NetMoST: A network-based machine learning approach for subtyping schizophrenia using polygenic SNP allele biomarkers

Subtyping neuropsychiatric disorders like schizophrenia is essential for improving the diagnosis and treatment of complex diseases. Subtyping schizophrenia is challenging because it is polygenic and genetically heterogeneous, rendering the standard symptom-based diagnosis often unreliable and unrepeatable. We developed a novel network-based machine-learning approach, netMoST, to subtyping psychiatric disorders. NetMoST identifies polygenic risk SNP-allele modules from genome-wide genotyping data as polygenic haplotype biomarkers (PHBs) for disease subtyping. We applied netMoST to subtype a cohort of schizophrenia subjects into three distinct biotypes with differentiable genetic, neuroimaging and functional characteristics. The PHBs of the first biotype (36.9% of all patients) were related to neurodevelopment and cognition, the PHBs of the second biotype (28.4%) were enriched for neuroimmune functions, and the PHBs of the third biotype (34.7%) were associated with the transport of calcium ions and neurotransmitters. Neuroimaging patterns provided additional support to the new biotypes, with unique regional homogeneity (ReHo) patterns observed in the brains of each biotype compared with healthy controls. Our findings demonstrated netMoST's capability for uncovering novel biotypes of complex diseases such as schizophrenia. The results also showed the power of exploring polygenic allelic patterns that transcend the conventional GWAS approaches.Comment: 21 pages,4 figure

Comparative effects of two in situ hybridization methods for the pinewood nematode (Bursaphelenchus xylophilus)

The gene localization technique of Bursaphelenchus xylophilus (pinewood nematode, PWN) is used for study gene expression in PWNs. Two in situ hybridization methods, namely, whole-mount in situ hybridization and the cut-off method are used widely. To compare the effects of these two in situ hybridization methods, the present study investigated the patterns of two functional genes expression in PWNs. The Bx-vap-2 gene (GenBank accession number: OR228482), related to pathogenicity, and the fem-2 gene (GenBank accession number: OR228481), related to sex determination, were selected to map related genes in the whole-mount and amputated PWNs at different ages using these in situ hybridization methods. Based on the overall statistical comparison, we found that compared to the cut-off method, the whole-mount method exhibited higher staining rates and correct staining rates for the fem-2 gene and Bx-vap-2 gene. However, considering the correct staining aspect, the cut-off method yielded better staining effects on pinewood nematode sections than the whole-mount method, with clearer hybridization signal locations and less non-specific staining. In other words, the cut-off method demonstrated more precise gene localization. Both methods are applicable for gene localization, but considering the overall staining pattern, analysis of experimental results, and comprehensive experimental operations, we believe that the whole-mount method is more suitable for gene localization and expression analysis of development-related genes in pinewood nematodes. This is because intact pinewood nematodes are better suited for showcasing the continuous developmental process of development-related genes. On the other hand, considering the experimental time, accuracy of staining site, and the amount of non-specific staining, the cut-off method is more suitable for disease-related genes. Additionally, to achieve better performance, the cut-off method can be selectively applied to samples during the experimental process

The Mechanism and Pathways of Dopamine and Dopamine Agonists in Prolactinomas

Dopamine agonists such as bromocriptine and cabergoline are the predominant treatment drugs for prolactinoma by inhibiting prolactin secretion and shrinking tumor size. However, the pathways of either dopamine or its agonists that lead to the death of cells are incompletely understood and some are even conflicting conclusions. The main aim of this paper is to review the different pathways of dopamine and its agonists in prolactinomas to help to gain a better understanding of their functions and drug resistance mechanisms

Early–middle Jurassic source to sink evolution and its tectonic significance in the northeastern Sichuan Basin

This paper discusses the sedimentary environment and source supply in the sedimentary area and their coupling relationship through a detailed description of the deposits from the Ziliujing Formation to Shaximiao Formation of the Lower–Middle Jurassic on the Tieshan section in the Dazhou City, northeastern Sichuan Province, through sedimentary characterization, determination of the paleocurrent direction, analysis of heavy minerals, and detrital zircon U–Pb dating. The results show that the Zhenzhuchong Member is sufficiently supplied with detrital sediments and is dominantly composed of fluvial-delta deposits. The Dongyuemiao Member—the first member of the Lianggaoshan Formation—is dominated by lacustrine deposits, with the detrital supply increased initially in the early Lianggaoshan. The second member of the Lianggaoshan Formation suggests a significant increase in detrital supply, with shrunken lake basin and changed paleocurrent direction. The Shaximiao Formation reveals a complete disappearance of the lake basin in the northern Sichuan Basin. The comprehensive analysis on source supply indicates that the change in source property is apparently coupled with the change in the sedimentary environment, both controlled by orogenesis around the basin. It is inferred from the zircon age distribution that the changes in the sedimentary environment and source supply during the late Ziliujing period and the middle and late Lianggaoshan period resulted from the uplifting of the Micangshan Mountain, Dabashan Mountain, and Qinling Mountain, respectively

Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis

High-density single nucleotide polymorphisms (SNPs) are used as highly favored makers to analyze genetic diversity and population structure, to construct high-density genetic maps and provide genotypes for genome-wide association analysis. In order to develop genome-wide SNP markers in oil palm (Elaeis guineensis), single locus amplified fragment sequencing (SLAF-seq) technology was performed in a diversity panel of 200 oil palm individuals and 1,261,501 SNPs were identified with minor allele frequency > 0.05 and integrity > 1. Among them, only 17.81% can be mapped within the genic region and the remaining was located into the intergenic region. A positive correlation was detected between the distribution of SNP markers and retrotransposons [transposable elements (TEs)]. Population structure analysis showed that the 200 individuals of oil palm can be divided into five subgroups based on cross-validation errors. However, the subpopulations divided for the 200 oil palm individuals based on the SNP markers were not accurately related to their geographical origins and 80 oil palm individuals from Malaysia showed highest genetic diversity. In addition, the physical distance of linkage disequilibrium (LD) decay in the analyzed oil palm population was 14.516 kb when r2 = 0.1. The LD decay distances for different chromosomes varied from 3.324 (chromosome 15) to 19.983 kb (chromosome 7). Our research provides genome-wide SNPs for future targeted breeding in palm oil

Value of Immediate Heart Rate Alteration From Supine to Upright in Differential Diagnosis Between Vasovagal Syncope and Postural Tachycardia Syndrome in Children

Objectives: To explore the predictive value of immediate heart rate alteration from supine to upright in the differential diagnosis between vasovagal syncope (VVS) and postural tachycardia syndrome (POTS) in children.Materials and Methods: A total of 76 pediatric outpatients or inpatients who visited the Peking University First Hospital from July 2016 to November 2017 were recruited in the study. Among them, 52 patients were diagnosed with VVS and 24 patients were diagnosed with POTS. The differential diagnostic value of acceleration index (AI) and 30/15 ratio was evaluated by the receiver operating characteristic (ROC) curve. An external validation test was performed in another 46 patients.Results: Compared with the cases in the VVS group, patients in the POTS group had a significantly increased AI but a decreased 30/15 ratio (33.495 ± 8.472 vs. 23.440 ± 8.693, p < 0.001; 0.962 ± 0.067 vs. 1.025 ± 0.084, p = 0.002; respectively). The ROC curves showed that AI and 30/15 ratio were useful for differentiating POTS from VVS. A cut-off value of AI set at 28.180 yielded a sensitivity of 79.2% and a specificity of 73.1%. A cut-off value of 30/15 ratio set at 1.025 yielded a sensitivity of 87.5% and a specificity of 61.5%. A combined use of these two indices improved the sensitivity to 95.8% when either AI or 30/15 was used, and specificity to 80.8% with the use of both AI and 30/15 at the same diagnosis. The external validation test showed that the positive and negative predictive values of the AI and 30/15 ratio were 77.3 and 79.2%, and 72.0 and 81.0%, respectively. The positive predictive value increased to 87.5% when both the AI and 30/15 ratio cut-off values were used together.Conclusions: The AI and 30/15 ratio, which are easy to perform and non-invasive, have proper sensitivity and specificity to differentiate patients with POTS from those with VVS. The combination of these two indices significantly improves the predictive value

Remarkable nucleation and growth of ultrafine particles from vehicular exhaust

High levels of ultrafine particles (UFPs; diameter of less than 50 nm) are frequently produced from new particle formation under urban conditions, with profound implications on human health, weather, and climate. However, the fundamental mechanisms of new particle formation remain elusive, and few experimental studies have realistically replicated the relevant atmospheric conditions. Previous experimental studies simulated oxidation of one compound or a mixture of a few compounds, and extrapolation of the laboratory results to chemically complex air was uncertain. Here, we show striking formation of UFPs in urban air from combining ambient and chamber measurements. By capturing the ambient conditions (i.e., temperature, relative humidity, sunlight, and the types and abundances of chemical species), we elucidate the roles of existing particles, photochemistry, and synergy of multipollutants in new particle formation. Aerosol nucleation in urban air is limited by existing particles but negligibly by nitrogen oxides. Photooxidation of vehicular exhaust yields abundant precursors, and organics, rather than sulfuric acid or base species, dominate formation of UFPs under urban conditions. Recognition of this source of UFPs is essential to assessing their impacts and developing mitigation policies. Our results imply that reduction of primary particles or removal of existing particles without simultaneously limiting organics from automobile emissions is ineffective and can even exacerbate this problem

Remarkable nucleation and growth of ultrafine particles from vehicular exhaust

High levels of ultrafine particles (UFPs; diameter of less than 50 nm) are frequently produced from new particle formation under urban conditions, with profound implications on human health, weather, and climate. However, the fundamental mechanisms of new particle formation remain elusive, and few experimental studies have realistically replicated the relevant atmospheric conditions. Previous experimental studies simulated oxidation of one compound or a mixture of a few compounds, and extrapolation of the laboratory results to chemically complex air was uncertain. Here, we show striking formation of UFPs in urban air from combining ambient and chamber measurements. By capturing the ambient conditions (i.e., temperature, relative humidity, sunlight, and the types and abundances of chemical species), we elucidate the roles of existing particles, photochemistry, and synergy of multipollutants in new particle formation. Aerosol nucleation in urban air is limited by existing particles but negligibly by nitrogen oxides. Photooxidation of vehicular exhaust yields abundant precursors, and organics, rather than sulfuric acid or base species, dominate formation of UFPs under urban conditions. Recognition of this source of UFPs is essential to assessing their impacts and developing mitigation policies. Our results imply that reduction of primary particles or removal of existing particles without simultaneously limiting organics from automobile emissions is ineffective and can even exacerbate this problem