Catfish is an important aquaculture species in the USA. Columnaris disease is distributed worldwide, affecting a wide variety of fish species including catfish . It leads to huge economic losses each ...year to the US catfish industry. Channel catfish in general is highly resistant to the disease, while blue catfish is highly susceptible. Genomic selection is an effective and accurate way to predict the breeding values and thus was expected to improve the prediction veracity of columnaris disease resistance in catfish effectively. In this study, two different methods, elastic net genomic best linear unbiased prediction (ENGBLUP) and genomic best linear unbiased prediction (GBLUP), were used to predict the columnaris disease resistance evaluated by binary survival status. Cross-validation showed that the prediction accuracy of ENGBLUP and GBLUP was 0.7347 and 0.4868, respectively, showing that ENGBLUP had a high prediction accuracy. It was shown that fitting QTL and polygenic effect with different distribution will improve genomic prediction accuracy for binary traits. In this study, an accurate and effective genomic selection method was proposed to predict the columnaris resistance in catfish, and its application should be beneficial to catfish breeding.
Diatoms and dinoflagellates dominate coastal marine phytoplankton communities as major players of marine biogeochemical cycles and their seasonal succession often leads to harmful algal blooms ...(HABs). What regulates their respective dominances and the development of the HABs remains elusive. Here we conducted time-sequential metatranscriptomic profiling on a natural assemblage that evolved from diatom dominance to a dinoflagellate bloom to interrogate the underlying major metabolic and ecological drivers. Data reveals similarity between diatoms and dinoflagellates in exhibiting high capacities of energy production, nutrient acquisition, and stress protection in their respective dominance stages. The diatom-to-dinoflagellate succession coincided with an increase in turbidity and sharp declines in silicate and phosphate availability, concomitant with the transcriptomic shift from expression of silicate uptake and urea utilization genes in diatoms to that of genes for light harvesting, diversified phosphorus acquisition and autophagy-based internal nutrient recycling in dinoflagellates. Furthermore, the diatom-dominant community featured strong potential to carbohydrate metabolism and a strikingly high expression of trypsin potentially promoting frustule building. In contrast, the dinoflagellate bloom featured elevated expression of xanthorhodopsin, and antimicrobial defensin genes, indicating potential importance of energy harnessing and microbial defense in bloom development. This study sheds light on mechanisms potentially governing diatom- and dinoflagellate-dominance and regulating bloom development in the natural environment and raises new questions to be addressed in future studies.
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•Chemical changes in the wine steaming processing of LLF were studied.•104 compounds were tentatively identified using UHPLC/Orbitrap-MS.•Chemical compositions were compared between ...LLF and wine-steamed LLF.•4 esters and 3 non-esters were determined by UPLC/UV in 21 commercial samples.•Ester hydrolysis is the major chemical change during wine steaming processing.
Ligustri Lucidi Fructus (LLF) is a traditional Chinese medicine to treat osteopathic and hepatic diseases. Wine steaming is the major processing method for LLF in Chinese Pharmacopoeia, but the chemical changes involved are still unclear. In this study, a research strategy was proposed to reveal the chemical changes during wine steaming processing of LLF. Firstly, in total 104 compounds were tentatively identified using UHPLC/Orbitrap-MS. Secondly, potential chemical changes were revealed by comparing the peak areas of the 104 compounds between LLF and the corresponding wine-steamed LLF (WLLF). The results indicated that iridoid and phenylethanoid esters were readily hydrolyzed during wine steaming processing, while organic acids, flavonoids, and triterpenes were stable. Finally, 7 selected compounds were simultaneously determined in 21 batches of LLF/WLLF samples using a 10-min UPLC/UV method. The contents of 4 esters decreased from 3.64% to 2.71%, and the contents of 3 potential hydrolysis products increased from 0.27% to 0.88% after processing. Our study indicated that hydrolysis of iridoid and phenylethanoid esters such as specneuzhenide was responsible for the chemical changes during the wine processing of LLF. The proposed strategy could be employed to investigate the chemical changes of other herbs during processing.
Exposure to PM2.5 is a leading environmental risk factor for many diseases and premature deaths, arousing growing public concerns. In this study, indoor and outdoor PM2.5 concentrations were ...investigated during the heating and non-heating seasons in an urban area in northwest China. Personal inhalation exposure levels among different age groups were evaluated, and the difference attributable to different cooking fuels including coal, gas and electricity, was discussed. The average concentrations of PM2.5 in the kitchen and the bedroom were 125±51 and 119±64μg/m3 during the heating season, and 80±67 and 80±50μg/m3 during the non-heating season, respectively. Indoor PM2.5, from indoor combustion sources but also outdoor penetration, contributed to about 75% of the total PM2.5 exposure. Much higher indoor concentrations and inhalation exposure levels were found in households using coal for cooking compared to those using gas and electricity. Changing from coal to gas or electricity for cooking could result in a reduction of PM2.5 in the kitchen by 40–70% and consequently lower inhalation exposure levels, especially for children and women.
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•Comparison and seasonal differences in indoor and outdoor PM2.5•Estimate personal inhalation exposure and indoor/outdoor contributions•Distinct indoor PM2.5 levels attributable to different cooking fuels•Use of coal for cooking leads to higher indoor pollution and exposure level.•Indoor PM2.5 exposure contributed to near 75% of total inhalation exposure.
During the past several decades, an increasing incidence of thyroid cancer has been reported in many parts of the world. To date, no study has compared the trends in thyroid cancer incidence across ...continents. We examined incidence data from cancer incidence in five continents (CI5) over the 30-year period 1973–2002 from 19 populations in the Americas, Asia, Europe, and Oceania. Thyroid cancer rates have increased from 1973–1977 to 1998–2002 for most of the populations except Sweden, in which the incidence rates decreased about 18% for both males and females. The average increase was 48.0% among males and 66.7% among females. More recently, the age-adjusted international thyroid cancer incidence rates from 1998 to 2002 varied 5-fold for males and nearly 10-fold for females by geographic region. Considerable variation in thyroid cancer incidence was present for every continent but Africa, in which the incidence rates were generally low. Our analysis of published CI5 data suggests that thyroid cancer rates increased between 1973 and 2002 in most populations worldwide, and that the increase does not appear to be restricted to a particular region of the world or by the underlying rates of thyroid cancer.
The associations between multiple sleep characteristics and smoking behavior are inconsistent, and it is unclear which sleep characteristics are most crucial for tobacco prevention. This study aimed ...to explore the associations between smoking status/intensity and multiple sleep characteristics and to identify the potential core domain of smoking-related sleep using network analysis. Data were obtained from a survey of cancer-related risk factors among Chinese adults. Logistic regression models were used to quantify the associations between sleep characteristics and smoking status/intensity. Network analyses were employed to identify the core sleep characteristics. A total of 5,228 participants with a median age of 44 years old were included in the study. Current smoking was significantly positively associated with long nap time, difficulty falling asleep, late bedtime, getting up after 7 am, and waking up earlier than expected. There was significant positive association between current smoking and short sleep duration in young adults under 45 years old. Late bedtime and getting up after 7 am were only associated with current heavy smoking, but not current light smoking. Network analyses showed that multiple smoking-related sleep characteristics were interconnected, with difficulty falling asleep and late bedtime as central characteristics in the network. The study found that the associations between sleep characteristics and smoking varied by age and smoking intensity and highlights the potential benefits of sleep health promotion in smoking cessation, with a particular focus on difficulty falling asleep and late bedtime.
Today, it is almost impossible to implement teaching processes without using information and communication technologies (ICT), especially in higher education. Education institutions often use ...learning management systems (LMS), such as Moodle, Edmodo, Canvas, Schoology, Blackboard Learn, and others. When accessing these systems with their personal account, each student’s activity is recorded in a log file. Moodle system allows not only information sav-ing. The plugins of this LMS provide a fast and accurate analysis of training sta-tistics. Within the study, the capabilities of several Moodle plugins providing the assessment of students' activity and success are reviewed. The research is aimed at discovering possibilities to improve the learning process and reduce the num-ber of underperforming students. The activity logs of 124 participants are ana-lyzed to identify the relations between the number of logs during the e-course and the final grades. In the study, a correlation analysis is performed to determine the impact of students' educational activity in the Moodle system on the final assess-ment. The results reveal that gender affiliation correlates with the overall perfor-mance but does not affect the selection of training materials. Furthermore, it is shown that students who got the highest grades performed at least 210 logs dur-ing the course. It is noted that the prevailing part of students prefers to complete the tasks before the deadline. The study concludes that LMSs can be used to pre-dict students' success and stimulate better results during the study. The findings are proposed to be used in higher education institutions for early detection of stu-dents experiencing difficulties in a course.
Prostate adenocarcinoma (PCa) is a complex genetic disease, and the implementation of personalized treatment in PCa faces challenges due to significant inter- and intrapatient tumor heterogeneities.
...To systematically explore the genomic complexity of tumor cells with different Gleason scores (GSs) in PCa.
We performed single-cell whole genome sequencing of 17 tumor cells from localized lesions with distinct GS and matched four normal samples from two prostatectomy patients.
All classes of genomic alterations were identified, including substitutions, insertions/deletions, copy number alterations, and rearrangements.
Significant spatial, intra- and intertumoral heterogeneities were observed at the cellular level. In the patient 1, all cells shared the same TP53 driver mutation, implying a monoclonal origin of PCa. In the patient 2, only a subpopulation of cells contained the TP53 driver mutation, whereas other cells carried different driver mutations, indicating a typical polyclonal model with separate clonal cell expansions. The tumor cells from different sides of prostate owned various mutation patterns. Considerable neoantigens were predicted among different cells, implying unknown immune editing components helping prostate tumor cells escaping from immune surveillance.
There is a significant spatial genomic heterogeneity even in the same PCa patient. Our study also provides the first genome-wide evidence at single-cell level, supporting that the origin of PCa could be either polyclonal or monoclonal, which has implications for treatment decisions for prostate cancer.
We reported the first single-cell whole genomic data of prostate adenocarcinoma (PCa) from different Gleason scores. Identification of these genetic alterations may help understand PCa tumor progression and clonal evolution.
Our study provides the first genome-wide evidence at cellular level supporting that the origin of prostate cancer could be either polyclonal or monoclonal. There is significant spatial genomic heterogeneity of prostate cancer even in the same patient.
Currently few studies have explored the relationship between exposure to gaseous pollutants and metabolic health indicators in patients, especially in patients with metabolic syndrome (Mets). This ...study collected 15,520 patients with Mets in a prospective cohort of nearly 50,000 people with 7 years of follow-up from 2011 to 2017, and matched air pollutants and meteorological data during the same period. The mixed effects model was used to analyze the relationship between different short exposure windows (1-week, 1-month, 2-month, and 3-month) of gaseous pollutants (SO2, NO2, and O3) and the metabolic health indicators of patients after controlled the confounding factors. Stratified analysis was performed by demographic characteristics and behavioral factors. The effects of gaseous pollutants on patients with different Met components were also analyzed. The results showed that the short-term exposure to SO2, NO2, and O3 had a certain effect on the metabolic health indicators of patients with Mets in different exposure windows, and with the extension of the exposure window period, the effects increased. The stratified analysis showed that gender, age, and life behaviors might modify these detrimental effects. In addition, the effects of gaseous pollutants on metabolic health indicators in G4 and G7 were more obvious than other Met components, and the effects of gaseous pollutants on the level of LDL-C were found to be statistically significant in most components. Therefore, patients with Mets should pay more attention to the influence of gaseous pollutants to take appropriate protection to reduce potential health risk.
•SO2, NO2 and O3 can affect metabolic health indicators of Metabolic syndrome.•With extension of exposure windows, effects of gaseous pollutants increased.•The elderly and males were more sensitive to gaseous pollutants.•Effects of pollutants on LDL-C levels were more significant in Met components.
Aberrant DNA methylation is an early event during tumorigenesis. In the present study, we aimed to construct a methylation diagnostic tool using urine sediment for the detection of urothelial bladder ...carcinoma, and improved the diagnostic performance of the model by incorporating single-nucleotide polymorphism (SNP) sites.
A three-stage analysis was carried out to construct the model and evaluate the diagnostic performance. In stage I, two small cohorts from Xiangya hospital were recruited to validate and identify the detailed regions of collected methylation biomarkers. In stage II, proof-of-concept study cohorts from the Hunan multicenter were recruited to construct a diagnostic tool. In stage III, a blinded cohort comprising suspicious UBC patients was recruited from Beijing single center to further test the robustness of the model.
In stage I, single NRN1 exhibited the highest AUC compared with six other biomarkers and the Random Forest model. At the best cutoff value of 5.16, a single NRN1 biomarker gave a diagnosis with a sensitivity of 0.93 and a specificity of 0.97. In stage II, the Random Forest algorithm was applied to construct a diagnostic tool, consisting of NRN1, TERT C228T and FGFR3 p.S249C. The tool exhibited AUC values of 0.953, 0.946 and 0.951 in training, test and all cohorts. At the best cutoff value, the model resulted in a sensitivity of 0.871 and a specificity of 0.947. In stage III, the diagnostic tool achieved a good discrimination in the external validation cohort, with an overall AUC of 0.935, sensitivity of 0.864 and specificity of 0.895. Additionally, the model exhibited a superior sensitivity and comparable specificity compared with conventional cytology and FISH.
The diagnostic tool exhibited a highly specific and robust performance. It may be used as a replaceable approach for the detection of UBC.
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