| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Feng, Shaohong, et al.
(author)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Journal article (peer-reviewed)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 3. |
- Guo, J., et al.
(author)
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Prenatal exposure to mixture of heavy metals, pesticides and phenols and IQ in children at 7 years of age : The SMBCS study
- 2020
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In: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 139
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Journal article (peer-reviewed)abstract
- 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.
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| 4. |
- Zhang, Jiming, et al.
(author)
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Early-life carbamate exposure and intelligence quotient of seven-year-old children
- 2020
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In: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 145
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Journal article (peer-reviewed)abstract
- Background: Early-life carbamate exposure during developmental period has been linked with adverse health effects and attracted attention.Methods: Three hundred and three children at age of seven were included in the current study. Urinary carbofuranphenol concentrations were measured using gas chromatography-tandem mass spectrometry. Verbal, performance and full-scale intelligence quotients (IQ(V), IQ(P), and IQ(FS)) were assessed using Wechsler Intelligence Scale for Children-Chinese Revised. Generalized linear models were used to explore the associations between carbofuranphenol levels and IQs. Generalized estimating equations were used to explore long-term health effect and sensitive time window.Results: Carbofuranphenol was detected in 96.6% of the seven-year-old urinary samples, the geometric mean, median, and inter quartile range of the carbofuranphenol concentrations were 0.67 mu g/L, 0.30 mu g/L, and 0.09-3.72 mu g/L, respectively, which were similar with the level of three-year-old children from the SMBCS cohort. Seven-year-old carbofuranphenol level was negatively associated with IQP [beta = -0.044; 95% confidence interval (CI): -0.087, -0.001; p = 0.045]. Three-year-old carbofuranphenol level was negatively associated with IQP (beta =-0.100; 95% CI: -0.186, -0.014; p= 0.022) and IQFS (beta =-0.087; 95% CI: -0.173, -0.001; p = 0.047). Carbamate exposure of maternal and children at both three and seven years old had negative associations with IQP (beta = -0.089; 95% CI: -0.171, -0.007; p = 0.034), and IQFS (beta = -0.064; 95% CI: -0.127, -0.000; p = 0.049) of children at age of seven.Conclusion: Results of the present study verify that children in an agricultural region of China were widely exposed to carbamate pesticides. Carbamate exposure in utero and at three and seven years may adversely impact children's neurodevelopment.
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| 5. |
- Chen, D., et al.
(author)
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A Muscle Teleoperation System of a Robotic Rollator Based on Bilateral Shared Control
- 2020
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In: IEEE Access. - : Institute of Electrical and Electronics Engineers (IEEE). - 2169-3536. ; 8, s. 151160-151170
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Journal article (peer-reviewed)abstract
- The approach that achieves the teleoperation between human muscle signals and the mobile robot is increasingly applied to transfer human muscle stiffness to enhance robotic performance. In this paper, we develop a mobile rollator control system applying a muscle teleoperation interface and a shared control method to enhance the obstacle avoidance in an effective way. In order to control intuitively, haptic feedback is utilized in the teleoperation interface and is integrated with EMG stiffness to provide a large composition force. Then the composition force is implemented with an artificial potential field method to keep the robotic rollator away from the obstacle in advance. This algorithm is superior to the traditional APF algorithm regardless of the required time and trajectory length. The experimental results demonstrate the effectiveness of the proposed muscle teleoperation system.
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| 6. |
- Cheng, Qiaoyun, et al.
(author)
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The conversion of nanocellulose into solvent-free nanoscale liquid crystals by attaching long side-arms for multi-responsive optical materials
- 2020
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In: Journal of Materials Chemistry C. - : ROYAL SOC CHEMISTRY. - 2050-7526 .- 2050-7534. ; 8:32, s. 11022-11031
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Journal article (peer-reviewed)abstract
- Nanocellulose, with its unique optical and chemical properties, has received increasing attention as feedstock to fabricate sustainable materials. However, achieving a nanocellulose-based solvent-free liquid crystal with good responsiveness still remains a challenge. Herein, for the first time, solvent-free supramolecular liquid crystals were fabricated by attaching long side-arms on the fiber-like nanocellulose derived from tunicate (TCNC) with an average width of 20 nm and 400-3000 nm in length. The side-arms were grafted via surface condensation with a charged organosilane, followed by further functionalization with a counter-ion polyoxyethylene ether. The nanoscale liquid crystals consisted of the stiff TCNC as the core and flexible side-arms as the soft shells, forming the core-shell structure with an average width of 34-36 nm. The resulting solvent-free liquid crystal exhibited transparent and viscous liquid-like fluidity, as well as a bright birefringence between the crossed polarizers at room temperature. In our findings, the stiff core provided crystal-like ordering, whereas the soft shells induced the high mobility of the TCNCs as a result of the increased fractional free volume, as shown by positron annihilation lifetime spectra. The unique flowability enables the possibility of multi-responsiveness to temperature, deformation, and alternating electric fields. In addition, the thermo-responsiveness can be regulated by tailoring the canopy. This work provides a novel strategy for the conversion of solid nanocellulose into a solvent-free nanoscale liquid crystal, which is promising for use as a responsive optical material.
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| 7. |
- Cukurova, Mutlu, et al.
(author)
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Modelling Collaborative Problem-solving Competence with Transparent Learning Analytics : Is Video Data Enough?
- 2020
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In: LAK20. - New York, NY, USA : Association for Computing Machinery (ACM). ; , s. 270-275
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Conference paper (peer-reviewed)abstract
- In this study, we describe the results of our research to model collaborative problem-solving (CPS) competence based on analytics generated from video data. We have collected similar to 500 mins video data from 15 groups of 3 students working to solve design problems collaboratively. Initially, with the help of OpenPose, we automatically generated frequency metrics such as the number of the face-in-the-screen; and distance metrics such as the distance between bodies. Based on these metrics, we built decision trees to predict students' listening, watching, making, and speaking behaviours as well as predicting the students' CPS competence. Our results provide useful decision rules mined from analytics of video data which can be used to inform teacher dashboards. Although, the accuracy and recall values of the models built are inferior to previous machine learning work that utilizes multimodal data, the transparent nature of the decision trees provides opportunities for explainable analytics for teachers and learners. This can lead to more agency of teachers and learners, therefore can lead to easier adoption. We conclude the paper with a discussion on the value and limitations of our approach.
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| 8. |
- Guo, Jianqiu, et al.
(author)
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Early life triclosan exposure and neurodevelopment of children at 3 years in a prospective birth cohort
- 2020
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In: International journal of hygiene and environmental health. - : Urban & Fischer. - 1438-4639 .- 1618-131X. ; 224
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Journal article (peer-reviewed)abstract
- BACKGROUND: Early life exposure to triclosan, an emerging endocrine disrupting chemical, may adversely impact childhood neurodevelopment, but limited epidemiologic studies have examined the associations.OBJECTIVE: We evaluated the associations between prenatal and postnatal triclosan exposure and child neurodevelopment at 3 years.METHODS: The study included 377 mother-child pairs who participated in Sheyang Mini Birth Cohort Study (SMBCS), a longitudinal birth cohort in China. Triclosan concentrations in maternal and 3-year-old child urine samples were quantified using gas chromatography-tandem mass spectrometry (GC-MS/MS). Gesell Developmental Schedules (GDS) were used to assess child neurodevelopment at 3 years of age. Multivariate linear regression models were applied to estimate associations of prenatal and postnatal urinary triclosan concentrations with children's developmental quotients (DQs).RESULTS: Detection frequencies of triclosan in maternal and childhood urine samples were 100% and 99.5%, respectively. The median values of prenatal and postnatal urinary triclosan levels were 0.65 and 0.44 μg/L, respectively. One ln-unit increase of maternal urinary triclosan concentration was associated with increase of DQ scores in motor area of children (regression coefficient, β = 0.28, 95% confidence interval, CI: 0.03, 0.54; p = 0.03). In sex-stratified analyses, maternal urinary triclosan levels were significantly related to increases in DQ scores in motor area among boys (β = 0.25, 95%CI: 0.01, 0.50; p = 0.04), while postnatal urinary triclosan concentrations were inversely associated with DQ scores in social area in boys (β = -0.37, 95%CI: -0.72, -0.03; p = 0.03).CONCLUSIONS: The findings suggested that prenatal triclosan exposure predicted increases in motor scores, while postnatal triclosan exposure was related to reductions in social scores of 3-year-old children. These associations were only observed in boys. The biological mechanisms linking triclosan exposure to neurodevelopment await further studies.
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| 9. |
- Guo, Jianqiu, et al.
(author)
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Maternal and childhood urinary phenol concentrations, neonatal thyroid function, and behavioral problems at 10 years of age : The SMBCS study
- 2020
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In: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 743
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Journal article (peer-reviewed)abstract
- BACKGROUND: Environmental phenols, bisphenol A (BPA), triclosan (TCS), and benzophenone-3 (BP-3), are known as emerging endocrine-disrupting chemicals; however, their impacts on thyroid hormones and children's neurobehaviors are still unclear.OBJECTIVES: We aimed to examine the associations of prenatal and childhood exposure to phenols with neonatal thyroid function and childhood behavioral problems aged 10 years.METHODS: A total of 386 mother-singleton pairs were included from Sheyang Mini Birth Cohort Study (SMBCS), a longitudinal birth cohort in China. We quantified urinary BPA, TCS and BP-3 concentrations in maternal and 10-year-old children's urine samples using gas chromatography tandem mass spectrometry and thyroid function parameters in cord serum samples. Caregivers completed the Strength and Difficulties Questionnaire (SDQ) for their children at 10 years of age. Multivariable linear regression models and logistic regression models were applied to estimate associations of urinary phenol concentrations with thyroid hormones and risks of children's behavioral problems, respectively.RESULTS: The median values of urinary BPA, TCS and BP-3 concentrations for pregnant women were 1.75 μg/L, 0.54 μg/L and 0.37 μg/L, while 1.29 μg/L, 6.64 μg/L and 1.39 μg/L for children, respectively. Maternal urinary BPA concentrations were in associations with 1.00% [95% confidence interval (CI): 0.20%, 1.92%] increases in cord serum FT4 concentrations and significantly associated with increased risks of total difficulties [odds ratio (OR): 1.45, 95% CI: 1.07, 1.97], while maternal urinary levels of BP-3 were significantly related to poorer prosocial behaviors (OR: 1.58, 95% CI: 1.04, 2.39) of children at 10 years of age. In sex-stratified analyses, maternal urinary BPA concentrations were related to increased total difficulty subscales only in boys.CONCLUSIONS: The findings indicated that higher prenatal urinary BPA concentrations were associated with increased risks of total difficulties, especially in boys and maternal urinary BP-3 concentrations were related to poorer prosocial behaviors at 10 years.
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| 10. |
- Guo, J., et al.
(author)
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Urinary bisphenol A concentrations and adiposity measures at age 7 years in a prospective birth cohort
- 2020
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In: Chemosphere. - : Pergamon Press. - 0045-6535 .- 1879-1298. ; 251
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Journal article (peer-reviewed)abstract
- 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.
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