Displaying publications 21 - 40 of 579 in total

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  1. Rajamanikam A, Isa MNM, Samudi C, Devaraj S, Govind SK
    PLoS Negl Trop Dis, 2023 Mar;17(3):e0011170.
    PMID: 36989208 DOI: 10.1371/journal.pntd.0011170
    Whilst the influence of intestinal microbiota has been shown in many diseases such as irritable bowel syndrome, colorectal cancer, and aging, investigations are still scarce on its role in altering the nature of other infective organisms. Here we studied the association and interaction of Blastocystis sp. and human intestinal microbiota. In this study, we investigated the gut microbiome of Blastocystis sp.-free and Blastocystis sp. ST3-infected individuals who are symptomatic and asymptomatic. We tested if the expression of phenotype and pathogenic characteristics of Blastocystis sp. ST3 was influenced by the alteration of its accompanying microbiota. Blastocystis sp. ST3 infection alters bacterial composition. Its presence in asymptomatic individuals showed a significant effect on microbial richness compared to symptomatic ones. Inferred metagenomic findings suggest that colonization of Blastocystis sp. ST3 could contribute to the alteration of microbial functions. For the first time, we demonstrate the influence of bacteria on Blastocystis sp. pathogenicity. When Blastocystis sp. isolated from a symptomatic individual was co-cultured with bacterial suspension of Blastocystis sp. from an asymptomatic individual, the parasite demonstrated increased growth and reduced potential pathogenic expressions. This study also reveals that Blastocystis sp. infection could influence microbial functions without much effect on the microbiota diversity itself. Our results also demonstrate evidence on the influential role of gut microbiota in altering the characteristics of the parasite, which becomes the basis for the contradictory findings on the parasite's pathogenic role seen across different studies. Our study provides evidence that asymptomatic Blastocystis sp. in a human gut can be triggered to show pathogenic characteristics when influenced by the intestinal microbiota.
    Matched MeSH terms: Phenotype
  2. Lin G, Dong L, Cheng KK, Xu X, Wang Y, Deng L, et al.
    Anal Chem, 2023 Aug 22;95(33):12505-12513.
    PMID: 37557184 DOI: 10.1021/acs.analchem.3c02246
    Metabolic pathways are regarded as functional and basic components of the biological system. In metabolomics, metabolite set enrichment analysis (MSEA) is often used to identify the altered metabolic pathways (metabolite sets) associated with phenotypes of interest (POI), e.g., disease. However, in most studies, MSEA suffers from the limitation of low metabolite coverage. Random walk (RW)-based algorithms can be used to propagate the perturbation of detected metabolites to the undetected metabolites through a metabolite network model prior to MSEA. Nevertheless, most of the existing RW-based algorithms run on a general metabolite network constructed based on public databases, such as KEGG, without taking into consideration the potential influence of POI on the metabolite network, which may reduce the phenotypic specificities of the MSEA results. To solve this problem, a novel pathway analysis strategy, namely, differential correlation-informed MSEA (dci-MSEA), is proposed in this paper. Statistically, differential correlations between metabolites are used to evaluate the influence of POI on the metabolite network, so that a phenotype-specific metabolite network is constructed for RW-based propagation. The experimental results show that dci-MSEA outperforms the conventional RW-based MSEA in identifying the altered metabolic pathways associated with colorectal cancer. In addition, by incorporating the individual-specific metabolite network, the dci-MSEA strategy is easily extended to disease heterogeneity analysis. Here, dci-MSEA was used to decipher the heterogeneity of colorectal cancer. The present results highlight the clustering of colorectal cancer samples with their cluster-specific selection of differential pathways and demonstrate the feasibility of dci-MSEA in heterogeneity analysis. Taken together, the proposed dci-MSEA may provide insights into disease mechanisms and determination of disease heterogeneity.
    Matched MeSH terms: Phenotype
  3. Majeed S, Iqbal M, Asi MR, Iqbal SZ, Selamat J
    J Food Prot, 2017 Dec;80(12):1993-1998.
    PMID: 29131682 DOI: 10.4315/0362-028X.JFP-17-117
    Recently, cultivation of high-yielding hybrid maize varieties has revolutionized maize production in Pakistan. Analyses of nutritional traits and aflatoxin (AF) contamination in these varieties can aid in the identification of susceptible and resistant varieties, particularly for cultivation in the Pakistani agro-climatic environment. Five spring maize varieties-Pioneer, Neelam, DK-919, Desi, and Hi-maize-were selected for analyses of their nutritional, tocopherol, and AF contents. Protein, carbohydrate, oil, ash, fiber, and moisture contents ranged between 8.7 and 10.8%, 68 and 71%, 3.72 and 5.56%, 1.09 and 1.81%, 1.1 and 3.1%, and 11.7 and 14.2%, respectively. Tocopherol levels in selected varieties were in the range of 461 to 1,430 μg/g. Hi-maize exhibited significantly higher protein and tocopherol contents than the other varieties, indicating its better suitability for feed and silage applications. The highest mean level of total AFs, 14.5 ± 0.12 μg/kg, was found in Desi, and results showed that the most dominant AF found in the maize varieties was AFB1. Furthermore, the results showed that the higher the level of tocopherol, the lower the concentration of total AFs and vice versa in maize varieties. The results can be used to investigate additional susceptible maize varieties that are resistant to fungal attack.
    Matched MeSH terms: Phenotype
  4. Kim SH, Seo J, Kwon SS, Teng LY, Won D, Shin S, et al.
    Epilepsia, 2024 Mar;65(3):766-778.
    PMID: 38073125 DOI: 10.1111/epi.17857
    OBJECTIVE: We aimed to identify common genes and recurrent causative variants in a large group of Asian patients with different epilepsy syndromes and subgroups.

    METHODS: Patients with unexplained pediatric-onset epilepsy were identified from the in-house Severance Neurodevelopmental Disorders and Epilepsy Database. All patients underwent either exome sequencing or multigene panels from January 2017 to December 2019, at Severance Children's Hospital in Korea. Clinical data were extracted from the medical records.

    RESULTS: Of the 957 patients studied, 947 (99.0%) were Korean and 570 were male (59.6%). The median age at testing was 4.91 years (interquartile range, 1.53-9.39). The overall diagnostic yield was 32.4% (310/957). Clinical exome sequencing yielded a diagnostic rate of 36.9% (134/363), whereas the epilepsy panel yielded a diagnostic rate of 29.9% (170/569). Diagnostic yield differed across epilepsy syndromes. It was high in Dravet syndrome (87.2%, 41/47) and early infantile developmental epileptic encephalopathy (60.7%, 17/28), but low in West syndrome (21.8%, 34/156) and myoclonic-atonic epilepsy (4.8%, 1/21). The most frequently implicated genes were SCN1A (n = 49), STXBP1 (n = 15), SCN2A (n = 14), KCNQ2 (n = 13), CDKL5 (n = 11), CHD2 (n = 9), SLC2A1 (n = 9), PCDH19 (n = 8), MECP2 (n = 6), SCN8A (n = 6), and PRRT2 (n = 5). The recurrent genetic abnormalities included 15q11.2 deletion/duplication (n = 9), Xq28 duplication (n = 5), PRRT2 deletion (n = 4), MECP2 duplication (n = 3), SCN1A, c.2556+3A>T (n = 3), and 2q24.3 deletion (n = 3).

    SIGNIFICANCE: Here we present the results of a large-scale study conducted in East Asia, where we identified several common genes and recurrent variants that varied depending on specific epilepsy syndromes. The overall genetic landscape of the Asian population aligns with findings from other populations of varying ethnicities.

    Matched MeSH terms: Phenotype
  5. Hazir MHM, Gloor E, Docherty E, Galbraith D
    Tree Physiol, 2024 Feb 11;44(3).
    PMID: 38349811 DOI: 10.1093/treephys/tpae022
    Land surface temperature is predicted to increase by 0.2 °C per decade due to climate change, although with considerable regional variability, and heatwaves are predicted to increase markedly in the future. These changes will affect where crops can be grown in the future. Understanding the thermal limits of plant physiological functioning and how flexible such limits are is thus important. Here, we report on the measurements of a core foliar thermotolerance trait, T50, defined as the temperature at which the maximum quantum yield (Fv/Fm) of photosystem II declines by 50%, across nine different Malaysian Hevea brasiliensis clones. We explore the relative importance of interclonal versus intraclonal variation in T50 as well as its association with leaf and hydraulic traits. We find very low variation in T50 within individual clones (mean intraclonal coefficient of variation (CoV) of 1.26%) and little variation across clones (interclonal CoV of 2.1%). The interclonal variation in T50 was lower than for all other functional traits considered. The T50 was negatively related to leaf mass per area and leaf dry matter content, but it was not related to hydraulic traits such as embolism resistance (P50) or hydraulic safety margins (HSM50). The range of T50 observed (42.9-46.2 °C) is well above the current maximum air temperatures Tmax,obs (T50 - Tmax,obs >5.8 °C), suggesting that H. brasiliensis is likely thermally safe in this south-east Asian region of Malaysia.
    Matched MeSH terms: Phenotype
  6. Lee YY, Erdogan A, Rao SS
    J Neurogastroenterol Motil, 2014 Oct 30;20(4):547-52.
    PMID: 25230902 DOI: 10.5056/jnm14056
    Management of chronic constipation with refractory symptoms can be challenging. Although new drugs and behavioral treat-ments have improved outcome, when they fail, there is little guidance on what to do next. At this juncture, typically most doc-tors may refer for surgical intervention although total colectomy is associated with morbidity including complications such as recurrent bacterial overgrowth. Recently, colonic manometry with sensory/tone/compliance assessment with a barostat study has been shown to be useful. Technical challenges aside, adequate preparation, and appropriate equipment and knowledge of co-lonic physiology are keys for a successful procedure. The test itself appears to be safe with little complications. Currently, colon-ic manometry is usually performed with a 6-8 solid state or water-perfused sensor probe, although high-resolution fiber-optic colonic manometry with better spatiotemporal resolutions may become available in the near future. For a test that has evolved over 3 decades, normal physiology and abnormal findings for common phenotypes of chronic constipation, especially slow transit constipation, have been well characterized only recently largely through the advent of prolonged 24-hour ambulatory colonic manometry studies. Even though the test has been largely restricted to specialized laboratories at the moment, emerg-ing new technologies and indications may facilitate its wider use in the near future.(J Neurogastroenterol Motil 2014;20:547-552).
    Matched MeSH terms: Phenotype
  7. Ramaiya SD, Bujang JS, Zakaria MH
    ScientificWorldJournal, 2014;2014:598313.
    PMID: 25050402 DOI: 10.1155/2014/598313
    This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edulis with high levels of genetic similarity; in contrast, P. foetida was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. foetida from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of morphological assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level.
    Matched MeSH terms: Phenotype*
  8. Ganesan J, Wan WP, Lie-Injo LE
    Med J Malaysia, 1975 Mar;30(3):163-8.
    PMID: 1160674
    Matched MeSH terms: Phenotype*
  9. Venkataraman VV, Yegian AK, Wallace IJ, Holowka NB, Tacey I, Gurven M, et al.
    Proc Biol Sci, 2018 11 07;285(1890).
    PMID: 30404871 DOI: 10.1098/rspb.2018.1492
    The convergent evolution of the human pygmy phenotype in tropical rainforests is widely assumed to reflect adaptation in response to the distinct ecological challenges of this habitat (e.g. high levels of heat and humidity, high pathogen load, low food availability, and dense forest structure), yet few precise adaptive benefits of this phenotype have been proposed. Here, we describe and test a biomechanical model of how the rainforest environment can alter gait kinematics such that short stature is advantageous in dense habitats. We hypothesized that environmental constraints on step length in rainforests alter walking mechanics such that taller individuals are expected to walk more slowly due to their inability to achieve preferred step lengths in the rainforest. We tested predictions from this model with experimental field data from two short-statured populations that regularly forage in the rainforest: the Batek of Peninsular Malaysia and the Tsimane of the Bolivian Amazon. In accordance with model expectations, we found stature-dependent constraints on step length in the rainforest and concomitant reductions in walking speed that are expected to compromise foraging efficiency. These results provide the first evidence that the human pygmy phenotype is beneficial in terms of locomotor performance and highlight the value of applying laboratory-derived biomechanical models to field settings for testing evolutionary hypotheses.
    Matched MeSH terms: Phenotype*
  10. Oon YY, Koh KT, Khaw CS, Mohd Amin NH, Ong TK
    Med J Malaysia, 2019 08;74(4):328-330.
    PMID: 31424042
    Arrhythmogenic right ventricular cardiomyopathy (ARVC) is primarily a familial disease with autosomal dominant inheritance. Incomplete penetrance and variable expression are common, resulting in broad disease spectrum. Three patterns of phenotypic expression have been described: (1) "classic" subtype, with predominant right ventricle involvement, (2) "left dominant" subtype, with early and dominant left ventricle involvement, and (3) "biventricular" subtype, with both ventricles equally affected. Genotypephenotype associations have been described, but there are other genetic and non-genetic factors that can affect disease expression. We describe two different phenotypic expressions of ARVC in a family.
    Matched MeSH terms: Phenotype*
  11. Abe A, Noma A
    Atherosclerosis, 1992 Sep;96(1):1-8.
    PMID: 1418098
    The frequency distribution for serum lipoprotein(a) (Lp(a)) concentrations in healthy Japanese was highly skewed, with a mean +/- S.D. of 14.6 +/- 13.6 mg/dl and a median of 11.0 mg/dl. The present study provides the first evidence on the frequencies of Lp(a) phenotypes and alleles in healthy Japanese subjects. There was a strong inverse relationship between the apparent molecular weights of apo(a) isoforms and plasma Lp(a) concentrations, as reported previously. However, because of the considerable overlap between the Lp(a) concentrations of the different phenotypes, it was impossible to predict Lp(a) concentration from Lp(a) phenotypes, or vice versa. The present results suggest that the distribution of Lp(a) concentrations, mean and median values and Lp(a) phenotype and allele frequencies in healthy Japanese are not significantly different from the results for Europeans, whereas they are significantly different from other Asian populations, i.e. Chinese, Indians and Malaysians.
    Matched MeSH terms: Phenotype*
  12. Hussain S, Berki DM, Choon SE, Burden AD, Allen MH, Arostegui JI, et al.
    J Allergy Clin Immunol, 2015 Apr;135(4):1067-1070.e9.
    PMID: 25458002 DOI: 10.1016/j.jaci.2014.09.043
    Matched MeSH terms: Phenotype*
  13. Boon WH, Seng CT
    Med J Malaya, 1968 Sep;23(1):20-8.
    PMID: 4237551
    Matched MeSH terms: Phenotype*
  14. Khang TF, Lau CY
    PeerJ, 2015;3:e1360.
    PMID: 26539333 DOI: 10.7717/peerj.1360
    Background. A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally, or use them for downstream systems biology analysis. Producing a coherent differential gene expression analysis from RNA-seq count data requires an understanding of how numerous sources of variation such as the replicate size, the hypothesized biological effect size, and the specific method for making differential expression calls interact. We believe an explicit demonstration of such interactions in real RNA-seq data sets is of practical interest to biologists. Results. Using two large public RNA-seq data sets-one representing strong, and another mild, biological effect size-we simulated different replicate size scenarios, and tested the performance of several commonly-used methods for calling differentially expressed genes in each of them. We found that, when biological effect size was mild, RNA-seq experiments should focus on experimental validation of differentially expressed gene candidates. Importantly, at least triplicates must be used, and the differentially expressed genes should be called using methods with high positive predictive value (PPV), such as NOISeq or GFOLD. In contrast, when biological effect size was strong, differentially expressed genes mined from unreplicated experiments using NOISeq, ASC and GFOLD had between 30 to 50% mean PPV, an increase of more than 30-fold compared to the cases of mild biological effect size. Among methods with good PPV performance, having triplicates or more substantially improved mean PPV to over 90% for GFOLD, 60% for DESeq2, 50% for NOISeq, and 30% for edgeR. At a replicate size of six, we found DESeq2 and edgeR to be reasonable methods for calling differentially expressed genes at systems level analysis, as their PPV and sensitivity trade-off were superior to the other methods'. Conclusion. When biological effect size is weak, systems level investigation is not possible using RNAseq data, and no meaningful result can be obtained in unreplicated experiments. Nonetheless, NOISeq or GFOLD may yield limited numbers of gene candidates with good validation potential, when triplicates or more are available. When biological effect size is strong, NOISeq and GFOLD are effective tools for detecting differentially expressed genes in unreplicated RNA-seq experiments for qPCR validation. When triplicates or more are available, GFOLD is a sharp tool for identifying high confidence differentially expressed genes for targeted qPCR validation; for downstream systems level analysis, combined results from DESeq2 and edgeR are useful.
    Matched MeSH terms: Phenotype
  15. Ismail I, Joo ST
    Korean J Food Sci Anim Resour, 2017;37(6):873-883.
    PMID: 29725209 DOI: 10.5851/kosfa.2017.37.6.87
    Variations in the definition of poultry meat quality exist because the quality traits are not solely based on intrinsic and extrinsic factors but also consumers' preference. Appearance quality traits (AQT), eating quality traits (EQT), and reliance quality traits (RQT) are the major factors focused by the consumer before buying good quality of poultry meat. AQT and EQT of poultry meat are controlled by physical and biochemical characteristics of muscle fibers which can be categorized into a total number of fibers (TNF), cross-sectional area of fibers (CSAF), and fiber type composition (FTC). In poultry meat, it has been shown that muscle fiber properties play a key role in meat quality because numerous studies have reported the relationships between quality traits and fiber characteristics. Despite intensive research has been carried out to manipulate the muscle fiber to improve poultry meat quality, demand in a rapid growth of poultry muscle has correlated to the deterioration in the meat quality. The present paper reviews the definition of poultry meat quality, meat quality traits, and variations of meat quality. Also, this review presents recent knowledge underlying the relationship between poultry meat quality traits and muscle fiber characteristics.
    Matched MeSH terms: Phenotype
  16. Ooi CS, Mukherjee TK, Wong WC, Jalaludin S
    Theor Appl Genet, 1975 Jan;46(3):149-55.
    PMID: 24419868 DOI: 10.1007/BF00264870
    A complete diallel cross of four broiler breeds was made to investigate whether there are breed differences in the combining abilities for the traits, body weight, weight gain and feed efficiency, measured during the growing period from 4 to 12 weeks of age. Data collected from male and female birds were analysed separately. General combining ability (GCA) was found to be the largest and most significant source of variation contributing to differences between crosses for all the traits, in both male and female birds. Specific combining ability (SCA) was important for body weight in both sexes and for weight gain in females. Feed efficiency in both sexes did not appear to be influenced by SCA effects. Reciprocal effects (RE) were generally absent in both sexes for all the traits, except possibly for feed efficiency.
    Matched MeSH terms: Phenotype
  17. Jahan N, Javed MA, Khan A, Manan FA, Tabassum B
    Ecotoxicology, 2021 Jul;30(5):794-805.
    PMID: 33871748 DOI: 10.1007/s10646-021-02413-6
    Aluminum (Al3+) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al3+ toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al3+ toxicity ranging from 0 to 20 mM at pH 4 ± 0.2 at germination. The favorable alleles for all new QTLs were analyzed based on germination traits, i.e., final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean germination time (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC), and growth traits, such as root length (RL), shoot length (SL), total dry biomass (TDB) and germination vigor index (GVI). The phenotypic evolution showed transgressive variations. For genome-wide mapping, 90 polymorphic SSRs with 4 gene-specific markers and Win QTL Cart were used for QTL analysis. In all, 35 QTLs for germination and 11 QTLs for seedling growth were detected in distinct chromosomal regions by composite interval mapping (CIM), and multiple interval mapping (MIM) confirmed the pleiotropy at region RM128 on chromosome 1. Based on our genetic mapping studies, the genes/QTLs underlying tolerance to Al3+ toxicity could differ for both the germination and seedling stages in segregated populations. The QTLs identified in this study could be a source of new alleles for improving tolerance to Al3+ toxicity in rice.
    Matched MeSH terms: Phenotype
  18. Daood U, Yiu CKY
    Dent Mater, 2019 02;35(2):206-216.
    PMID: 30509480 DOI: 10.1016/j.dental.2018.11.018
    OBJECTIVE: To evaluate the transdentinal cytotoxicity and macrophage phenotype response to a novel quaternary ammonium silane (QAS) cavity disinfectant.

    METHODS: NIH 3T3 mouse fibroblasts were cultured in Dulbecco's Modified Eagle's Medium and incubated for 3 days. The cells (3×104) were seeded on the pulpal side of dentine discs and the occlusal side of the discs were treated with different cavity disinfectants: Group 1: de-ionized water (control); Group 2: 2% chlorhexidine (CHX); Group 3: 2% QAS; Group 4: 5% QAS, and Group 5: 10% QAS. Cell morphology of NIH 3T3 cells was examined using scanning electron microscopy (SEM) and cell viability was assessed using Trypan blue assay. The eluates were collected and applied on cells seeded in 24-well plates. The total protein production, alkaline phosphatase activity and deposition of mineralized nodules were evaluated after 7 and 14 days. Immunofluorescence staining was performed on the samples with primary antibodies of CD68+, CD80+, and CD163+ assessing the macrophage M1/M2 phenotypes. The macrophages were imaged using a confocal scanning light microscope with an excitation wavelength of 488nm.

    RESULTS: No significant difference in cell viability (p<0.0001), total protein production (p<0.01) and mineralized nodule production (p<0.05) was found between 2% QAS and the control, which was significantly higher than 2% CHX, 5% and 10% QAS after 14 days. Alkaline phosphatase production of 2% QAS was significantly lower than the control (p<0.001), but higher than 2% CHX at 14 days. The M1/M2 macrophage ratio was also significantly lower in the 2% and 10% QAS groups (p<0.05) compared to the control and 2% CHX groups.

    SIGNIFICANCE: The 2% QAS cavity disinfectant does not have cytotoxic effects on 3T3 NIH mouse fibroblast cells and the predominance of the anti-inflammatory phenotype after its application may stimulate healing and tissue repair.

    Matched MeSH terms: Phenotype
  19. Koya Kutty S, Mulroy E, Magrinelli F, Di Lazzaro G, Latorre A, Bhatia KP
    Parkinsonism Relat Disord, 2021 09;90:120-122.
    PMID: 33640251 DOI: 10.1016/j.parkreldis.2021.02.022
    Matched MeSH terms: Phenotype
  20. Kalman JL, Yoshida T, Andlauer TFM, Schulte EC, Adorjan K, Alda M, et al.
    Eur Arch Psychiatry Clin Neurosci, 2022 Dec;272(8):1611-1620.
    PMID: 35146571 DOI: 10.1007/s00406-021-01366-5
    Personality traits influence risk for suicidal behavior. We examined phenotype- and genotype-level associations between the Big Five personality traits and suicidal ideation and attempt in major depressive, bipolar and schizoaffective disorder, and schizophrenia patients (N = 3012) using fixed- and random-effects inverse variance-weighted meta-analyses. Suicidal ideations were more likely to be reported by patients with higher neuroticism and lower extraversion phenotypic scores, but showed no significant association with polygenic load for these personality traits. Our findings provide new insights into the association between personality and suicidal behavior across mental illnesses and suggest that the genetic component of personality traits is unlikely to have strong causal effects on suicidal behavior.
    Matched MeSH terms: Phenotype
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