group were significantly lower than those of the mild AD group and healthy control group in the right hippocampus. Compared with the gFA(α), gFA(H), α, and H, the ROC analysis showed larger areas under the curves for combination of α + gFA(α) and the combination of H + gFA(H) in differentiating the mild AD and moderate AD groups, and larger area under the curves for combination of α + gFA(α) in differentiating the healthy controls and AD groups. Conclusion: The anisotropy of anomalous diffusion could significantly differentiate and grade patients with AD, and the diagnostic performance was improved when the anisotropy metric was combined with commonly used directionally averaged values. The utility of anisotropic anomalous diffusion may provide novel insights to profoundly understand the neuropathology of AD.

Self-Healing Material with Reversible Luminescence Switch Behavior

Luminescent materials with dynamic responsiveness to external stimuli have attracted extensive attention for the development of advanced sensors and smart materials; however, self-healing capability is also of great importance for functional soft materials. An acid/base vapor reversibly triggered luminescence switch with self-healing ability is achieved by incorporating dynamic lanthanide metal-ligand (Ln-L) coordination into the soft polydimethylsiloxane polymer network. The emission color of the resultant luminescent material could be modulated by altering either the Eu³⁺/Tb³⁺ molar ratio or the excitation wavelength. The luminescence "On-Off" reversible switch is realized via direct alternating exposure to acid and base vapor, realizing reversible information encryption and decryption. The dynamic Ln-L cross-link as well as the hydrogen bond in the luminescent material endow it with excellent self-healing capability, high toughness, and stretchability. We believe this acid/base vapor-triggered self-healing switching strategy provides new insights for expanding the application range of luminescent materials.

Rare variant analysis of essential tremor-associated genes in early-onset Parkinson's disease

Objective

Parkinson’s disease (PD) and essential tremor (ET) are the two most common movement disorders. A significant overlap in clinical features, epidemiology, imaging, and pathology suggests that PD and ET may also share common genetic risk factors. Previous studies have only assessed a limited number of ET‐associated genes in PD patients and vice versa. Consequently, the genetic association between PD and ET remains incompletely characterized. In this study, we systematically investigated a potential association between rare coding variants in ET‐associated genes and PD, in a relatively large Chinese population cohort.

Methods

To investigate the genetic association between ET and PD, we performed the sequence kernel association testing (SKAT‐O) to explore the variant burden of 33 ET‐associated genes, using whole‐exome sequencing (WES) data from 1494 early‐onset PD (EOPD) patients and 1357 control subjects from mainland China.

Results

We report that rare loss‐of‐function and damaging missense variants of TNEM4 are suggestively associated with EOPD (P = 0.026), damaging missense variants of TNEM4 alone are also suggestively associated with EOPD (P = 0.032). No other rare damaging variants in ET‐related genes were significantly associated with EOPD.

Interpretation

This is the first systematic analysis of ET‐associated genes in EOPD. The suggestive association between TNEM4 and EOPD provides new evidence for a genetic link between ET and PD.

Association of rare heterozygous PLA2G6 variants with the risk of Parkinson's disease

The PLA2G6 gene has been identified as a causative gene for autosomal recessive early-onset dystonia-parkinsonism. Possible association was reported between single heterozygous PLA2G6 mutation and the risk of Parkinson's disease (PD), which, however, remained inconclusive. To clarify the effect of heterozygous PLA2G6 variants on the risk of PD, a total of 3710 patients with PD and 2636 controls of Chinese mainland population were recruited and genotyped by whole-exome sequencing or whole-genome sequencing. Variants in the PLA2G6 coding region were extracted and subjected to burden analysis using the optimal sequence kernel association test. In total, we identified 86 rare heterozygous variants in the PLA2G6 coding region, whereas no significant difference was found between cases and controls. Therefore, we found no supportive evidence for heterozygous PLA2G6 variants being a risk factor for PD in Chinese mainland population.

Identification and Classification of Alzheimer's Disease Patients Using Novel Fractional Motion Model

Most diffusion magnetic resonance imaging (dMRI) techniques use the mono-exponential model to describe the diffusion process of water in the brain. However, the observed dMRI signal decay curve deviates from the mono-exponential form. To solve this problem, the fractional motion (FM) model has been developed, which is regarded as a more appropriate model for describing the complex diffusion process in brain tissue. It is still unclear in the identification and classification of Alzheimer's disease (AD) patients using the FM model. The purpose of this study was to investigate the potential feasibility of FM model for differentiating AD patients from healthy controls and grading patients with AD. Twenty-four patients with AD and 11 healthy controls were included. The left and right hippocampus were selected as regions of interest (ROIs). The apparent diffusion coefficient (ADC) values and FM-related parameters, including the Noah exponent (α), the Hurst exponent (H), and the memory parameter (μ=H-1/α), were calculated and compared between AD patients and healthy controls and between mild AD and moderate AD patients using a two-sample t-test. The correlations between FM-related parameters α, H, μ, and ADC values and the cognitive functions assessed by mini-mental state examination (MMSE) and Montreal cognitive assessment (MoCA) scales were investigated using Pearson partial correlation analysis in patients with AD. The receiver-operating characteristic analysis was used to assess the differential performance. We found that the FM-related parameter α could be used to distinguish AD patients from healthy controls (P < 0.05) with greater sensitivity and specificity (left ROI, 0.917 and 0.636; right ROI, 0.917 and 0.727) and grade AD patients (P < 0.05) showed higher sensitivity and specificity (right ROI, 0.917, 0.75). The α was found to be positively correlated with MMSE (P < 0.05) and MoCA (P < 0.05) scores in patients with AD, indicating that the α values in the bilateral hippocampus were a potential MRI-based biomarker of disease severity in AD patients. This novel diffusion model may be useful for further understanding neuropathologic changes in patients with AD.

No relationship between SRY variants and risk of Parkinson's disease in Chinese population

Parkinson's disease (PD) is a common neurodegenerative disease with inherent sex differences, and sex-determining region Y (SRY) is a gene located in the Y chromosome which encodes a transcription factor involving the regulation of the dopamine system. In this study, we investigated whether SRY variants were associated with PD in Chinese population. A total of 2058 male patients with PD and 1650 male control participants were recruited, and variants in SRY transcript and flanking regions were genotyped by whole-exome sequencing or whole-genome sequencing. Analysis of rare variants by the optimal sequence kernel association test showed no difference in variant burden of coding, 5'-noncoding and 3'-noncoding between the case and control group. In addition, of the 6 common variants identified, none showed a significant effect in altering PD risk in our population using logistic regression. Our results suggested SRY variants were not associated with the risk of PD in Chinese population.

GCH1 variants contribute to the risk and earlier age-at-onset of Parkinson's disease: a two-cohort case-control study

Background

Common and rare variants of guanosine triphosphate cyclohydrolase 1 (GCH1) gene may play important roles in Parkinson’s disease (PD). However, there is a lack of comprehensive analysis of GCH1 genotypes, especially in non-coding regions. The aim of this study was to explore the genetic characteristics of GCH1, including rare and common variants in coding and non-coding regions, in a large population of PD patients in Chinese mainland, as well as the phenotypic characteristics of GCH1 variant carriers.

Methods

In the first cohort of this case-control study, we performed whole-exome sequencing in 1555 patients with early-onset or familial PD and 2234 healthy controls; then in the second cohort, whole-genome sequencing was performed in sporadic late-onset PD samples (1962 patients), as well as 1279 controls. Variants at target GCH1 regions were extracted, and then genetic and detailed phenotypic data were analyzed using regression models and the sequence kernel association test. We also performed a meta-analysis to correlate deleterious GCH1 variants with age at onset (AAO) in PD patients.

Results

For coding variants, we identified a significant burden of GCH1 deleterious variants in early-onset or familial PD cases compared to controls (1.2% vs 0.1%, P < 0.0001). In the analysis of possible regulatory variants in GCH1 non-coding regions, rs12323905 (P = 0.001, odds ratio = 1.19, 95%CI 1.07–1.32) was significantly associated with PD, and variant sets in untranslated regions and intron regions, GCH1 brain-specific expression quantitative trait loci, and two possible promoter/enhancer (GH14J054857 and GH14J054880) were suggestively associated with PD. Genotype-phenotype correlation analysis revealed that the carriers of GCH1 deleterious variants manifested younger AAO (P < 0.0001), and had milder motor symptoms, milder fatigue symptoms and more autonomic nervous dysfunctions. Meta-analysis of six studies demonstrated 6.4-year earlier onset in GCH1 deleterious variant carriers (P = 0.0009).

Conclusions

The results highlight the importance of deleterious variants and non-coding variants of GCH1 in PD in Chinese mainland and suggest that GCH1 mutation can influence the PD phenotype, which may help design experimental studies to elucidate the mechanisms of GCH1 in the pathogenesis of PD.

Enhancement of charge-mediated magnetoelectric coupling in Fe3O4/SrTiO3/Ba0.6Sr0.4TiO3 heterostructure

The in-plane magnetic hysteresis loops of Fe₃O₄/SrTiO₃(STO) and Fe₃O₄/STO/Ba_0.6Sr_0.4TiO₃(BSTO) heterostructures have been investigated at 200 K under various electric fields. The bottom BSTO layer of the STO/BSTO bilayer is used to improve the dielectric properties of the top STO layer. The polarization of the STO/BSTO bilayer is ∼78% larger than that of the STO layer at room temperature due to the improvement of surface topography and the contribution of electrostatic interlayer coupling. A significant enlargement (∼70%) in the magnetoelectric response of Fe₃O₄/STO/BSTO heterostructure has been achieved at 200 K and 300 kV cm^-1 after introducing the BSTO layer, since the STO/BSTO bilayer with larger dielectric constant supplies more polarization charges at its interface to the Fe₃O₄ layer than the STO layer. It indicates that the dielectric bilayer improves the polarization and thus benefits the magnetoelectric coupling in the multiferroic heterostructure.

Effect of plant hedgerows on agricultural non-point source pollution: a meta-analysis

Eutrophication has been a critical environmental issue due to soil nitrogen (N) and phosphorus (P) loss in runoff from agricultural lands. Plant hedgerow is an important measure to prevent soil erosion and reduce agricultural non-point source pollution (NPSP). In the present study, we searched 3683 research papers on plant hedgerows published from 1980 to March 2020. After screening, we used 53 effective papers on plant hedgerows for the meta-analysis by using Stata 15.1. The results showed that plant hedgerows significantly increased soil organic matter (SOM) (standardized mean difference (SMD) = 1.46; 95% confidence interval (CI) = 1.12-1.80 > 0), total N (TN) (SMD = 1.33; 95% CI 0.98-1.68 > 0), total P (SMD = 0.73; 95% CI 0.26-1.20 > 0), alkali N (SMD = 0.86; 95% CI 0.52-1.21 > 0), available P (SMD = 1.28; 95% CI 0.75-1.81 > 0) and readily available potassium (K) (SMD = 1.20; 95% CI 0.75-1.65 > 0) concentrations but exhibited no significant effects on soil total K concentration (SMD = 0.17; 95% CI - 0.13-0.47 < 0). Plant hedgerows showed a greater effect on SOM increase than soil N, P, and K, and soil TN increase than the available state, but the opposite trend was observed for P and K. This meta-analysis can clarify the influence of plant hedgerows on soil nutrients and provide ideas for the prevention and control of agricultural NPSP.

Luminescent Ag+ exchanged SOD zeolites with their potential applications in white LEDs

Ag+ exchanged zeolites (Ag-zeolites) combining the advantages of high stability of microporous zeolites with the unique optical properties of silver clusters are attractive as promising functional materials. In this work, we systematically studied the optical properties of Ag+ exchanged SOD zeolites, obtaining tuned emission from yellow to blue and for the first time acquired white-emitting Ag-zeolite phosphors at a mild temperature (<300 °C). This tunable emission color was found to be caused by lattice shrinkage and lattice expansion of the framework in SOD zeolites. The obtained white emitting phosphors show Commission Internationale de I'Eclairage (CIE) chromaticity coordinates of (0.33, 0.34) under 395 nm excitation. In addition, we fabricated warm white LEDs with these white emitting phosphors, which show CIE coordinates of (0.37, 0.34), with a lower correlated color temperature (CCT) of 4329 K and a higher color rendering index (CRI) of 91.