Publications by authors named "Haiming Tang"

31 Publications

Effects of different short-term tillage managements on rhizosphere soil autotrophic CO -fixing bacteria in a double-cropping rice paddy field.

Environ Microbiol Rep 2022 Jan 12. Epub 2022 Jan 12.

Hunan Soil and Fertilizer Institute, Changsha, 410125, China.

Soil autotrophic bacteria community plays an important role in carbon (C) cycling process in soil, but there is still limited information about how the rhizosphere soil microbe that drives this process respond to combined application of tillage with crop residue incorporation managements under a double-cropping rice (Oryza sativa L.) paddy field in southern China. Therefore, the 6-years short-term tillage treatment on rhizosphere soil autotrophic bacteria community [RubisCO gene (cbbL)] under the double-cropping rice paddy field in southern China was studied using the high-throughput sequencing method in the present article. The field experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that abundance, composition and activity of rhizosphere soil cbbL-carrying bacteria were obviously influenced by application of different tillage treatments. The rhizosphere soil abundant cbbL and 16S rRNA genes as well as RubisCO activity with CT, RT and NT treatments were higher than that of RTO treatment. The cbbL sequences in rhizosphere soil with CT, RT and NT treatments mainly included Azoarcus_sp._KH33C, Ralstonia_pickettii, Thermomonospora_curvata, Variovorax_paradoxus and uncultured_proteobacterium. Meanwhile, the results indicated that cbbL-carrying bacterial composition was significantly affected by soil organic carbon, microbial biomass carbon, dissolved organic carbon contents and soil bulk density. There had an obvious difference in characteristics of rhizosphere soil autotrophic bacteria community between CT, RT, NT treatments and RTO treatment. Therefore, it was a beneficial practice for improving rhizosphere soil autotrophic bacteria community in the double-cropping rice paddy field in southern China by combined application of tillage with crop residue incorporation practices.
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http://dx.doi.org/10.1111/1758-2229.13044DOI Listing
January 2022

Excessive and less complex body movement in children with autism during face-to-face conversation: An objective approach to behavioral quantification.

Autism Res 2021 Nov 27. Epub 2021 Nov 27.

Department of Child Psychiatry of Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, China.

The majority of existing studies investigating characteristics of overt social behavior in individuals with autism spectrum disorder (ASD) relied on informants' evaluation through questionnaires and behavioral coding techniques. As a novelty, this study aimed to quantify the complex movements produced during social interactions in order to test differences in ASD movement dynamics and their convergence, or lack thereof, during social interactions. Twenty children with ASD and twenty-three children with typical development (TD) were videotaped while engaged in a face-to-face conversation with an interviewer. An image differencing technique was utilized to extract the movement time series. Spectral analyses were conducted to quantify the average power of movement, and the fractal scaling of movement. The degree of complexity matching was calculated to capture the level of behavioral coordination between the interviewer and children. Results demonstrated that the average power was significantly higher (p < 0.01), and the fractal scaling was steeper (p < 0.05) in children with ASD, suggesting excessive and less complex movement as compared to the TD peers. Complexity matching occurred between children and interviewers, but there was no reliable difference in the strength of matching between the ASD and TD children. Descriptive trends in the interviewer's behavior suggest that her movements adapted to match both ASD and TD movements equally well. The findings of our study might shed light on seeking novel behavioral markers of ASD, and on developing automatic ASD screening techniques during daily social interactions.
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http://dx.doi.org/10.1002/aur.2646DOI Listing
November 2021

Restricted Kinematics in Children With Autism in the Execution of Complex Oscillatory Arm Movements.

Front Hum Neurosci 2021 3;15:708969. Epub 2021 Nov 3.

Developmental Behavioral Pediatric Department, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China.

Restricted and repetitive behavior is a core symptom of autism spectrum disorder (ASD) characterized by features of restrictedness, repetition, rigidity, and invariance. Few studies have investigated how restrictedness is manifested in motor behavior. This study aimed to address this question by instructing participants to perform the utmost complex movement. Twenty children with ASD and 23 children with typical development (TD) performed one-dimensional, left-right arm oscillations by demonstrating varying amplitudes and frequencies. The entropy of amplitude and velocity was calculated as an index of kinematic complexity. Results showed that the velocity entropy, but not the amplitude entropy, was significantly lower in ASD than in TD ( < 0.01), suggesting restricted kinematics. Further analysis demonstrated that a significantly higher proportion of the velocity values was allocated at a low-speed level in the children with ASD ( < 0.01). A qualitative comparison of the complex movement with movement at preferred frequency suggested that the children with ASD might be less likely to shift away from the preferred movement. However, our study can be improved in terms of recruiting a larger sample of participants, measuring the level of motivation, and collecting both complex and preferred movements of the same participant.
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http://dx.doi.org/10.3389/fnhum.2021.708969DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8597710PMC
November 2021

Impact of long-term tillage management on utilization of microbial carbon sources in rhizosphere and non-rhizosphere soils under a double-cropping rice paddy field.

Environ Sci Pollut Res Int 2021 Oct 9. Epub 2021 Oct 9.

College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.

In order to reveal the mechanism of microbial carbon (C) sequestration in paddy soil under different tillage management and to provide an important theoretical basis for perfecting the mechanism of C sequestration in paddy soil. C can indicate changes of soil nutrient content and soil microbial community, but more research is needed to study how C sources utilization characteristics respond to different tillage management under a double-cropping rice (Oryza sativa L.) paddy field in southern China. Hence, the impact of long-term (2005-2018) tillage management on utilization of microbial carbon sources in rhizosphere and non-rhizosphere soils under a double-cropping rice paddy field was studied by using O-HO method in this study. The tillage treatments were included: (1) moldboard plow with all crop residue removed as a control (CT), (2) moldboard plow with all crop residue incorporated (CTS), (3) no-tillage with all crop residue retained on the soil surface (NTS), and (4) rotary tillage with all crop residue incorporated (RTS). The results indicated that Richness, Shannon, and McIntosh indices were increased by application of crop residue management, compared with treatment without crop residue, and soil microbial growth rate, soil microbial biomass C content, and soil microbial basal respiration with CT treatment were significantly lower (p < 0.05) than that of NTS, RTS, and CTS treatments. And the soil C utilization efficiency in rhizosphere soil with NTS, RTS, and CTS treatments was significantly lower (p < 0.05) than that of CT treatment. Compared with CT and CTS treatments, the metabolic capacity of soil microorganisms to exogenous C sources with NTS and RTS treatments was increased, and the different types of exogenous C sources were showed as following: complex compounds < carbohydrate < amino acid < carboxylic acids. The redundancy analysis results showed that utilization characteristics of soil microorganisms to exogenous C sources were significantly changed under tillage and crop residue incorporated conditions. Hence, this result indicated that characteristics of soil C sources utilization were significantly increased combined applied with tillage and crop residue incorporated management.
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http://dx.doi.org/10.1007/s11356-021-16886-9DOI Listing
October 2021

Effects of fertilizer practice on fungal and actinobacterial cellulolytic community with different humified particle-size fractions in double-cropping field.

Sci Rep 2021 09 16;11(1):18441. Epub 2021 Sep 16.

Hunan Soil and Fertilizer Institute, Changsha, 410125, China.

Cellulose plays an important role in maintaining or improving soil carbon (C) cycling and soil fertility of paddy field. There had close relationship between functional cellulose genes (cbhI and GH48) with characterize of soil organic matter chemical components (fulvic acid and humic acid) and soil physical fractions. However, there is still limited information about how functional cellulose degradation response to long-term fertilizer management and their relative importance for C sequestration under the double-cropping rice paddy field in southern of China. Therefore, the objective of this study were investigated the effects of 34-years long-term fertilizer regime on community abundance of cbhI and GH48 genes in five soil particle-size fractions (> 2000 μm, 2000-200 μm, 200-50 μm, 50-2 μm and 2-0.1 μm) by using polarization magic angle spinning C nuclear magnetic resonance spectroscopy. The field experiment was included four different fertilizer treatments: chemical fertilizer alone (MF), rice straw and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that distribution of soil humus and cellulolytic microbial community abundance was significant increased under long-term application of crop residue and organic manure condition. And the FA, HA and HM C contents in > 2000 μm and 2000-50 μm fractions with MF, RF and OM treatments were significant higher than that of CK treatment. Meanwhile, the alkyl C and Oalkyl C groups of FA and HA in > 2000 μm fraction with MF, RF, OM and CK treatments were higher than that of the other fractions. There had higher AL% and lower ARO% of FA and HA in different particle-size fractions with MF, RF, OM and CK treatments. The results indicated that abundance of cbhI and GH48 genes in different particle-size fractions with RF and OM treatments were significant increased, compared with CK treatment. There had significant positive correlation between soil humus C components (FA and HA) with abundance of cbhI and GH48 genes, and the o-alkyl C and AL% of FA were positively correlated with abundance of cbhI and GH48 genes. As a result, the community abundance of cbhI and GH48 genes were significant increased under combined application of crop residue and organic manure with chemical fertilizer condition.
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http://dx.doi.org/10.1038/s41598-021-97975-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8446020PMC
September 2021

Improving Generalization of Deep Learning Models for Diagnostic Pathology by Increasing Variability in Training Data: Experiments on Osteosarcoma Subtypes.

J Pathol Inform 2021 4;12:30. Epub 2021 Aug 4.

Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA.

Background: Artificial intelligence has an emerging progress in diagnostic pathology. A large number of studies of applying deep learning models to histopathological images have been published in recent years. While many studies claim high accuracies, they may fall into the pitfalls of overfitting and lack of generalization due to the high variability of the histopathological images.

Aims And Objects: Use the model training of osteosarcoma as an example to illustrate the pitfalls of overfitting and how the addition of model input variability can help improve model performance.

Materials And Methods: We use the publicly available osteosarcoma dataset to retrain a previously published classification model for osteosarcoma. We partition the same set of images into the training and testing datasets differently than the original study: the test dataset consists of images from one patient while the training dataset consists images of all other patients. We also show the influence of training data variability on model performance by collecting a minimal dataset of 10 osteosarcoma subtypes as well as benign tissues and benign bone tumors of differentiation.

Results: The performance of the re-trained model on the test set using the new partition schema declines dramatically, indicating a lack of model generalization and overfitting. We show the additions of more and moresubtypes into the training data step by step under the same model schema yield a series of coherent models with increasing performances.

Conclusions: In conclusion, we bring forward data preprocessing and collection tactics for histopathological images of high variability to avoid the pitfalls of overfitting and build deep learning models of higher generalization abilities.
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http://dx.doi.org/10.4103/jpi.jpi_78_20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8404558PMC
August 2021

Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.

J Appl Microbiol 2022 Feb 14;132(2):1307-1318. Epub 2021 Sep 14.

Hunan Soil and Fertilizer Institute, Changsha, China.

Aims: The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5 years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction.

Methods And Results: The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management.

Conclusions: The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition.

Significance And Impact Of Study: The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.
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http://dx.doi.org/10.1111/jam.15289DOI Listing
February 2022

Effect of different long-term fertilizer managements on soil nitrogen fixing bacteria community in a double-cropping rice paddy field of southern China.

PLoS One 2021 1;16(9):e0256754. Epub 2021 Sep 1.

Hunan Soil and Fertilizer Institute, Changsha, China.

Soil microorganism plays an important role in nitrogen (N) fixation process of paddy field, but the related information about how soil microorganism that drive N fixation process response to change of soil phy-chemical characteristics under the double-cropping rice (Oryza sativa L.) paddy field in southern of China is need to further study. Therefore, the impacts of 34-years different long-term fertilization system on soil N-fixing bacteria community under the double-cropping rice paddy field in southern of China were investigated by taken chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method in this paper. The field experiment were set up four different fertilizer treatments: chemical fertilizer alone (MF), rice straw and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and unfertilized as a control (CK). This results showed that compared with CK treatment, the diversity index of cbbLR and nifH genes with OM and RF treatments were significantly increased (p<0.05), respectively. Meanwhile, the abundance of cbbLR gene with OM, RF and MF treatments were increased by 23.94, 12.19 and 6.70×107 copies g-1 compared to CK treatment, respectively. Compared with CK treatment, the abundance of nifH gene with OM, RF and MF treatments were increased by 23.90, 8.82 and 5.40×109 copies g-1, respectively. This results indicated that compared with CK treatment, the soil autotrophic azotobacter and nitrogenase activities with OM and RF treatments were also significantly increased (p<0.05), respectively. There were an obvious difference in features of soil N-fixing bacteria community between application of inorganic fertilizer and organic manure treatments. Therefore, this results demonstrated that abundance of soil N-fixing bacteria community in the double-cropping rice paddy field were increased by long-term applied with organic manure and crop residue managements.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0256754PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8409621PMC
November 2021

Classification of Children With Autism and Typical Development Using Eye-Tracking Data From Face-to-Face Conversations: Machine Learning Model Development and Performance Evaluation.

J Med Internet Res 2021 08 26;23(8):e29328. Epub 2021 Aug 26.

Department of Child Psychiatry of Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, China.

Background: Previous studies have shown promising results in identifying individuals with autism spectrum disorder (ASD) by applying machine learning (ML) to eye-tracking data collected while participants viewed varying images (ie, pictures, videos, and web pages). Although gaze behavior is known to differ between face-to-face interaction and image-viewing tasks, no study has investigated whether eye-tracking data from face-to-face conversations can also accurately identify individuals with ASD.

Objective: The objective of this study was to examine whether eye-tracking data from face-to-face conversations could classify children with ASD and typical development (TD). We further investigated whether combining features on visual fixation and length of conversation would achieve better classification performance.

Methods: Eye tracking was performed on children with ASD and TD while they were engaged in face-to-face conversations (including 4 conversational sessions) with an interviewer. By implementing forward feature selection, four ML classifiers were used to determine the maximum classification accuracy and the corresponding features: support vector machine (SVM), linear discriminant analysis, decision tree, and random forest.

Results: A maximum classification accuracy of 92.31% was achieved with the SVM classifier by combining features on both visual fixation and session length. The classification accuracy of combined features was higher than that obtained using visual fixation features (maximum classification accuracy 84.62%) or session length (maximum classification accuracy 84.62%) alone.

Conclusions: Eye-tracking data from face-to-face conversations could accurately classify children with ASD and TD, suggesting that ASD might be objectively screened in everyday social interactions. However, these results will need to be validated with a larger sample of individuals with ASD (varying in severity and balanced sex ratio) using data collected from different modalities (eg, eye tracking, kinematic, electroencephalogram, and neuroimaging). In addition, individuals with other clinical conditions (eg, developmental delay and attention deficit hyperactivity disorder) should be included in similar ML studies for detecting ASD.
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http://dx.doi.org/10.2196/29328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8440949PMC
August 2021

Identifying Autism with Head Movement Features by Implementing Machine Learning Algorithms.

J Autism Dev Disord 2021 Jul 11. Epub 2021 Jul 11.

Institute of Human Factors and Ergonomics, College of Mechatronics and Control Engineering, Shenzhen University, 3688 Nanhai, Avenue, Shenzhen City, Guangdong Province, China.

Our study investigated the feasibility of using head movement features to identify individuals with autism spectrum disorder (ASD). Children with ASD and typical development (TD) were required to answer ten yes-no questions, and they were encouraged to nod/shake head while doing so. The head rotation range (RR) and the amount of rotation per minute (ARPM) in the pitch (head nodding direction), yaw (head shaking direction) and roll (lateral head inclination) directions were computed, and further fed into machine learning classifiers as the input features. The maximum classification accuracy of 92.11% was achieved with the decision tree classifier with two features (i.e., RR_Pitch and ARPM_Yaw). Our study suggests that head movement dynamics contain objective biomarkers that could identify ASD.
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http://dx.doi.org/10.1007/s10803-021-05179-2DOI Listing
July 2021

Characteristics of Visual Fixation in Chinese Children with Autism During Face-to-Face Conversations.

J Autism Dev Disord 2021 Jun 8. Epub 2021 Jun 8.

Department of Child Psychiatry of Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, China.

Few eye tracking studies have examined how people with autism spectrum disorder (ASD) visually attend during live interpersonal interaction, and none with the Chinese population. This study used an eye tracker to record the gaze behavior in 20 Chinese children with ASD and 23 children with typical development (TD) when they were engaged in a structured conversation. Results demonstrated that children with ASD looked significantly less at the interlocutor's mouth and whole-face, and more at background. Additionally, gaze behavior was found to vary with the conversational topic. Given the great variability in eye tracking findings in existing literature, future explorations might consider investigating how fundamental factors (i.e., participant's characteristics, tasks, and context) influence the gaze behavior in people with ASD.
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http://dx.doi.org/10.1007/s10803-021-04985-yDOI Listing
June 2021

Functional soil organic matter fraction in response to short-term tillage management under the double-cropping rice paddy field in southern of China.

Environ Sci Pollut Res Int 2021 Sep 28;28(35):48438-48449. Epub 2021 Apr 28.

Hunan Soil and Fertilizer Institute, Changsha, 410125, China.

Soil organic matter (SOM) and its fraction play an important role in maintaining and improving soil fertility of paddy field. However, there is still limited information about how SOM fraction response to carbon (C) sequestration with different short-term tillage practices under the double-cropping rice paddy field in southern of China. Therefore, the effects of 5-year short-term tillage treatments on different SOM fractions (physically protected, physico-chemically protected, physico-biochemically protected, chemically protected, biochemically protected, and unprotected) under the double-cropping rice paddy field in southern of China were studied in this paper. The field experiment included four different tillage treatments: rotary tillage with crop residue removed as a control (RTO), conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), and no-tillage with crop residue retention (NT). The results showed that soil unprotected (cPOM), biochemically (NH-dSilt), physically-biochemically (NH-μSilt), and chemically protected (H-dSilt) fractions with different tillage treatments were the mainly C storage fraction in paddy field. The soil organic carbon (SOC) content in unprotected (cPOM and fPOM), physically protected (iPOM), and physico-chemically protected (H-μClay) fractions with CT treatment was increased by 1.45, 2.13, 1.91, and 1.42 times higher than that of RTO treatment, respectively. The results showed that largest proportion of fraction to SOC content was biochemically protected, followed by unprotected and physically-biochemically protected, and physically protected was the lowest. These results indicated that soil physically protected, physically-chemically protected, and physically-biochemically protected fractions with CT and RT treatments were higher than that of NT and RTO treatments. In summary, it was a benefit practice for increasing SOM fraction under the double-cropping rice paddy field in southern of China by combined application of conventional tillage and rotary tillage with crop residue incorporation management.
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http://dx.doi.org/10.1007/s11356-021-14173-1DOI Listing
September 2021

Microbial carbon source utilization in rice rhizosphere soil with different tillage practice in a double cropping rice field.

Sci Rep 2021 03 3;11(1):5048. Epub 2021 Mar 3.

Hunan Soil and Fertilizer Institute, Changsha, 410125, China.

Carbon (C) plays an important role in maintaining soil fertility and increasing soil microbial community, but there is still limited information about how source utilization characteristics respond to soil fertility changes under double-cropping rice (Oryza sativa L.) system in southern China paddy field. Therefore, the effects of different short-term (5-years) tillage management on characteristics of C utilization in rice rhizosphere and non-rhizosphere soils under double-cropping rice field in southern China were investigated by using O incorporation into DNA. Therefore, a field experiment were included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), rotary tillage with crop residue removed as control (RTO). The results showed that soil microbial biomass C content with CT, RT, NT treatments were increased by 29.71-47.27% and 3.77-21.30% in rhizosphere and non-rhizosphere soils, compared with RTO treatment, respectively. Compared with RTO treatment, soil microbial basal respiration and microbial growth rate with CT treatment were increased 30.56%, 30.94% and 11.91%, 12.34% in rhizosphere and non-rhizosphere soils, respectively. The soil microbial C utilization efficiency were promoted with NT treatment. Compared with RTO treatment, the metabolic capacity of soil microorganism to exogenous C source with CT, RT and NT treatments were increased. The largest type of exogenous C source was saccharides, followed by amino acid and polymers, and complex compounds was the smallest. The redundancy analysis results indicated that tillage treatments significantly changed the utilization characteristics of soil microorganism to exogenous C source. Compared with RTO treatment, the grain yield of early rice and late rice with CT treatment were increased by 409.5 kg ha and 387.0 kg ha, respectively. Therefore, the CT and RT treatments could significantly increase soil microbial biomass C content, but the NT treatment promote microbial C utilization efficiency in the double-cropping paddy field of southern China.
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http://dx.doi.org/10.1038/s41598-021-84425-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7930054PMC
March 2021

Atypical Head Movement during Face-to-Face Interaction in Children with Autism Spectrum Disorder.

Autism Res 2021 06 2;14(6):1197-1208. Epub 2021 Feb 2.

Institute of Human Factors and Ergonomics, College of Mechatronics and Control Engineering, Shenzhen University, Shenzhen, China.

The present study implemented an objective head pose tracking technique-OpenFace 2.0 to quantify the three dimensional head movement. Children with autism spectrum disorder (ASD) and typical development (TD) were engaged in a structured conversation with an interlocutress while wearing an eye tracker. We computed the head movement stereotypy with multiscale entropy analysis. In addition, the head rotation range (RR) and the amount of rotation per minute (ARPM) were calculated to quantify the extent of head movement. Results demonstrated that the ASD group had significantly higher level of movement stereotypy, RR and ARPM in all the three directions of head movement. Further analyses revealed that the extent of head movement could be significantly explained by movement stereotypy, but not by the amount of visual fixation to the interlocutress. These results demonstrated the atypical head movement dynamics in children with ASD during live interaction. It is proposed that head movement might potentially provide novel objective biomarkers of ASD. LAY SUMMARY: Our study used an objective tool to quantify head movement in children with autism. Results showed that children with autism had more stereotyped and greater head movement. We suggest that head movement tracking technique be widely used in autism research.
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http://dx.doi.org/10.1002/aur.2478DOI Listing
June 2021

Effect of different short-term tillage management on nitrogen-fixing bacteria community in a double-cropping paddy field of southern China.

J Basic Microbiol 2021 Mar 22;61(3):241-252. Epub 2020 Dec 22.

Hunan Soil and Fertilizer Institute, Changsha, China.

Soil nitrogen (N)-fixing bacteria community plays an important role in the N cycling process in soil, but there is still limited information about how the soil microbes that drive this process to respond to combined application of tillage and crop residue management under the double-cropping rice (Oryza sativa L.) paddy field in southern of China. Therefore, the effects of 6-years short-term tillage treatment on soil N-fixing bacteria community under the double-cropping rice paddy field in southern China were studied by using the polymerase chain reaction-denaturing gradient gel electrophoresis method. The field experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), rotary tillage with crop residue removed as control (RTO). The results showed that the diversity index and richness index of cbbLR and nifH genes with CT, RT, and NT treatments were increased, compared with RTO treatment. Compared with RTO treatment, the abundance of cbbLR gene with CT, RT, and NT treatments were increased by 6.54, 4.73, and 2.78 times, respectively. Meanwhile, the abundance of nifH gene with CT, RT, and NT treatments were 5.32, 3.71, and 2.45 times higher than that of RTO treatment. The results also indicated that soil autotrophic Azotobacter and nitrogenase activity with CT and RT treatments were significantly higher (p < .05) than that of RTO treatment. There was an obvious difference in characteristic of soil N-fixing bacteria community between the application of crop residue and without crop residue input treatments. In summary, the results indicated that the abundance of N-fixing bacteria community in the double-cropping rice paddy field increased with conventional tillage and rotary tillage practice.
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http://dx.doi.org/10.1002/jobm.202000608DOI Listing
March 2021

Microbial carbon source utilization in rice rhizosphere and non-rhizosphere soils in a 34-year fertilized paddy field.

J Basic Microbiol 2020 Nov 1;60(11-12):1004-1013. Epub 2020 Nov 1.

Hunan Soil and Fertilizer Institute, Changsha, China.

Carbon (C) is playing an important role in regulating soil nutrient cycling, maintaining soil fertility and crop yield, but there is still need to further study on how C source utilization characteristic respond to soil physical and chemical properties change with different fertilizer treatments under a double-cropping rice (Oryza sativa L.) field in southern China. Therefore, the effects of 34-year long-term fertilizer regime on C source utilization characteristic in rice rhizosphere and non-rhizosphere soils under a double-cropping rice field in southern China were studied by using O-H O method in the present paper. The field experiments were included four fertilizer treatments: mineral fertilizer alone (MF), rice straw and mineral fertilizer (RF), 30% organic manure and 70% mineral fertilizer (OM), and without fertilizer input as control (CK). The results showed that microbial biomass C content, basal respiration of soil microorganism and microbial growth rate in rice rhizosphere and non-rhizosphere soils with OM and RF treatments were significantly higher (p < .05) than that of CK treatment. The microbial C utilization efficiency (CUE) in rhizosphere soil with MF and CK treatments were significantly higher (p < .05) than that of OM treatment, but there was no significantly difference (p > .05) in microbial CUE in non-rhizosphere soil between MF, RF, OM, and CK treatments. In the different parts of soil, the microbial biomass C content and basal respiration of soil microorganism in rhizosphere soil were higher than that of non-rhizosphere soil, but the microbial growth rate and microbial CUE in non-rhizosphere soil were higher than that of rhizosphere soil. Compared with CK and MF treatments, the metabolic capacity of soil microorganism to exogenic C source with RF and OM treatments were significantly higher (p < .05) than that of MF and CK treatments. The largest type of exogenic C source used by soil microorganism was carboxylic acids, followed by amino acid and carbohydrate, and complex compounds was the smallest. In the different parts of soil, the metabolic capacity of soil microorganism to the types of exogenic C source in non-rhizosphere soil was higher than that of rhizosphere soil. The redundancy analysis results indicated that there had obvious difference in utilization characteristic of soil microorganism to exogenic C source among different fertilizer treatments. In conclusion, this results indicated that characteristic of soil C source utilization were significantly changed under different long-term fertilizer condition.
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http://dx.doi.org/10.1002/jobm.202000452DOI Listing
November 2020

Haematological and serum biochemical reference values in Chinese water deer (Hydropotes inermis): a preliminary study.

BMC Vet Res 2020 Oct 20;16(1):395. Epub 2020 Oct 20.

School of Life Sciences, Institute of Eco-Chongming, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China.

Background: A selection of haematological and serum biochemical profile was first presented from the 81 samples of Chinese water deer (Hydropotes inermis). The deer health assessment database was initially established, especially in relation to determining potential effects associated with diseases diagnosis.

Results: Blood samples were analyzed for different haematological parameters viz. white blood cells (WBC), red blood cells (RBC), haemoglobin (HGB), packed-cell volume (PCV), platelet count (PLT), mean corpuscular haemoglobin (MCH), mean corpuscular haemoglobin concentration (MCHC), mean corpuscular volume (MCV), mean red blood cells distribution width coefficient of variation (RDW) and different hematological parameters viz. total protein (TP), albumin (ALB), globulin (GLB), albumin to globulin ratio (A/G), total bilirubin (TBIL), alkaline phosphatase (ALP), γ-glutamyl transferase (GGT), alanine aminotransferase (ALT), aspartate aminotransferase (AST), AST/ALT, creatinine, urea (BUN), uric acid, total cholesterol (TC), triglyceride, creatine kinase (CK), lactate dehydrogenase (LDH) and cortisol. The adult females had higher values than adult males in albumin, mean corpuscular volume, packed-cell volume, and hemoglobin content values. The deer from Shanghai had higher urea nitrogen values than those from Zhoushan.

Conclusion: To our knowledge this is the first report about the haematological and serum biochemical parameters in Chinese water deer. We had initially established a profile of Chinese water deer on haematological and serum biochemical parameters based on 81 samples we had collected. The findings can serve as a primary reference for health monitoring and disease prevention in this species.
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http://dx.doi.org/10.1186/s12917-020-02601-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7574586PMC
October 2020

Effects of Short-Term Soil Tillage Management on Activity and Community Structure of Denitrifiers under Double- Cropping Rice Field.

J Microbiol Biotechnol 2020 Nov;30(11):1688-1696

Hunan Soil and Fertilizer Institute, Changsha 410125, P.R. China.

Soil physical and chemical characteristics, soil potential denitrification rates (PDR), community composition and -, - and -encoding denitrifiers were studied by using MiSeq sequencing, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment polymorphism (T-RFLP) technologies base on short-term (5-year) tillage field experiment. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), and rotary tillage with crop residue removed as control (RTO). The results indicated that soil organic carbon, total nitrogen and NH-N contents were increased with CT, RT and NT treatments. Compared with RTO treatment, the copies number of , and in paddy soil with CT, RT and NT treatments were significantly increased. The principal coordinate analysis indicated that tillage management and crop residue returning management were the most and the second important factors for the change of denitrifying bacteria community, respectively. Meanwhile, this study indicated that activity and community composition of denitrifiers with CT, RT and NT treatments were increased, compared with RTO treatment. This result showed that , and -type denitrifiers communities in crop residue applied soil had higher species diversity compared with crop residue removed soil, and denitrifying bacteria community composition were dominated by , , and . Therefore, it is a beneficial practice to increase soil PDR level, abundance and community composition of nitrogen-functional soil microorganism by combined application of tillage with crop residue management.
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http://dx.doi.org/10.4014/jmb.2007.07012DOI Listing
November 2020

Effects of short-term manure nitrogen input on soil microbial community structure and diversity in a double-cropping paddy field of southern China.

Sci Rep 2020 08 11;10(1):13540. Epub 2020 Aug 11.

Hunan Soil and Fertilizer Institute, Changsha, 410125, People's Republic of China.

The soil physicochemical properties and soil microbial communities were affected by different fertilizer management. Fertilizer regime were closely relative to the soil texture and nutrient status in a double-cropping paddy field of southern China. However, there was limited information about the influence of different manure nitrogen (N) input on soil microbial communities in a double-cropping rice (Oryza sativa L.) field. Therefore, the short-term different manure N input rate management on soil bacterial and fungal diversity in a double-cropping paddy field of southern China were studied by using Illumina sequencing and quantitative real-time polymerase chain reaction technology in the present paper. The filed experiment were including 100% N of chemical fertilizer (M0), 30% N of organic manure and 70% N of chemical fertilizer (M30), 50% N of organic manure and 50% N of chemical fertilizer (M50), 100% N of organic manure (M100), and without N fertilizer input as control (CK). The results showed that diversity indices of soil microbial communities with application of organic manure and chemical N fertilizer treatments were higher than that of CK treatment. Application of organic manure and chemical N fertilizer management increase soil bacterial abundance of the phylum Actinobacteria, Proteobacteria and Gammaproteobacteria, and soil fungi abundance of the phylum Basidiomycota and Zygomycota were also increased. Compared with CK treatment, the value of Richness, Shannon and McIntosh indices, and taxonomic diversity were increased with M30, M50 and M100 treatments. This finding demonstrated that M30, M50 and M100 treatments modify soil bacterial and fungal diversity. Therefore, the combined application of organic manure and chemical fertilizer N management could significantly increase the abundance of profitable functional bacteria and fungi species in a double-cropping rice field of southern China.
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http://dx.doi.org/10.1038/s41598-020-70612-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419555PMC
August 2020

Functional diversity of rhizosphere soil microbial communities in response to different tillage and crop residue retention in a double-cropping rice field.

PLoS One 2020 21;15(5):e0233642. Epub 2020 May 21.

Hunan Soil and Fertilizer Institute, Changsha, China.

Microbial community functional diversity is a sensitive indicator of soil quality, soil management such as tillage and crop residue which can affect the microbial community functional diversity of paddy field. However, there is still limited information about the influence of different tillage and crop residue management on rhizosphere soil microbial community functional diversity in a double-cropping rice (Oryza sativa L.) field. Therefore, four tillage treatments were set up in paddy field, tillage treatments were included: conventional tillage with residue incorporation (CT), rotary tillage with residue incorporation (RT), no-tillage with residue retention (NT), and rotary tillage with residue removed as control (RTO). And the effects of CT, RT, NT, and RTO treatments on the average well color development (AWCD), genetic diversity indices and carbon source utilization of rhizosphere soil were studied in the present paper. The results showed that the values of AWCD with CT, RT and NT treatments were higher than that of RTO treatment. It was implied that application of crop residue management resulted in the variation of the carbon utilization efficiency of rhizosphere soil microbial communities. At maturity stages of early and late rice, the Richness indices, Shannon indices and McIntosh indices with CT treatment were significantly higher than that of RTO treatment, and with the order as CT>RT>NT>RTO. Principal component analysis (PCA) results indicated that there were significant differences in carbon substrate utilization patterns among different tillage treatments. Carbohydrates and amino acids were the main carbon resources utilized by rhizosphere soil microbes. Therefore, the combined application of tillage with crop residue management could significantly increase the rhizosphere soil microbial community functional diversity in the double-cropping paddy field of southern China.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0233642PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241825PMC
August 2020

Microbial carbon source utilization in rice rhizosphere and nonrhizosphere soils with short-term manure N input rate in paddy field.

Sci Rep 2020 04 16;10(1):6487. Epub 2020 Apr 16.

Hunan Soil and Fertilizer Institute, Changsha, 410125, P. R. China.

Carbon (C) plays a vital role in regulating soil nutrient cycling and increasing soil microbial community, but there is still limited information on how C source utilization characteristics responds to soil physical and chemical properties changes under double-cropping rice (Oryza sativa L.) paddy field in southern China. Therefore, the effects of different short-term manure nitrogen (N) input rate managements on C source utilization characteristics in rice rhizosphere and non-rhizosphere soils under double-cropping rice field in southern China were studied by using O-HO method. Therefore, a field experiment were established in Ningxiang city of Hunan Province, and five different fertilizer treatments were applied: (1) 100% N of chemical fertilizer (M0), (2) 30% N of organic manure and 70% N of chemical fertilizer (M30), (3) 50% N of organic manure and 50% N of chemical fertilizer (M50), (4) 100% N of organic manure (M100), and (5) without N fertilizer input as control (CK). The results showed that soil microbial biomass C content, soil microbial growth rate, and soil microbial basal respiration with application of organic manure treatments (M30, M50, M100) were significantly higher (p < 0.05) than that of CK treatment. And the soil C utilization efficiency with M0 treatment were significantly higher (p < 0.05) than that of M100 treatment. Compared with CK and M0 treatments, the metabolic capacity of soil microorganisms to exogenous C sources with M30, M50 and M100 treatments were increased. The largest types of exogenous C source was carboxylic acids, followed by amino acid and carbohydrate, and complex compounds was the smallest. The RDA analysis results indicated that fertilizer treatments significantly changed the utilization characteristics of soil microorganisms to exogenous C sources. As a result, this study found that characteristics of soil C source utilization were significantly affected by different short-term manure N input rate managements.
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http://dx.doi.org/10.1038/s41598-020-63639-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162909PMC
April 2020

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.

Neuron 2019 07 3;103(2):217-234.e4. Epub 2019 Jun 3.

Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, 08025 Barcelona, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain.

Synapses are fundamental information-processing units of the brain, and synaptic dysregulation is central to many brain disorders ("synaptopathies"). However, systematic annotation of synaptic genes and ontology of synaptic processes are currently lacking. We established SynGO, an interactive knowledge base that accumulates available research about synapse biology using Gene Ontology (GO) annotations to novel ontology terms: 87 synaptic locations and 179 synaptic processes. SynGO annotations are exclusively based on published, expert-curated evidence. Using 2,922 annotations for 1,112 genes, we show that synaptic genes are exceptionally well conserved and less tolerant to mutations than other genes. Many SynGO terms are significantly overrepresented among gene variations associated with intelligence, educational attainment, ADHD, autism, and bipolar disorder and among de novo variants associated with neurodevelopmental disorders, including schizophrenia. SynGO is a public, universal reference for synapse research and an online analysis platform for interpretation of large-scale -omics data (https://syngoportal.org and http://geneontology.org).
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http://dx.doi.org/10.1016/j.neuron.2019.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764089PMC
July 2019

Utilization of carbon sources in the rice rhizosphere and nonrhizosphere soils with different long-term fertilization management.

J Basic Microbiol 2019 Jun 25;59(6):621-631. Epub 2019 Apr 25.

Farming Ecology, Hunan Academy of Agricultural Sciences, Institute of Soil and Fertilizer, Changsha, China.

Carbon (C) plays an important role in the interaction between plant and rhizosphere microbial communities, but there is still limited information about how C source utilization soil microbial structure responds to soil fertility changes under the double-cropping rice (Oryza sativa L.) system in Southern China paddy fields. Therefore, the effects of long-term (33 years) fertilizer regimes on the characteristics of C utilization in both rhizosphere and nonrhizosphere soils under double-cropping rice fields in Southern China were investigated by using the metagenome sequencing technology. The experiment began in 1986, and included five fertilizer treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic matter, and 70% chemical fertilizer (LOM), and 60% organic matter and 40% chemical fertilizer (HOM). The results showed that the relative abundance of Gemmatimonadetes and Planctomycetia in both the rhizosphere and nonrhizosphere soils was increased by application of rice straw residue and organic manure, whereas the relative abundance of Gammaproteobacteria and Nitrospira was promoted by application of inorganic fertilizers. The largest group of clusters of orthologous groups of proteins categories was "amino acid transport and metabolism" with 16.46% unigenes, followed by "general function prediction only" (12.23%). Regarding the gene ontology categories, biological process were the largest category (174 949, 46.40%), followed by cellular component (126 766, 33.62%), and molecular function (110 353, 29.26%). The principal coordinate analysis indicated that different parts of the root zone were the most important factors affecting the variation of C source utilization bacteria community, and the different fertilizer treatments were the second important factor affecting the variation of C source utilization bacteria community. As a result, the application of fertilization practices had significant effects on the abundance and community composition of C source utilization microbes in paddy soils. The results showed that the combined application of rice straw residue or organic manure with chemical fertilizer practices significantly increases the C source utilization of soil microorganisms in double-cropping rice fields.
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http://dx.doi.org/10.1002/jobm.201800736DOI Listing
June 2019

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life.

Nucleic Acids Res 2019 01;47(D1):D271-D279

Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA.

A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these 'fossil genomes'. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life. The reconstructed genes are based on the extensive library of over 15 000 gene family trees from the PANTHER database, and are updated on a yearly basis. For each ancestral gene, we assign a stable identifier, and provide additional information designed to facilitate analysis: an inferred name, a reconstructed protein sequence, a set of inferred Gene Ontology (GO) annotations, and a 'proxy gene' for each ancestral gene, defined as the least-diverged descendant of the ancestral gene in a given extant genome. On the Ancestral Genomes website, users can browse the Ancestral Genomes by selecting nodes in a species tree, and can compare an extant genome with any of its reconstructed ancestors to understand how the genome evolved.
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http://dx.doi.org/10.1093/nar/gky1009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323951PMC
January 2019

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.

Bioinformatics 2019 02;35(3):518-520

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.

Summary: TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable to any annotations that have been made to internal nodes of a reference phylogenetic tree. TreeGrafter takes each input query protein sequence, finds the best matching homologous family in a library of pre-calculated, pre-annotated gene trees, and then grafts it to the best location in the tree. It then annotates the sequence by propagating annotations from ancestral nodes in the reference tree. We show that TreeGrafter outperforms subfamily HMM scoring for correctly assigning subfamily membership, and that it produces highly specific annotations of GO terms based on annotated reference phylogenetic trees. This method will be further integrated into InterProScan, enabling an even broader user community.

Availability And Implementation: TreeGrafter is freely available on the web at https://github.com/pantherdb/TreeGrafter, including as a Docker image.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361231PMC
February 2019

Effects of long-term fertilization practices on heavy metal cadmium accumulation in the surface soil and rice plants of double-cropping rice system in Southern China.

Environ Sci Pollut Res Int 2018 Jul 8;25(20):19836-19844. Epub 2018 May 8.

Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, Hunan, China.

Fertilizer regime is playing an important role in heavy metal cadmium (Cd) accumulation in paddy soils and crop plant. It is necessary to assess the Cd accumulation in soils and rice (Oryza sativa L.) plants under long-term fertilization managements, and the results which help to assess the environmental and food risk in Southern China. However, the effects of different organic manure and chemical fertilizers on Cd accumulation in soils and rice plant remain unclear under intensively cultivated rice conditions. Therefore, the objective was to explore Cd accumulation in paddy soils and rice plant at mature stage under different long-term fertilization managements in the double-cropping rice system. Cd accumulation in the surface soils (0-20 cm) and rice plant with chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic matter and 70% chemical fertilizer (LOM), 60% organic matter and 40% chemical fertilizer (HOM), and without fertilizer input (CK) basis on 32 years long-term fertilization experiment were analyzed. The results showed that the soil total Cd content was increased by 0.296 and 0.351 mg kg and 0.261 and 0.340 mg kg under LOM and HOM treatments at early and late rice mature stages, respectively, compared with the CK treatment. And the soil available Cd content was increased by 0.073 and 0.137 mg kg and 0.102 and 0.160 mg kg under LOM and HOM treatments at early and late rice mature stages, respectively, compared with the CK treatment. The bioconcentration factor of Cd across different parts of rice plant was the highest in root, followed by stem and grain, and the lowest in leaves. At early and late rice mature stages, the root Cd concentration of rice plant was increased by 0.689 and 0.608 mg kg with HOM treatment, the stem Cd concentration of rice plant was increased by 0.666 and 0.758 mg kg with RF treatment, and the leaf and grain Cd concentration of rice plant was increased 0.094 and 0.082 mg kg and 0.086 and 0.083 mg kg with LOM treatment, respectively, compared with the CK treatment. The soil Cd single-factor contaminant index (P) under different fertilization treatments was as the following HOM > LOM > RF > MF > CK. Meanwhile, the P with LOM and HOM treatments was higher than that of the MF, RF, and CK treatments, but there is no significant difference between that of MF and RF treatments. Therefore, long-term application of rice straw residue and chemical fertilizer had no obvious effect on the accumulation of Cd in paddy soils and grain, and soil Cd accumulation was increased as application of organic fertilizer.
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http://dx.doi.org/10.1007/s11356-018-2175-zDOI Listing
July 2018

Impact of long-term fertilization practices on the soil aggregation and humic substances under double-cropped rice fields.

Environ Sci Pollut Res Int 2018 Apr 6;25(11):11034-11044. Epub 2018 Feb 6.

Hunan Soil and Fertilizer Institute, Changsha, 410125, People's Republic of China.

Soil organic matter (SOM) content and soil aggregation are essential components of soil structure, which plays an important role in soil quality and fertility. Also, the SOM content, aggregation, and humus substances in paddy field were affected by application of fertilization practices. However, there is still limited information about the effects of long-term different fertilization practices on soil aggregation and carbon content in the humic acid (C-HAF), fulvic acid (C-FAF), and humin (C-HUM) fractions under double-cropping rice (Oryza sativa L.) system in Southern China paddy fields. Therefore, the effects of long-term fertilizer application on soil aggregation and C-HUM, C-HAF, and C-FAF contents in 0-5-, 5-10-, and 10-20-cm soil depth under double-cropped rice fields in Southern China were investigated. The experiment located at NingXiang County in Hunan Province, China begins in 1986 and the experiment includes five treatments: without fertilizer input (CK), mineral fertilizer alone (MF), rice straw residues and mineral fertilizer (RF), 30% organic matter and 70% mineral fertilizer (LOM), and 60% organic matter and 40% mineral fertilizer (HOM). The results showed that the soil total organic carbon content in paddy soils with RF, LOM, and HOM treatments was significant higher (P < 0.05) than that of the CK treatment at early and late rice maturity stages. The different sizes of soil aggregates with different fertilization treatments were decreased as HOM > LOM > RF > MF > CK. The HOM treatment had the highest percentage of soil aggregates in each size class and the CK treatment had the lowest percentage of soil aggregates in each size class in 0-5-, 5-10-, and 10-20-cm soil depth at early and late rice maturity stages. The soil C-HAF, C-FAF, and C-HUM contents were increased by long-term combined application of manure with mineral fertilizer practices. Meanwhile, the results indicated that the soil C-HAF, C-FAF, and C-HUM contents with RF, LOM, and HOM treatments were significantly higher (P < 0.05) than that of the CK treatment at early and late rice maturity stages. As a result, the soil total organic carbon content, each size class of soil aggregates, and soil C-HAF, C-FAF, and C-HUM contents were increased by long-term combined application of manure with mineral fertilizer in double-cropped rice fields.
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http://dx.doi.org/10.1007/s11356-018-1365-zDOI Listing
April 2018

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

Nucleic Acids Res 2017 01 29;45(D1):D183-D189. Epub 2016 Nov 29.

Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA

The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools. Protein subfamily functional classifications have more than doubled due to progress of the Gene Ontology Phylogenetic Annotation Project. For human genes (as well as a few other organisms), PANTHER now also supports enrichment analysis using pathway classifications from the Reactome resource. The gene list enrichment tools include a new 'hierarchical view' of results, enabling users to leverage the structure of the classifications/ontologies; the tools also allow users to upload genetic variant data directly, rather than requiring prior conversion to a gene list. The updated coding single-nucleotide polymorphisms (SNP) scoring tool uses an improved algorithm. The hidden Markov model (HMM) search tools now use HMMER3, dramatically reducing search times and improving accuracy of E-value statistics. Finally, the PANTHER Tree-Attribute Viewer has been implemented in JavaScript, with new views for exploring protein sequence evolution.
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http://dx.doi.org/10.1093/nar/gkw1138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210595PMC
January 2017

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation.

Genetics 2016 06;203(2):635-47

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90033

As personal genome sequencing becomes a reality, understanding the effects of genetic variants on phenotype-particularly the impact of germline variants on disease risk and the impact of somatic variants on cancer development and treatment-continues to increase in importance. Because of their clear potential for affecting phenotype, nonsynonymous genetic variants (variants that cause a change in the amino acid sequence of a protein encoded by a gene) have long been the target of efforts to predict the effects of genetic variation. Whole-genome sequencing is identifying large numbers of nonsynonymous variants in each genome, intensifying the need for computational methods that accurately predict which of these are likely to impact disease phenotypes. This review focuses on nonsynonymous variant prediction with two aims in mind: (1) to review the prioritization methods that have been developed to date and the principles on which they are based and (2) to discuss the challenges to further improving these methods.
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http://dx.doi.org/10.1534/genetics.116.190033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896183PMC
June 2016

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation.

Bioinformatics 2016 07 18;32(14):2230-2. Epub 2016 May 18.

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.

Unlabelled: PANTHER-PSEP is a new software tool for predicting non-synonymous genetic variants that may play a causal role in human disease. Several previous variant pathogenicity prediction methods have been proposed that quantify evolutionary conservation among homologous proteins from different organisms. PANTHER-PSEP employs a related but distinct metric based on 'evolutionary preservation': homologous proteins are used to reconstruct the likely sequences of ancestral proteins at nodes in a phylogenetic tree, and the history of each amino acid can be traced back in time from its current state to estimate how long that state has been preserved in its ancestors. Here, we describe the PSEP tool, and assess its performance on standard benchmarks for distinguishing disease-associated from neutral variation in humans. On these benchmarks, PSEP outperforms not only previous tools that utilize evolutionary conservation, but also several highly used tools that include multiple other sources of information as well. For predicting pathogenic human variants, the trace back of course starts with a human 'reference' protein sequence, but the PSEP tool can also be applied to predicting deleterious or pathogenic variants in reference proteins from any of the ∼100 other species in the PANTHER database.

Availability And Implementation: PANTHER-PSEP is freely available on the web at http://pantherdb.org/tools/csnpScoreForm.jsp Users can also download the command-line based tool at ftp://ftp.pantherdb.org/cSNP_analysis/PSEP/ CONTACT: [email protected]

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btw222DOI Listing
July 2016
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