Effects of prenatal exposure to five parabens on neonatal thyroid function and birth weight: Evidence from SMBCS study

BACKGROUND

Parabens, suspected as endocrine-disrupting chemicals, are nearly ubiquitous in the human body and exposure to these chemicals during pregnancy may disrupt thyroid hormones homeostasis and even affect fetal growth, although the impacts are still unclear.

OBJECTIVES

We aimed to estimate associations of maternal urinary paraben concentrations with cord serum thyroid hormones and birth weight.

METHODS

A subset of 437 mother-newborn pairs were included from a prospective birth cohort with five parabens quantified in maternal urine and seven thyroid function indicators measured in cord serum samples. Multivariable linear regression models and elastic net regression (ENR) models were applied to explore associations between individual and mixtures of prenatal urinary paraben concentrations and thyroid hormones and birth weight, respectively.

RESULTS

Maternal urinary ethyl-paraben (EtP) concentrations were associated with increased cord serum total triiodothyronine levels (TT3) [percent change: 1.51%; 95% confidence interval (CI): 0.20%, 2.74%; p=0.017]. Urinary propyl-paraben (PrP) levels predicted higher thyroid peroxidase antibodies (percent change: 4.19%, 95%CI: 0.20%, 8.44%; p=0.041). Maternal urinary EtP and butyl-paraben (BuP) concentrations were significantly positively associated with birth weight [regression coefficient, (β)=40.9g, 95%CI: 3.99, 76.6; p=0.030; β=62.1g, 95%CI: 8.70, 115; p=0.023, for EtP and BuP, respectively]. In sex-stratified analyses, positive relationship between EtP levels and birth weight was observed in boys. Urinary EtP concentrations predicted higher TT3 levels in cord serum samples, assessing parabens as a chemical mixture with ENR models.

CONCLUSIONS

Prenatal exposure to parabens may affect thyroid hormone indicators with increased serum TT3 levels and associate with higher birth weight, especially in boys. The underlying biological mechanisms and effects of prenatal paraben exposures on disruption of thyroid function homeostasis and potential impacts of childhood growth and development needed to be further investigated.

Predicting plant cuticle-water partition coefficients for organic pollutants using pp-LFER model

Predicting plant cuticle-water partition coefficients (K_cw) and understanding the partition mechanisms are crucial to assess environmental fate and risk of organic pollutants. Up to now, experimental K_cw values are determined for only hundreds of compounds because of high experimental cost. For this reason, computational models, which can predict K_cw values based on chemical structures, are promising approaches to evaluate new compounds. In this study, a large dataset consisting of 279 logK_cw values for 125 unique compounds were collected and curated. A poly-parameter linear free energy relationship (pp-LFER) model was developed with stepwise multiple linear regression based on this dataset. The resulted pp-LFER model has good predictability and robustness as indicated by determination coefficient (R²_adj,tra) of 0.93, bootstrapping coefficient (Q²_BOOT) of 0.92, external validation coefficient (Q²_ext) of 0.94 and root mean square error of 0.52 log units. Contribution analysis of different interactions indicated that dispersion and hydrophobic interactions have the highest positive contribution (56%) to increase the partition of pollutants onto plant cuticles. In addition, for organic pollutions containing benzene ring (13-31%), double bond (9-17%) or nitrogen-containing heterocycles (9-17%), π/n-electron pairs interactions exhibit obvious positive contributions to logK_cw. In conclusion, the proposed pp-LFER model is beneficial for predicting logK_cw of potential organic pollutants directly from their molecular structures.

Urinary bisphenol A concentrations and adiposity measures at age 7 years in a prospective birth cohort

Bisphenol A (BPA) exposure during early life may increase risk of childhood obesity, however, prospective evidence of birth cohort is limited and inconclusive. We aimed to explore the associations of maternal and childhood BPA exposure with child adiposity measures, including body mass index, waist circumference and skinfold thickness and waist to height ratio of children at 7 years. 430 mother-child pairs were examined from a population-based prospective cohort in a rural area of East China. BPA concentrations of spot urine samples were quantified in mothers and their children aged 3 and 7 years. Maternal urinary BPA concentration was significantly positively associated with waist circumference in children aged 7 years (β = 0.508 cm, 95% CI: 0.067, 0.950). These significant associations were not modified by child sex, but they were only observed among girls in sex-stratified analyses. Risk of central obesity related to prenatal BPA exposure was significantly higher in the second and the third tertile than those in the first tertile (odds ratio, OR = 2.510, 95% CI = 1.146, 5.499; OR = 2.584, 95% CI = 1.186, 5.631, respectively; p for trend = 0.022). The present findings suggested that prenatal exposure to BPA may enhance waist circumference of children and thereby increase risk of central obesity in school-age girls.

LepR-Expressing Stem Cells Are Essential for Alveolar Bone Regeneration

Stem cells play a critical role in bone regeneration. Multiple populations of skeletal stem cells have been identified in long bone, while their identity and functions in alveolar bone remain unclear. Here, we identified a quiescent leptin receptor–expressing (LepR+) cell population that contributed to intramembranous bone formation. Interestingly, these LepR+ cells became activated in response to tooth extraction and generated the majority of the newly formed bone in extraction sockets. In addition, genetic ablation of LepR+ cells attenuated extraction socket healing. The parabiosis experiments revealed that the LepR+ cells in the healing sockets were derived from resident tissue rather than peripheral blood circulation. Further studies on the mechanism suggested that these LepR+ cells were responsive to parathyroid hormone/parathyroid hormone 1 receptor (PTH/PTH1R) signaling. Collectively, we demonstrate that LepR+ cells, a postnatal skeletal stem cell population, are essential for alveolar bone regeneration of extraction sockets.

[Impact of gender on hepatic pathology and antibody - mediated immunity caused by Schistosoma japonicum infection in C57BL/6 mice]

OBJECTIVE

To investigate the effect of gender on hepatic pathology and antibody-mediated immunity in Schistosoma japonicum-infected C57BL/6 mice.

METHODS

Female and male C57BL/6 mice were infected with S. japonicum, and the hepatic pathological changes were observed using HE and picrosirius red staining in mice 8 weeks post-infection. The serum specific IgG antibody levels against the soluble adult worm antigen (SWA) and soluble egg antigen (SEA) were measured in mice using enzyme-linked immunosorbent assay (ELISA), and the percentages of follicular helper T (Tfh) cells and regulatory T (Treg) cells were detected in mouse spleen and lymph nodes using flow cytometry.

RESULTS

HE staining showed no significant difference in the mean area of a single hepatic egg granuloma between female and male mice 8 weeks post-infection with S. japonicum [(28.050 ± 3.576) × 10⁴ μm² vs. (26.740 ± 4.093) × 10⁴ μm²; t = 0.241, P = 0.821], and picrosirius red staining revealed no statistical differences between female and male mice in terms of the mean proportion of picrosirius red stained hepatic tissues [(7.667 ± 1.856)% vs. (7.667 ± 1.764)%; t = 0, P = 1] or the mean optical density [(0.023 ± 0.003) vs. (0.027 ± 0.007); t = 0.447, P = 0.678]. ELISA detected no significant differences in the serum IgG antibody levels against SWA [(2.098 ± 0.037) vs. (1.970 ± 0.071); t = 1.595, P = 0.162] or SEA [(3.738 ± 0.039) vs. (3.708 ± 0.043); t = 0.512, P = 0.623] between female and male mice 8 weeks post-infection with S. japonicum. Flow cytometry detected significantly greater percentages of Tfh cells in the spleen [female mice, (8.645 ± 1.356)% vs. (1.730 ± 0.181)%, t = 5.055, P = 0.002; male mice, (8.470 ± 1.161)% vs. (1.583 ± 0.218)%, t = 5.829, P = 0.001] and lymph nodes [female mice, (3.218 ± 0.153)% vs. (1.095 ± 0.116)%, t = 11.040, P < 0.001; male mice, (3.673 ± 0.347)% vs. (0.935 ± 0.075)%, t = 8.994, P = 0.001) of both female and male mice 8 weeks post-infection with S. japonicum than in uninfected mice; however, no significant differences were seen between female and male mice 8 weeks post-infection with S. japonicum in terms of the percentages of Tfh cells in the spleen [(8.645 ± 1.356)% vs. (8.470 ± 1.161)%; t = 0.098, P = 0.925] or lymph nodes [(3.218 ± 0.153)% vs. (3.673 ± 0.347)%; t = 1.332, P = 0.241]. There was no significant difference in the proportion of Treg cells in the spleen of male mice between infected and uninfected mice [(10.060 ± 0.361)% vs. (10.130 ± 0.142)%; t = 0.174, P = 0.867], while a higher proportion of Treg cells was seen in the spleen of female mice 8 weeks post-infection with S. japonicum than in uninfected mice [(10.530 ± 0.242)% vs. (9.450 ± 0.263)%; t = 3.021, P = 0.023]. There was no significant difference in the proportion of Treg cells in the spleen between female and male mice infected with S. japonicum [(10.530 ± 0.242)% vs. (10.060 ± 0.361)%; t =1.077, P = 0.323]. In addition, the proportions of Treg cells were significantly greater in the lymph node of S. japonicum -infected female [(17.150 ± 0.805)% vs. (13.100 ± 0.265)%; t = 4.781, P = 0.003] and male mice [(18.550 ± 0.732)% vs. (12.630 ± 0.566)%; t = 6.402, P = 0.001] than in uninfected mice; however, no significant difference was seen between female and male mice 8 weeks post-infection [(17.150 ± 0.805)% vs. (18.550 ± 0.732)%; t = 1.287, P = 0.246].

CONCLUSIONS

There are no gender-specific hepatic pathological changes or antibody-mediated immunity in C57BL/6 mice post-infection with S. japonicum.

Prenatal exposure to mixture of heavy metals, pesticides and phenols and IQ in children at 7 years of age: The SMBCS study

OBJECTIVE

Prenatal exposure to heavy metals, pesticides and phenols has been suggested to interfere with neurodevelopment, but the neurotoxicity of their mixtures is still unclear. We aimed to elucidate the associations of maternal urinary concentrations of selected chemical mixtures with intelligence quotient (IQ) in children.

METHODS

Maternal urinary concentrations of selected heavy metals, pesticide metabolites, and phenols were quantified in pregnant women who participated in the Sheyang Mini Birth Cohort Study (SMBCS) from June 2009 to January 2010. At age 7 years, child's IQ score was assessed using the Chinese version of Wechsler Intelligence Scale for Children (C-WISC) by trained pediatricians. Generalized linear regression models (GLM), Bayesian kernel machine regression (BKMR) models and elastic net regression (ENR) models were used to assess the associations of urinary concentrations individual chemicals and their mixtures with IQ scores of the 7-year-old children.

RESULTS

Of 326 mother-child pairs, single-chemical models indicated that prenatal urinary concentrations of lead (Pb) and bisphenol A (BPA) were significantly negatively associated with full intelligence quotient (FIQ) among children aged 7 years [β = -2.31, 95% confidence interval (CI): -4.13, -0.48; p = 0.013, sex interaction p-value = 0.076; β = -1.18, 95% CI: -2.21, -0.15; p = 0.025; sex interaction p-value = 0.296, for Pb and BPA, respectively]. Stratified analysis by sex indicated that the associations were only statistically significant in boys. In multi-chemical BKMR and ENR models, statistically significant inverse association was found between prenatal urinary Pb level and boy's FIQ scores at 7 years. Furthermore, BKMR analysis indicated that the overall mixture was associated with decreases in boy's IQ when all the chemicals' concentrations were at their 75th percentiles or higher, compared to at their 50th percentiles. ENR models revealed that maternal urinary Pb levels were statistically significantly associated with lower FIQ scores (β = -2.20, 95% CI: -4.20, -0.20; p = 0.031).

CONCLUSIONS

Prenatal exposure to selected chemical mixtures may affect intellectual performance at 7 years of age, particularly in boys. Pb and BPA were suspected as primary chemicals associated with child neurodevelopment.

An Adversarial Perturbation Oriented Domain Adaptation Approach for Semantic Segmentation

We focus on Unsupervised Domain Adaptation (UDA) for the task of semantic segmentation. Recently, adversarial alignment has been widely adopted to match the marginal distribution of feature representations across two domains globally. However, this strategy fails in adapting the representations of the tail classes or small objects for semantic segmentation since the alignment objective is dominated by head categories or large objects. In contrast to adversarial alignment, we propose to explicitly train a domain-invariant classifier by generating and defensing against pointwise feature space adversarial perturbations. Specifically, we firstly perturb the intermediate feature maps with several attack objectives (i.e., discriminator and classifier) on each individual position for both domains, and then the classifier is trained to be invariant to the perturbations. By perturbing each position individually, our model treats each location evenly regardless of the category or object size and thus circumvents the aforementioned issue. Moreover, the domain gap in feature space is reduced by extrapolating source and target perturbed features towards each other with attack on the domain discriminator. Our approach achieves the state-of-the-art performance on two challenging domain adaptation tasks for semantic segmentation: GTA5 → Cityscapes and SYNTHIA → Cityscapes.

[WITHDRAWN: Potential false-positive rate among the 'asymptomatic infected individuals' in close contacts of COVID-19 patients]

Editor office’s response for Ahead of Print article withdrawn The article “Potential false-positive rate among the ‘asymptomatic infected individuals’ in close contacts of COVID-19 patients” was under strong discussion after pre-published. Questions from the readers mainly focused on the article’s results and conclusions were depended on theoretical deduction, but not the field epidemiology data and further researches were needed to prove the current theory. Based on previous discussions, the article was decided to be offline by the editorial board from the pre-publish lists. Objective: As the prevention and control of COVID-19continues to advance, the active nucleic acid test screening in the close contacts of the patients has been carrying out in many parts of China. However, the false-positive rate of positive results in the screening has not been reported up to now. But to clearify the false-positive rate during screening is important in COVID-19 control and prevention. Methods: Point values and reasonable ranges of the indicators which impact the false-positive rate of positive results were estimated based on the information available to us at present. The false-positive rate of positive results in the active screening was deduced, and univariate and multivariate-probabilistic sensitivity analyses were performed to understand the robustness of the findings. Results: When the infection rate of the close contacts and the sensitivity and specificity of reported results were taken as the point estimates, the positive predictive value of the active screening was only 19.67%, in contrast, the false-positive rate of positive results was 80.33%. The multivariate-probabilistic sensitivity analysis results supported the base-case findings, with a 75% probability for the false-positive rate of positive results over 47%. Conclusions: In the close contacts of COVID-19 patients, nearly half or even more of the 'asymptomatic infected individuals' reported in the active nucleic acid test screening might be false positives.

[Analysis on the consciousness of the cancer early detection and its influencing factors among urban residents in China from 2015 to 2017]

Objective: To understand the consciousness of the cancer early detection among urban residents and identify the influencing factors from 2015 to 2017. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. Self-designed questionnaires were used to collect population, socioeconomic indicators, self-cancer risk assessment, regular participation in physical examination and other information. The multivariate logistic regression model was used to identify the factors of people who had not regularly participated in the regular physical examination in the past five years. Results: The self-assessment results of 32 357 residents showed that there were 27.54% (8 882) of total study population with self-reported cancer risk, 45.48% (14 671) without cancer risk and 26.98% (8 704) with unclear judgement on their own cancer risk. Among population with cancer risk, 79.84% (7 091) considered physical examination accounted. In the past five years, there were 21 105 (65.43%) residents participated in regular physical examination and 11 148 (34.56%) participated in non-scheduled one, respectively. The multivariate logistic regression analysis showed that compared with unmarried and western region residents, divorced, middle and eastern region residents had a stronger consciousness to participate in the regular physical examination (P<0.05). Compare with residents with annual household income less than 20 000 CNY in 2014, cancer risk assessment/screening intervention population, and self-assessment with cancer risk, residents with annual household income between 20 000 CNY and 59 000 CNY in 2014, occupational population, community residents, cancer patients, self-reported cancer-free risk, and self-assessment with unclear judgement of cancer risk were less likely to participate in the regular physical examination (all P values <0.05). Conclusion: From 2015 to 2017, the Chinese urban residents had a acceptable consciousness of the cancer early detection. The marital status, annual household income, population group and self-assessment of cancer risk were related to the consciousness of the cancer early detection of people who had not participated in the regular physical examination in the past five years.

[Analysis on the demand, access and related factors of cancer prevention and treatment knowledge among urban residents in China from 2015 to 2017]

Objective: To investigate the demand and access to the cancer prevention and treatment knowledge and related factors among urban residents in China from 2015 to 2017. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The self-designed questionnaire was used to collect the information of general demographic characteristics, the demand and access to cancer prevention and treatment knowledge, and the influencing factors of the attitude. The Chi-square test was used to analyze the difference of the demand of the cancer prevention knowledge among different groups and the corresponding factors of the cancer prevention and treatment knowledge were analyzed by using the logistic regression model. Results: The proportion of residents who need the cancer prevention and treatment knowledge was 79.5%. The demand rate of the inducement, symptom and diagnosis methods of cancer in the occupational population was highest, about 66.8%, 71.0% and 20.8%, respectively. The demand rate of treatment methods and cost in current cancer patients was the highest, about the 45.9% and 21.9%, respectively. The top three sources to acquire the cancer prevention and treatment knowledge were "broadcast or television" (69.5%), "books, newspapers, posters or brochures" (44.7%) and "family and friends" (33.8%). The multivariate analysis showed that compared with public institution personnel/civil servants, unmarried/cohabiting/divorced/widowed and others, annual household income less than 20 000 CNY, from the eastern region, people without cancer diagnosis and people with self-assessment of cancer risk, the demand rate of cancer prevention and treatment knowledge was higher in enterprise personnel/workers, married, annual household income between 60 000 CNY and 150 000 CNY, from the central region, people with cancer and people with unclear cancer risk (all P values <0.05). Conclusion: There was a high demand for the cancer prevention and treatment knowledge among urban residents in China from 2015 to 2017. The main access to the knowledge is from the radio or television. The occupation, marital status, annual household income, residential region, health status and risk of disease were the main factors of the demand of the cancer prevention and treatment knowledge.

[Study on the health literacy and related factors of the cancer prevention consciousness among urban residents in China from 2015 to 2017]

Objective: To understand the health literacy and relevant factors of cancer prevention consciousness in Chinese urban residents from 2015 to 2017. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The self-designed questionnaire was used to collect the information of demographic characteristics and cancer prevention consciousness focusing on nine common risk factors, including smoking, alcohol, fiber food, food in hot temperature or pickled food, chewing betel nut, helicobacter pylori, moldy food, hepatitis B infection, estrogen, and exercise. The logistic regression model was adopted to identify the influencing factors. Results: The overall health literacy of the cancer prevention consciousness was 77.4% (24 980 participants), with 77.4% (12 018 participants), 79.9% (6 406 participants), 77.2% (1 766 participants) and 74.5% (4 709 participants) in each group (P<0.001). The correct response rates for nine risk factors ranged from 55.2% to 93.0%. The multivariate logistic regression analysis showed that compared with community residents, people with primary school level education or below, and the number of people living together in the family <3, the cancer risk assessment/screening intervention population, cancer patients, those with junior high school level educationor above and the number of people living in the family ≥3 had better health literacy of the cancer prevention consciousness (all P values <0.05). Compared with females, 39 years old and below, government-affiliated institutions or civil servants, from the eastern region, males, older than 40 years, company or enterprise employees, and from the middle or western region had worse health literacy of the cancer prevention consciousness (all P values <0.05). Conclusion: The health literacy of the cancer prevention consciousness in Chinese urban residents should be improved. The cancer screening intervention, gender, age, education, occupation, the number of people co-living in the family, and residential region were associated with the health literacy of the cancer prevention consciousness.

[Analysis on the health literacy of the cancer prevention and treatment and its related factors among urban residents in China from 2015 to 2017]

Objective: To understand the health literacy of the cancer prevention and treatment among urban residents of China, and explore the related factors. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China (CanSPUC) from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The health literacy of the cancer prevention, early discovery, early diagnosis, early treatment and the demands of cancer prevention and treatment knowledge was analyzed. The level of health literacy among different groups were calculated and compared. The binary logistic regression model was used to analyze the influencing factors of the health literacy of the cancer prevention and treatment. Results: The level of health literacy of the cancer prevention and treatment was 56.97% among all study population; in each group it was 55.01% for community residents, 59.08% for cancer risk assessment/screening population, 61.99% for cancer patients and 57.31% for occupational population, respectively (P<0.001). The level of health literacy of the cancer prevention and treatment of residents aged 50 to 69 years old, other occupational groups, unmarried, the central and western region residents and the group with unclear self-assessment of cancer risk was significantly lower than that of residents younger than 40 years old, personnel of public institutions/civil servants, married, the eastern region residents and the group whose self-assessment without cancer risk (P<0.05) . The level of health literacy of cancer prevention and treatment of females, people who went to high school or over, cancer risk assessment/screening population, cancer patients and occupational population was significantly higher than that of males, people who had an education level of primary school or below and community residents (P<0.05) . Conclusion: The health literacy of the cancer prevention and treatment of urban residents in China was relatively high, but there was still room for improvement. Gender, age, educational level, occupation, region, marital status, self-assessment of cancer risk, and type of respondents were the key influencing factors of the health literacy of the cancer prevention and treatment. Male, 50-69 years old, lower educational level, central and western regions, unclear cancer risk self-assessment, and without specific environmental exposure to cancer prevention and treatment knowledge or related risk factors were the characteristics of the key intervention group of the health literacy of the cancer prevention and treatment.

[Analysis on the consciousness of the early cancer treatment and its influencing factors among urban residents in China from 2015 to 2017]

Objective: To understand the consciousness of the cancer early treatment and its demographic and socioeconomic factors. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China (CanSPUC) from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The questionnaire collected personal information, the consciousness of the cancer early treatment and relevant factors. The Chi square test was used to compare the difference between the consciousness of the cancer early treatment and relevant factors among the four groups. The logistic regression model was used to analyze the influencing factors related to the consciousness of the cancer early treatment. Results: With the assumption of being diagnosed as precancer or cancer, 89.97% of community residents, 91.84% of cancer risk assessment/screening population, 93.00% of cancer patients and 91.52% of occupational population would accept active treatments (P<0.001). If the immediate family members were diagnosed as precancer or cancer, people who would encourage their family members to receive early treatment in the four groups accounted for 91.96%, 91.94%, 92.44% and 91.55%, respectively (P<0.001). The company employees, annual household income with 40 000 yuan and more and other three groups had a relatively better consciousness of the cancer early treatment (P<0.05). Male, widowed, unemployed and from the central and western regions had a relatively worse consciousness of the cancer early treatment (P<0.05). Conclusion: Residents in urban China participants had a good consciousness of the cancer early treatment. The marital status, occupation, annual household income and residential regions were major factors related to the consciousness of the cancer early treatment.

Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay

The diversity of disease presentations warrants one single assay for detection and delineation of various genomic disorders. Herein, we describe a gel-free and biotin-capture-free mate-pair method through coupling Controlled Polymerizations by Adapter-Ligation (CP-AL). We first demonstrated the feasibility and ease-of-use in monitoring DNA nick translation and primer extension by limiting the nucleotide input. By coupling these two controlled polymerizations by a reported non-conventional adapter-ligation reaction 3′ branch ligation, we evidenced that CP-AL significantly increased DNA circularization efficiency (by 4-fold) and was applicable for different sequencing methods but at a faction of current cost. Its advantages were further demonstrated by fully elimination of small-insert-contaminated (by 39.3-fold) with a ∼50% increment of physical coverage, and producing uniform genome/exome coverage and the lowest chimeric rate. It achieved single-nucleotide variants detection with sensitivity and specificity up to 97.3 and 99.7%, respectively, compared with data from small-insert libraries. In addition, this method can provide a comprehensive delineation of structural rearrangements, evidenced by a potential diagnosis in a patient with oligo-atheno-terato-spermia. Moreover, it enables accurate mutation identification by integration of genomic variants from different aberration types. Overall, it provides a potential single-integrated solution for detecting various genomic variants, facilitating a genetic diagnosis in human diseases.

Sex-Specific Differences in Cognitive Abilities Associated with Childhood Cadmium and Manganese Exposures in School-Age Children: a Prospective Cohort Study

To examine sex-specific associations of neonatal and childhood exposure to eight trace elements with cognitive abilities of school-age children. The association between exposure and effects was assessed among 296 school-age children from a population-based birth cohort study, who had manganese (Mn), cadmium (Cd), and lead (Pb) exposure measured in cord blood and chromium (Cr), manganese, cobalt (Co), copper (Cu), arsenic (As), selenium (Se), cadmium, and lead exposure quantified in spot urine. Cognitive abilities were assessed using the Wechsler Intelligence Scale for Children-Chinese Revised (WISC-CR). Generalized linear models were performed to analyze associations of intelligence quotient (IQ) with trace element concentrations in cord blood and urinary trace element levels. General linear models were used to evaluate association between exposure fluctuation and children's IQ. Urinary Cd concentrations were negatively associated with full-scale IQ (β = - 3.469, 95% confidence interval (CI) - 6.291, - 0.647; p = 0.016) and performance IQ (β = - 4.012, 95% CI - 7.088, - 0.936; p = 0.011) in girls; however, neonatal Cd exposure expressed as Cd concentrations in cord blood was in inverse associations with verbal IQ (β = - 2.590, 95% CI - 4.570, - 0.609; p = 0.010) only in boys. Positive association between urinary Mn concentrations and performance IQ (β = 1.305, 95% CI 0.035, 2.575; p = 0.044) of children was observed, especially in girls. In addition, inverse association of urinary Cu concentrations with verbal IQ (β = - 2.200, 95% CI - 4.360, - 0.039; p = 0.046) was only found in boys. Childhood Cd exposure may adversely affect cognitive abilities, while Mn exposure may beneficially modify cognitive abilities of school-age children, particularly in girls.

Impaired bone microarchitecture in distal interphalangeal joints in patients with primary hypertrophic osteoarthropathy assessed by high-resolution peripheral quantitative computed tomography

This study aimed to investigate the bone impairment in finger joints in PHO patients by HR-pQCT. Results showed distinguished differences in bone architecture and biomechanics parameters at DIPs between PHO patients and healthy controls using HR-pQCT assessment. Besides, serum PGE2, hsCRP and ESR levels were found negatively correlated with total vBMD.

INTRODUCTION

This study aimed to investigate the bone impairment in finger joints in primary hypertrophic osteoarthropathy (PHO) patients firstly by high-resolution peripheral quantitative computed tomography (HR-pQCT).

METHODS

Fifteen PHO patients and 15 healthy controls were enrolled in this study. Bone erosions in hands at distal interphalangeal joints (DIPs) in both PHO patients and controls were evaluated by X-ray. Bone geometry, vBMD, microstructure parameters, and size of individual bone erosion were also measured at the 3rd DIP by HR-pQCT as well. Blood biochemistry levels between the two groups were also compared.

RESULTS

Compared to X-ray, HR-pQCT assessment were more sensitive for detection of bone erosions, with 14 PHO patients by HR-pQCT versus ten PHO patients by X-ray judged at the 3rd DIP. The average depth, width, and volume of erosions size in PHO patients were 1.38 ± 0.80 mm, 0.79 ± 0.27 mm, and 1.71 ± 0.52 mm³, respectively. The bone cross-areas including total area (+ 25.3%, p ≤ 0.05), trabecular area (+ 56.2%, p ≤ 0.05), and cortical perimeter (+ 10.7%, p ≤ 0.05) at the defined region of interest of 3rd DIP was significantly larger than controls. Total vBMD was 11.9% lower in PHO patients compared with the controls (p ≤ 0.05). Biochemical test results showed the increased levels of inflammatory cytokines, bone resorption markers, and joint degeneration markers in PHO patients. Serum prostaglandin PGE2, high-sensitive C-reactive protein (hsCRP) and erythrocyte sedimentation rate (ESR) levels were found negatively correlated with total vBMD.

CONCLUSIONS

This study demonstrated higher sensitivity of the HR-pQCT measurement at DIPs by showing the differences in architecture and biomechanics parameters at DIPs between the PHO patients and healthy controls, which would be of interest clinically to investigate bone deterioration in PHO patients.

Integrating transcriptome-wide association study and mRNA expression profiling identified candidate genes and pathways associated with osteomyelitis

Objective: Osteomyelitis (OM) is an acute or chronic inflammatory process, characterized by severe inflammation and progressive bone destruction. Limited efforts have been made to explore the genetic basis of OM.Method: The genome-wide association study data set of OM was obtained from the UK Biobank. A transcriptome-wide association study (TWAS) of OM was conducted by the FUSION tool using the gene expression reference weights of lymphocytes and blood. The OM-associated genes identified by TWAS were subjected to gene ontology (GO) enrichment analysis to explore OM-related gene sets. The TWAS results of OM were finally compared with a genome-wide mRNA expression profiling of OM to detect common genes and gene sets.Results: TWAS of OM detected 86 genes for lymphocytes and 387 genes for blood. Comparing the genes identified by TWAS and mRNA expression profiling detected eight common genes for OM, including VWF (p_TWAS = 0.0030, p_mRNA = 3.44 × 10^-9), CCDC50 (p_TWAS = 0.0130, p_mRNA = 0.0003), and TPD52 (p_TWAS = 0.0180, p_mRNA = 1 × 10^-6). GO analysis of the genes identified by TWAS detected multiple OM-associated GO terms, e.g. peroxisomal matrix (p_TWAS = 0.0082), extracellular exosome (p_TWAS = 0.0248), and monooxygenase activity (p_TWAS = 0.0040). Further comparing the GO results of TWAS and mRNA expression profiling detected one common GO term, named extracellular exosome (p_TWAS = 0.0248, p_mRNA = 0.0027).Conclusion: This integrative study of TWAS and mRNA expression profiling detected multiple candidate genes and GO terms for OM. Our results provide novel clues for understanding the pathogenesis of OM.

[Overview of logistic regression model analysis and application]

Logistic regression is a kind of multiple regression method to analyze the relationship between a binary outcome or categorical outcome and multiple influencing factors, including multiple logistic regression, conditional logistic regression, polytomous logistic regression, ordinal logistic regression and adjacent categorical logistic regression. This paper illustrates the basic principle, independent variable selection and assignment, applied condition, model evaluation and diagnosis for multiple logistic regression model. Moreover, the principle and application for polytomous logistic regression and ordinal logistic regression models were also introduced. By providing SAS codes and detailed explanations of the result for an example of obesity, readers could be able to better understand logistic regression model, and apply this method correctly to their research and daily work, so as to improve their capacity of the data analysis.

Exposure to carbamate and neurodevelopment in children: Evidence from the SMBCS cohort in China

BACKGROUND

Carbamate pesticides exposure have been linked with adverse health effects during developmental period. Based on 377 mother-child pairs from Sheyang Mini Birth Cohort Study, the present study aimed to assess carbofuranphenol exposure of three-year-old children and explore the associations between prenatal or postnatal carbofuranphenol exposures and neurodevelopmental indicators.

METHODS

Urinary carbofuranphenol concentrations were measured by gas chromatography-tandem mass spectrometry. Neural developmental quotient (DQ) of children was evaluated using Gesell Developmental Schedules. Generalized linear models were used to examine the associations between carbofuranphenol concentrations and neurodevelopment.

RESULTS

Geometric mean, geometric standard deviation, median, inter quartile range of postnatal urinary carbofuranphenol concentrations were 0.653 μg/L, 9.345 μg/L, 0.413 μg/L, 0.150-1.675 μg/L, respectively. Postnatal carbofuranphenol level showed negatively significant trend in language DQ [beta (β) = -0.121; 95% confidence interval (95% CI): 0.212, -0.031; p value (p) = 0.008] and total average DQ (β = -0.059, 95% CI: 0.115, -0.003; p = 0.035). Prenatal carbofuranphenol level showed negative correlations with children's adaptive DQ (β = -0.755; 95% CI: 1.257, -0.254; p = 0.003), social DQ (β = -0.341; 95% CI: 0.656, -0.027; p = 0.032) and total average DQ (β = -0.349; 95% CI: 0.693, -0.005; p = 0.047).

CONCLUSION

The results of the present study supposed children in agricultural region of China are widely exposed to carbamate pesticides, and both prenatal and postnatal exposure to carbamate pesticides may lead to neurodevelopmental effect.