Open Innovation Web-Based Platform for Evaluation of Water Quality Based on Big Data Analysis

There are many models presented that assess water quality. However, the applications of the models are limited due to the difficulty of preparing input data and interpreting model output. In this paper, we developed a Web-based platform to assist researchers in analyzing water quality. The data from sensors can be automatically imported to the platform according to the configured information of data structures. The platform also provides conventional methods and big data methods for the users to analyze water quality. Moreover, the users can choose the water quality parameters according to the water usage. The presented platform can show the model output in a text format and a graphic format, which allows for the analysis to be better understood by the user. The platform integrates the input, analysis, and output together well and brings great convenience to the research on water quality

Predicting the impacts of Mississippi River diversions and sea-level rise on spatial patterns of eastern oyster growth rate and production

© 2017 There remains much debate regarding the perceived tradeoffs of using freshwater and sediment diversions for coastal restoration in terms of balancing the need for wetland restoration versus preserving eastern oyster (Crassostrea virginica) production. Further complicating the issue, climate change-induced sea-level rise (SLR) and land subsidence are also expected to affect estuarine water quality. In this study, we developed a process-based numerical modeling system that couples hydrodynamic, water quality, and oyster population dynamics. We selected Breton Sound Estuary (BSE) (∼2740 km2) in the eastern Mississippi River Deltaic Plain since it is home to several of the largest public oyster seed grounds and private leases for the Gulf coast. The coupled oyster population model was calibrated and validated against field observed oyster growth data. We predicted the responses of oyster population in BSE to small- (142 m3 s−1) and large-scale (7080 m3 s−1) river diversions at the Caernarvon Freshwater Diversion structure planned in the 2012 Coastal Master Plan (Louisiana) under low (0.38 m) and high (1.44 m) relative sea-level rise (RSLR = eustatic SLR + subsidence) compared to a baseline condition (Year 2009). Model results showed that the large-scale diversion had a stronger negative impact on oyster population dynamics via freshening of the entire estuary, resulting in reduced oyster growth rate and production than RSLR. Under the large-scale diversion, areas with optimal oyster growth rates (\u3e15 mg ash-free dry weight (AFDW) oyster−1 wk−1) and production (\u3e500 g AFDW m−2 yr−1) would shift seaward to the southeastern edge of the estuary, turning the estuary into a very low oyster production system. RSLR however played a greater role than the small-scale diversion on the magnitude and spatial pattern of oyster growth rate and production. RSLR would result in an overall estuary-wide decrease in oyster growth rate and production as a consequence of decreased salinities in the middle and lower estuary because rising sea level likely causes increased stage and overbank flow downstream along the lower Mississippi River

Genetic parameters analysis of milk citrate for Holstein cows in early lactation

peer reviewedDelivering innovative and holistic monitoring and decision-making PLF tools relies on the availability of critical biomarkers. Negative energy balance is a difficult trait complex as there is a difference between perceived imbalance and physiological imbalance. Milk citrate is considered to be an early biomarker of negative energy balance for dairy cows in early lactation, but its genetic analysis is lacking. The objectives of this study were to (1) show the distribution of milk citrate content in early lactation; (2) analyze the genetic parameters of milk citrate. The coefficient of determination (R2) and root mean square error (RMSE) of the predicted milk citrate model by milk mid-infrared (MIR) spectra in external validation were 0.86 and 0.76 mmol/L, and available from DIM 5 to 50 d. Records were divided into three traits according to the first (citrate1), second (citrate2), and from third to fifth party (citrate3+). After editing, the data included 134,517 records, from 52,198 cows, and 4,479 animals in the pedigree with 566,170 SNPs. A multiple-trait repeatability model was used in this study. The citrate is decreasing in early lactation, on average from 10.04 to 8.58 mmol/L from DIM 5 to 50 d. When cows start to be in energy balance (DIM ≈ 40 d), milk citrate was 8.82 mmol/l. The average of citrate1 was 8.93 mmol/l; citrate2 was 8.93 mmol/l; citrate3+ was 9.17 mmol/l. The heritability for citrate1 was 0.40; for citrate2, 0.37 and for citrate3+, 0.35. The ranges of genetic correlations between the three traits were from 0.98 to 0.99, and of phenotypic correlations, from 0.41 to 0.42. This study shows that considering MIR-based milk citrate as an indicator to identify negative energy balance should be possible in early lactation and that this indicator could help select for animals less affected by negative energy balance

Correlation analysis of diabetes based on Copula

IntroductionThe ratio of Triglyceride (TG) to high-density lipoprotein cholesterol (HDL-C) is a crucial indicator for diabetes diagnosis.MethodsThis study utilizes the Copula function to model and fit the non-linear correlation among fasting blood glucose (Glu), glycosylated hemoglobin (HbA1C), and TG/HDL-C in patients with diabetes. The Copula function chosen for this study includes the two-dimensional Archimedes and Elliptical distribution family, as well as the multidimensional Vine Copula function, for fitting the data. The evaluation of the fitting effect is performed using the mean absolute error (MAE) and mean square error (MSE).ResultsThe results indicate that the Clayton Copula exhibits the highest effectiveness in fitting the pairwise relationship between Glu and TG/HDL-C, as well as HbA1C and TG/HDL-C, displaying the smallest fitting error. Additionally, the Vine Copula function produces a satisfactory fit for the relationship among all three indicators. Compared to linear analysis methods, the Copula function more accurately depicts the correlation among these three types of indicators.DiscussionMoreover, our findings indicate a stronger correlation in the lower tail between Glu and HbA1C, as well as TG/HDL-C, suggesting that the Copula function provides greater accuracy and applicability in depicting the relationship among these indicators. As a result, it can offer a more precise auxiliary diagnosis and serve as a valuable reference in clinical judgment

Relationship between proxies of energy states and nitrogen use efficiency for Holstein cows in early lactation

peer reviewedThe purposes of this study were to estimate the genetic parameters of the energy status indicator (C18:1 cis-9) of Holstein cows in early lactation and its relationship with nitrogen use efficiency (NUE) (predicted NUE and milk urea concentration). After editing, the data included 143,517 records within 5 to 50 days in milk from 52,198 cows, and 3,546 animals in the pedigree with 28,427 SNPs. Two multiple-trait repeatability models were used in this study. In early lactation, the average C18:1 cis-9 was gradually decreasing and was highest in May. The heritabilities of C18:1 cis-9 for primiparous and multiparous cows were 0.12 and 0.09, respectively. The C18:1 cis-9 had positive genetic correlations with predicted NUE (from 0.28 to 0.67), and weak genetic correlations with milk yield, milk urea concentration (from-0.15 to 0.14). This study suggests that breeding for NUE alone may enhance energy troubles in early lactation

Defining a nitrogen efficiency index in Holstein cows and assessing its potential effect on the breeding program of bulls.

peer reviewedThe purposes of this study were (1) to explore the relationship between 3 milk mid-infrared predicted features including nitrogen intake (NINT), milk true protein N (MTPN), and milk urea-N yield (MUNY); (2) to integrate these 3 features into an N efficiency index (NEI) and analyses approximate genetic correlations between the NEI and 37 traits (indices) of interest; and (3) to assess the potential effect of including the NEI into breeding programs of bulls. The edited data were 1,043,171 test-day records on 342,847 cows in 1,931 herds and 143,595 test-day records on 53,660 cows in 766 herds used for estimating breeding values (EBV) and variance components, respectively. The used records were within 5 to 50 d in milk. The records were grouped into primiparous and multiparous. The genetic parameters for the included mid-infrared features and EBV of the animals included in the pedigree were estimated using a multiple-trait repeatability animal model. Then, the EBV of the NINT, MTPN, MUNY were integrated into the NEI using a selection index assuming weights based on the N partitioning. The approximate genetic correlations between the NEI and 37 traits of interest were estimated using the EBV of the selected bulls. The bulls born from 2011 to 2014 with NEI were selected and the NEI distribution of these bulls having EBV for the 8 selected traits (indices) was checked. The heritability and repeatability estimates for NINT, MTPN, and MUNY ranged from 0.09 to 0.13, and 0.37 to 0.65, respectively. The genetic and phenotypic correlations between NINT, MTPN, and MUNY ranged from -0.31 to 0.87, and -0.02 to 0.42, respectively. The NEI ranged from -13.13 to 12.55 kg/d. In total, 736 bulls with reliability ≥0.50 for all included traits (NEI and 37 traits) and at least 10 daughters distributed in at least 10 herds were selected to investigate genetic aspects of the NEI. The NEI had positive genetic correlations with production yield traits (0.08-0.46), and negative genetic correlations with the investigated functional traits and indices (-0.71 to -0.07), except for the production economic index and functional type economic index. The daughters of bulls with higher NEI had lower NINT and MUNY, and higher MTPN. Furthermore, 26% of the bulls (n = 50) with NEI born between 2011 to 2014 had higher NEI and global economic index than the average in the selected bulls. Finally, the developed NEI has the advantage of large-scale prediction and therefore has the potential for routine application in dairy cattle breeding in the future.13. Climate actio

Genetic analysis of milk citrate predicted by milk mid-infrared spectra of Holstein cows in early lactation.

peer reviewedMilk citrate is regarded as an early biomarker of negative energy balance (NEB) in dairy cows during early lactation and serves as a suitable candidate phenotype for genomic selection due to its wide availability across a large number of cows through milk mid-infrared spectra prediction. However, its genetic background is not well known. Therefore, the objectives of this study were to (1) analyze the genetic parameters of milk citrate; (2) identify genomic regions associated with milk citrate; (3) analyze the functional annotation of candidate genes and quantitative trait loci (QTL) related to milk citrate in Walloon Holstein cows. In total, 134,517 test-day milk citrate phenotypes (mmol/L) collected within the first 50 d in milk (DIM) on 52,198 Holstein cows were used. These milk citrate phenotypes, predicted by milk mid-infrared spectra, were divided into 3 traits according to the first (citrate1), second (citrate2), and third to fifth parity (citrate3+). Genomic information for 566,170 SNPs was available for 4,479 animals. A multiple-trait repeatability model was used to estimate genetic parameters. A single-step genome-wide association study (GWAS) was used to identify candidate genes for citrate and post-GWAS analysis was done to investigate relationship and function of the identified candidate genes. The heritabilities estimated for citrate1, citrate2 and citrate3+ were 0.40, 0.37 and 0.35, respectively. The genetic correlations between the 3 traits ranged from 0.98 to 0.99. The genomic correlations between the 3 traits were also nearly 1.00 across the genomic regions (1 Mb) in the whole genome, which means that citrate can be considered as a single trait in the first 5 parities. In total, 603 significant SNPs located on 3 genomic regions (chromosome7 68.569 - 68.575 Mb, 14 1.31 - 3.05 Mb, and 20 54.00 - 64.28 Mb), were identified to be associated with milk citrate. We identified 89 candidate genes including GPT, ANKH, PPP1R16A and 32 QTL reported in the literature related to the identified significant SNPs. These identified QTL were mainly reported associated with milk fatty acids and metabolic diseases in dairy cows. This study suggests that milk citrate in Holstein cows is highly heritable and has the potential to be used as an early proxy for the NEB of Holstein cows in a breeding objective

Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation.

peer reviewedNitrogen (N) use efficiency (NUE) is an economically important trait for dairy cows. Recently, we proposed a new N efficiency index (NEI), that simultaneously considers both NUE and N pollution. This study aimed to validate the genomic prediction for NEI and its composition traits and investigate the relationship between SNP effects estimated directly from NEI and indirectly from its composition traits. The NEI composition included genomic estimated breeding value of N intake (NINT), milk true protein N (MTPN) and milk urea N yield. The edited data were 132,899 records on 52,064 cows distributed in 773 herds. The pedigree contained 122,368 animals. Genotypic data of 566,294 SNP was available for 4514 individuals. A total of 4413 cows (including 181 genotyped) and 56 bulls (including 32 genotyped) were selected as the validation populations. The linear regression method was used to validate the genomic prediction of NEI and its composition traits using best linear unbiased prediction (BLUP) and single-step genomic BLUP (ssGBLUP). The mean theoretical accuracies of validation populations obtained from ssGBLUP were higher than those obtained from BLUP for both NEI and its composition traits, ranging from 0.57 (MTPN) to 0.72 (NINT). The highest mean prediction accuracies for NEI and its composition traits were observed for the genotyped cows estimated under ssGBLUP, ranging from 0.48 (MTPN) to 0.66 (NINT). Furthermore, the SNP effects estimated from NEI composition traits, multiplied by the relative weight were the same as those estimated directly from NEI. This study preliminary showed that genomic prediction can be used for NEI, however, we acknowledge the need for further validation of this result in a larger dataset. Moreover, the SNP effects of NEI can be indirectly calculated using the SNP effects estimated from its composition traits. This study provided a basis for adding genomic information to establish NEI as part of future routine genomic evaluation programs

Entire Spectrum Measurement Of Kerr Constant And Birefringence Dispersion In A Polymer-Stabilized Blue-Phase Liquid Crystal Composite

A new method is proposed and implemented experimentally for measuring the electric-field induced birefringence together with the Kerr constant of a polymer-stabilized blue-phase liquid crystal (PSBPLC) composite. The conventional Senarmont compensation method is only suitable for the single wavelength measurement limited by the achromatic zero order quarter wavelength plate (QWP). In our new method, the QWP is removed so that a broad band light source can be used instead of monochromatic incident light. Herein planar ITO electrodes are employed, producing a uniformly distributed vertical electric field. Thus the fitting data is accurate and convincing prior to that from the IPS cell measurement. By rotating the sample to an oblique angle and using the spectrometer to scan the voltage dependent optical transmission, the induced birefringence and the Kerr constant for the entire visible spectrum can be carried out using the single band model. Quantitative experimental results have been obtained and presented in this paper to support this proposed scheme. © 2013 Society for Information Display