New Phytol , IF:8.512 , 2021 Feb , V229 (4) : P2324-2338 doi: 10.1111/nph.16997
The land plant-specific MIXTA-MYB lineage is implicated in the early evolution of the plant cuticle and the colonization of land.
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.; Genetics and Genomics of Plants, Center for Biotechnology & Faculty of Biology, Bielefeld University, Bielefeld, 33615, Germany.; Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Universitatsstrasse, Bochum, 44801, Germany.; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430047, China.
The evolution of a lipid-based cuticle on aerial plant surfaces that protects against dehydration is considered a fundamental innovation in the colonization of the land by the green plants. However, key evolutionary steps in the early regulation of cuticle synthesis are still poorly understood, owing to limited studies in early-diverging land plant lineages. Here, we characterize a land plant specific subgroup 9 R2R3 MYB transcription factor MpSBG9, in the early-diverging land plant model Marchantia polymorpha, that is homologous to MIXTA proteins in vascular plants. The MpSBG9 functions as a key regulator of cuticle biosynthesis by preferentially regulating expression of orthologous genes for cutin formation, but not wax biosynthesis genes. The MpSBG9 also promotes the formation of papillate cells on the adaxial surface of M. polymorpha, which is consisitent with its canonical role in vascular plants. Our observations imply conserved MYB transcriptional regulation in the control of the cutin biosynthesis pathway as a core genetic network in the common ancestor of all land plants, implicating the land plant-specific MIXTA MYB lineage in the early origin and evolution of the cuticle.
PMID: 33051877
Sci Total Environ , IF:6.551 , 2021 Feb , V757 : P143786 doi: 10.1016/j.scitotenv.2020.143786
Changes in soil organic carbon status and microbial community structure following biogas slurry application in a wheat-rice rotation.
College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Sustainable Agriculture Sciences, North Wyke, Rothamsted Research, Okehampton EX20 2SB, UK.; College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.; Sustainable Agriculture Sciences, North Wyke, Rothamsted Research, Okehampton EX20 2SB, UK.; COFCO Meat (Jiangsu) Co., Ltd., Dongtai 224200, China.; College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China. Electronic address: jghan.njfu@outlook.com.
Biogas slurry is widely used as a crop fertilizer due to its available nitrogen content. However, it remains unclear how biogas slurry application affects soil organic carbon (SOC) status and soil microbial community under typical agricultural systems. Here, under a wheat-rice field experiment, we examined the responses of SOC and soil bacterial and fungal communities to biogas slurry application, both with (BSS) and without (BS) straw return, relative to chemical nitrogen fertilizer with (CFS) and without (CF) straw return. The BS treatment significantly increased total organic carbon (TOC) at all soil depths (0-60 cm), compared to CF. Greater TOC occurred at 20-40 cm depth under BSS relative to all other treatments. However, straw return had no impact on soil TOC content under the CF and CFS treatments. Labile organic carbon (LOC) in the topsoil and recalcitrant organic carbon (ROC) at 20-60 cm depth was significantly greater under BS relative to CF. The bacterial class Gammaproteobacteria and family Hyphomicrobiaceae were found to be specifically abundant under biogas slurry application after one year of wheat-rice double cropping. Network analyses showed that the soil bacterial community under biogas slurry application was more complex than under chemical fertilizer application, while the opposite was true for the fungal community. Correlations between network modules and the SOC fractions indicated that biogas slurry application stimulated soil bacteria and fungi to participate in SOC cycling. The module functionality supports our speculation that soil microorganisms degraded the biogas slurry derived-ROC in the topsoil. Overall, we conclude that substitution of chemical fertilizer with biogas slurry can be beneficial for increasing SOC stocks and, in systems with straw return, enhancing straw decomposition.
PMID: 33223165
Epilepsia , IF:6.04 , 2021 Feb , V62 (2) : P492-503 doi: 10.1111/epi.16811
Interictal electroencephalographic functional network topology in drug-resistant and well-controlled idiopathic generalized epilepsy.
Department of Neurology, Manchester Centre for Clinical Neurosciences, Salford, UK.; Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine, and Health, School of Biological Sciences, University of Manchester, Manchester, UK.; Manchester Academic Health Sciences Centre, Manchester, UK.; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.; Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.
OBJECTIVE: The study aim was to compare interictal encephalographic (EEG) functional network topology between people with well-controlled idiopathic generalized epilepsy (WC-IGE) and drug-resistant IGE (DR-IGE). METHODS: Nineteen participants with WC-IGE, 18 with DR-IGE, and 20 controls underwent a resting state, 64-channel EEG. An artifact-free epoch was bandpass filtered into the frequency range of high and low extended alpha. Weighted functional connectivity matrices were calculated. Mean degree, degree distribution variance, characteristic path length (L), clustering coefficient, small world index (SWI), and betweenness centrality were measured. A Kruskal-Wallis H-test assessed effects across groups. Where significant differences were found, Bonferroni-corrected Mann-Whitney pairwise comparisons were calculated. RESULTS: In the low alpha band (6-9 Hz), there was a significant difference in L at the three-group level (p < .0001). This was lower in controls than both WC-IGE and DR-IGE (p < .0001 for both), with no difference in L between WC-IGE and DR-IGE. Mean degree (p = .031), degree distribution variance (p = .032), and SWI (p = .023) differed across the three groups in the high alpha band (10-12 Hz). Mean degree and degree distribution variance were lower in WC-IGE than controls (p = .029 for both), and SWI was higher in WC-IGE compared with controls (p = .038), with no differences in other pairwise comparisons. SIGNIFICANCE: IGE network topology is more regular in the low alpha frequency band, potentially reflecting a more vulnerable structure. WC-IGE network topology is different from controls in the high alpha band. This may reflect drug-induced network changes that have stabilized the WC-IGE network by rendering it less likely to synchronize. These results are of potential importance in advancing the understanding of mechanisms of epilepsy drug resistance and as a possible basis for a biomarker of DR-IGE.
PMID: 33501642
Mol Ecol , IF:5.163 , 2021 Feb , V30 (4) : P926-937 doi: 10.1111/mec.15773
Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.
State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.; Gladstone Institute, University of California, San Francisco, CA, USA.; Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon degradation, especially the old, chemically recalcitrant carbon. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect carbon stability of tundra. In a 2-year winter soil warming experiment of 2 degrees C by snow fences, we investigated responses of fungal communities to warming in the active layer of an Alaskan tundra. Although fungal community composition, revealed by the 28S rRNA gene amplicon sequencing, remained unchanged (p > .05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (p < .05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (canonical correlation analysis, p < .05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase and vanillin dehydrogenase significantly increased (p < .05), indicating higher carbon degradation capacities of fungal communities under warming. Accordingly, we detected changes in fungal gene networks under warming, including higher average path distance, lower average clustering coefficient and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study reveals higher carbon degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on tundra ecosystem respiration, and consequently future carbon stability of high-latitude tundra.
PMID: 33305411
J Transl Med , IF:4.124 , 2021 Feb , V19 (1) : P49 doi: 10.1186/s12967-021-02716-6
The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis.
Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China.; Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Vascular Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China. yuehongzheng@yahoo.com.
BACKGROUND: Thoracic aortic aneurysm (TAA) can be life-threatening due to the progressive weakening and dilatation of the aortic wall. Once the aortic wall has ruptured, no effective pharmaceutical therapies are available. However, studies on TAA at the gene expression level are limited. Our study aimed to identify the driver genes and critical pathways of TAA through gene coexpression networks. METHODS: We analyzed the genetic data of TAA patients from a public database by weighted gene coexpression network analysis (WGCNA). Modules with clinical significance were identified, and the differentially expressed genes (DEGs) were intersected with the genes in these modules. Gene Ontology and pathway enrichment analyses were performed. Finally, hub genes that might be driving factors of TAA were identified. Furthermore, we evaluated the diagnostic accuracy of these genes and analyzed the composition of immune cells using the CIBERSORT algorithm. RESULTS: We identified 256 DEGs and two modules with clinical significance. The immune response, including leukocyte adhesion, mononuclear cell proliferation and T cell activation, was identified by functional enrichment analysis. CX3CR1, C3, and C3AR1 were the top 3 hub genes in the module correlated with TAA, and the areas under the curve (AUCs) by receiver operating characteristic (ROC) analysis of all the hub genes exceeded 0.7. Finally, we found that the proportions of infiltrating immune cells in TAA and normal tissues were different, especially in terms of macrophages and natural killer (NK) cells. CONCLUSION: Chemotaxis and the complement system were identified as crucial pathways in TAA, and macrophages with interactive immune cells may regulate this pathological process.
PMID: 33531038
Genes (Basel) , IF:3.759 , 2021 Feb , V12 (2) doi: 10.3390/genes12020216
The Genetics of Sudden Infant Death Syndrome-Towards a Gene Reference Resource.
Department of Biology, Lund University, 22362 Lund, Sweden.; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.; Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Sudden infant death syndrome (SIDS) is the unexpected death of an infant under one year of age that remains unexplained after a thorough investigation. Despite SIDS remaining a diagnosis of exclusion with an unexplained etiology, it is widely accepted that SIDS can be caused by environmental and/or biological factors, with multiple underlying candidate genes. However, the lack of biomarkers raises questions as to why genetic studies on SIDS to date are unable to provide a clearer understanding of the disease etiology. We sought to improve the identification of SIDS-associated genes by reviewing the SIDS genetic literature and objectively categorizing and scoring the reported genes based on the strength of evidence (from C1 (high) to C5 (low)). This was followed by analyses of function, associations between genes, the enrichment of gene ontology (GO) terms, and pathways and gender difference in tissue gene expression. We constructed a curated database for SIDS gene candidates consisting of 109 genes, 14 of which received a category 4 (C4) and 95 genes received the lowest category of C5. That none of the genes was classified into the higher categories indicates the low level of supporting evidence. We found that genes of both scoring categories show distinct networks and are highly diverse in function and involved in many GO terms and pathways, in agreement with the perception of SIDS as a heterogeneous syndrome. Genes of both scoring categories are part of the cardiac system, muscle, and ion channels, whereas immune-related functions showed enrichment for C4 genes. A limited association was found with neural development. Overall, inconsistent reports and missing metadata contribute to the ambiguity of genetic studies. Considering those parameters could help improve the identification of at-risk SIDS genes. However, the field is still far from offering a full-pledged genetic test to identify at-risk infants and is still hampered with methodological challenges and misunderstandings of the vulnerabilities of vital biological mechanisms.
PMID: 33540853
FEMS Microbiol Ecol , IF:3.675 , 2021 Feb , V97 (2) doi: 10.1093/femsec/fiaa222
Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant - microbiome - soil continuum.
Soils and Soil Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75 st., Athens 11855, Greece.; Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
Mutualistic relationships of legume plants with, either bacteria (like rhizobia) or fungi (like arbuscular mycorrhizal fungi), have been investigated intensively, usually as bi-partite interactions. However, diverse symbiotic interactions take place simultaneously or sequentially under field conditions. Their collective, but not additive, contribution to plant growth and performance remains hard to predict, and appears to be furthermore affected by crop species and genotype, non-symbiotic microbial interactions and environmental variables. The challenge is: (i) to unravel the complex overlapping mechanisms that operate between the microbial symbionts as well as between them, their hosts and the rhizosphere (ii) to understand the dynamics of the respective mechanisms in evolutionary and ecological terms. The target for agriculture, food security and the environment, is to use this insight as a solid basis for developing new integrated technologies, practices and strategies for the efficient use of beneficial microbes in legumes and other plants. We review recent advances in our understanding of the symbiotic interactions in legumes roots brought about with the aid of molecular and bioinformatics tools. We go through single symbiont-host interactions, proceed to tripartite symbiont-host interactions, appraise interactions of symbiotic and associative microbiomes with plants in the root-rhizoplane-soil continuum of habitats and end up by examining attempts to validate community ecology principles in the legume-microbe-soil biosystem.
PMID: 33155054
BMC Genomics , IF:3.594 , 2021 Jan , V22 (1) : P93 doi: 10.1186/s12864-021-07406-7
Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa.
College of Life Sciences, Huzhou University, NO.1 Xueshi Road, Huzhou, 313000, P.R. China.; Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.; College of Life and Environmental Sciences, Hangzhou Normal University, Xuelin Street 16#, Xiasha, Hangzhou, 310036, P. R. China. mengyijun@zju.edu.cn.; College of Life Sciences, Huzhou University, NO.1 Xueshi Road, Huzhou, 313000, P.R. China. shaocg@zjhu.edu.cn.
BACKGROUND: The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network. RESULTS: In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development. CONCLUSIONS: These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.
PMID: 33516199
Plant Mol Biol , IF:3.302 , 2021 Feb doi: 10.1007/s11103-021-01121-3
Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice.
Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, 330045, Jiangxi Province, China.; Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang City, 330045, Jiangxi Province, China.; Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, Hunan Province, China.; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, 330045, Jiangxi Province, China. yjhuang_cn@126.com.; Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang City, 330045, Jiangxi Province, China. yjhuang_cn@126.com.; Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, Hunan Province, China. yjhuang_cn@126.com.; Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, 330045, Jiangxi Province, China. zhaohai_wang@163.com.; Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang City, 330045, Jiangxi Province, China. zhaohai_wang@163.com.; Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, Hunan Province, China. zhaohai_wang@163.com.
KEY MESSAGE: This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation-reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.
PMID: 33569692
Plant Mol Biol , IF:3.302 , 2021 Feb doi: 10.1007/s11103-021-01122-2
Comparative transcriptome analyses between cultivated and wild grapes reveal conservation of expressed genes but extensive rewiring of co-expression networks.
Embrapa Uva e Vinho (Brazilian Agricultural Research Corporation, Grape and Wine Research Center), Rua Livramento, 515, Bento Goncalves, RS, 95701-008, Brazil.; Embrapa Uva e Vinho (Brazilian Agricultural Research Corporation, Grape and Wine Research Center), Rua Livramento, 515, Bento Goncalves, RS, 95701-008, Brazil. vera.quecini@embrapa.br.
KEY MESSAGE: The transcriptomes of wild and cultivated grapes consists of similar expressed genes but distinct wiring of co-expressed modules associated with environmental conditions. Grapevine is an important fruit crop worldwide, with high economic value and widespread distribution. Commercial production is based on Vitis vinifera, and, to a lesser extent, on hybrids with American grapes, such as V. labrusca. Wild grape relatives are important sources of resistance against biotic and abiotic factors; however, their global gene expression patterns remain poorly characterized. We associated genome-wide transcript profiling to phenotypic analyses to investigate the responses of cultivated and wild vines to vineyard conditions. The expressed genes in the Vitis reference transcriptome are largely shared by wild grapes, V. labrusca hybrids and vinifera cultivars. In contrast, significant differential regulation between wild and vinifera genotypes represents 80% of gene expression variation, regardless of the environment. In wild grapes, genes associated to regulatory processes are downregulated, whereas those involved in metabolic pathways are upregulated, in comparison to vinifera. Photosynthesis-related ontologies are overrepresented in the induced genes, in agreement with higher contents of chlorophyll in wild grapes. Co-regulated gene network analyses provide evidence of more complex transcriptome organization in vinifera. In wild grapes, genes involved in signaling pathways of stress-related hormones are overrepresented in modules associated with the environment. Consensus network analyses revealed high preservation within co-regulated gene modules between cultivated and wild grapes, but divergent relationships among the expression clusters. In conclusion, the distinct phenotypes of wild and cultivated grapes are underlain by differences in gene expression, but also by distinct higher-order organization of the transcriptome and contrasting association of co-expressed gene clusters with the environment.
PMID: 33538951
Waste Manag Res , IF:2.771 , 2021 Feb , V39 (2) : P279-290 doi: 10.1177/0734242X20945375
Quantification of geographical proximity of sugarcane bagasse ash sources to ready-mix concrete plants for sustainable waste management and recycling.
Department of Civil Engineering, Birla Institute of Technology and Science Pilani, Hyderabad, India.
As stated in the European Commission's waste framework directive, the geographic proximity of wastes to the potential recovery/disposal site is of paramount importance in attaining an effective resource recycling paradigm. The global interest in achieving an end-of-waste scenario encourages the recovery of useful products/secondary raw materials from locally available waste materials. Sugarcane bagasse ash is an abundantly available waste (44,200 tonnes day(-1)) from sugar plants in India which has the potential to be used as a partial replacement to cement in ready-mix concrete plants. Although pozzolanic performance of sugarcane bagasse ash and its ability in reducing the carbon emissions associated with concrete production have been reported in earlier research studies, its use in concrete is hindered due to the lack of availability and accessibility data. In this study, the geographical distribution of sugar plants and the available quantity of sugarcane bagasse ash in India have been determined. In addition, a detailed network analysis using a geographic information system was conducted to quantify the geographic proximity of bagasse ash, fly ash and slag sources to ready-mix concrete plants. The study results indicate that for most of the ready-mix concrete plants in India, the probability of having a bagasse ash source in proximity is higher than the probability of encountering slag/fly ash sources.
PMID: 32787672
Multivariate Behav Res , IF:2.75 , 2021 Feb : P1-9 doi: 10.1080/00273171.2021.1886897
On Unreplicable Inferences in Psychopathology Symptom Networks and the Importance of Unreliable Parameter Estimates.
Centre for Emotional Health, Department of Psychology, Macquarie University.; Department of Psychology, University of Pittsburgh.; Department of Psychological and Brain Sciences, University of Iowa.; Department of Psychology, University of Minnesota.
We recently wrote an article comparing the conclusions that followed from two different approaches to quantifying the reliability and replicability of psychopathology symptom networks. Two commentaries on the article have raised five core criticisms, which are addressed in this response with supporting evidence. 1) We did not over-generalize about the replicability of symptom networks, but rather focused on interpreting the contradictory conclusions of the two sets of methods we examined. 2) We closely followed established recommendations when estimating and interpreting the networks. 3) We also closely followed the relevant tutorials, and used examples interpreted by experts in the field, to interpret the bootnet and NetworkComparisonTest results. 4) It is possible for statistical control to increase reliability, but that does not appear to be the case here. 5) Distinguishing between statistically significant versus substantive differences makes it clear that the differences between the networks affect the inferences we would make about symptom-level relationships (i.e., the basis of the purported utility of symptom networks). Ultimately, there is an important point of agreement between our article and the commentaries: All of these applied examples of cross-sectional symptom networks are demonstrating unreliable parameter estimates. While the commentaries propose that the resulting differences between networks are not genuine or meaningful because they are not statistically significant, we propose that the unreplicable inferences about the symptom-level relationships of interest fundamentally undermine the utility of the symptom networks.
PMID: 33599559
Br J Math Stat Psychol , IF:2.388 , 2021 Feb , V74 (1) : P34-63 doi: 10.1111/bmsp.12192
Deterministic blockmodelling of signed and two-mode networks: A tutorial with software and psychological examples.
Florida State University, Tallahassee, Florida, USA.; University of Ljubljana, Ljubljana, Slovenia.; Univerity of Pittsburgh, Pittsburgh, Pennsylvania, USA.; University of Missouri, Columbia, Missouri, USA.
Deterministic blockmodelling is a well-established clustering method for both exploratory and confirmatory social network analysis seeking partitions of a set of actors so that actors within each cluster are similar with respect to their patterns of ties to other actors (or, in some cases, other objects when considering two-mode networks). Even though some of the historical foundations for certain types of blockmodelling stem from the psychological literature, applications of deterministic blockmodelling in psychological research are relatively rare. This scarcity is potentially attributable to three factors: a general unfamiliarity with relevant blockmodelling methods and applications; a lack of awareness of the value of partitioning network data for understanding group structures and processes; and the unavailability of such methods on software platforms familiar to most psychological researchers. To tackle the first two items, we provide a tutorial presenting a general framework for blockmodelling and describe two of the most important types of deterministic blockmodelling applications relevant to psychological research: structural balance partitioning and two-mode partitioning based on structural equivalence. To address the third problem, we developed a suite of software programs that are available as both Fortran executable files and compiled Fortran dynamic-link libraries that can be implemented in the R software system. We demonstrate these software programs using networks from the literature.
PMID: 31705539
Front Psychol , 2021 , V12 : P623970 doi: 10.3389/fpsyg.2021.623970
The Network Theory of Psychiatric Disorders: A Critical Assessment of the Inclusion of Environmental Factors.
Department of Philosophy, Radboud University, Nijmegen, Netherlands.; Department of Philosophy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.; Department of Anatomy and Neurosciences, Amsterdam University Medical Centers (Location VUmc), Amsterdam, Netherlands.
Borsboom and colleagues have recently proposed a "network theory" of psychiatric disorders that conceptualizes psychiatric disorders as relatively stable networks of causally interacting symptoms. They have also claimed that the network theory should include non-symptom variables such as environmental factors. How are environmental factors incorporated in the network theory, and what kind of explanations of psychiatric disorders can such an "extended" network theory provide? The aim of this article is to critically examine what explanatory strategies the network theory that includes both symptoms and environmental factors can accommodate. We first analyze how proponents of the network theory conceptualize the relations between symptoms and between symptoms and environmental factors. Their claims suggest that the network theory could provide insight into the causal mechanisms underlying psychiatric disorders. We assess these claims in light of network analysis, Woodward's interventionist theory, and mechanistic explanation, and show that they can only be satisfied with additional assumptions and requirements. Then, we examine their claim that network characteristics may explain the dynamics of psychiatric disorders by means of a topological explanatory strategy. We argue that the network theory could accommodate topological explanations of symptom networks, but we also point out that this poses some difficulties. Finally, we suggest that a multilayer network account of psychiatric disorders might allow for the integration of symptoms and non-symptom factors related to psychiatric disorders and could accommodate both causal/mechanistic and topological explanations.
PMID: 33613399
J Intell , 2021 Feb , V9 (1) doi: 10.3390/jintelligence9010008
Investigating the Structure of Intelligence Using Latent Variable and Psychometric Network Modeling: A Commentary and Reanalysis.
Department of Psychology, Claremont Graduate University, Claremont, CA 91711, USA.; Institute of Psychology, ELTE Eotvos Lorand University, 1064 Budapest, Hungary.
In a recent publication in the Journal of Intelligence, Dennis McFarland mischaracterized previous research using latent variable and psychometric network modeling to investigate the structure of intelligence. Misconceptions presented by McFarland are identified and discussed. We reiterate and clarify the goal of our previous research on network models, which is to improve compatibility between psychological theories and statistical models of intelligence. WAIS-IV data provided by McFarland were reanalyzed using latent variable and psychometric network modeling. The results are consistent with our previous study and show that a latent variable model and a network model both provide an adequate fit to the WAIS-IV. We therefore argue that model preference should be determined by theory compatibility. Theories of intelligence that posit a general mental ability (general intelligence) are compatible with latent variable models. More recent approaches, such as mutualism and process overlap theory, reject the notion of general mental ability and are therefore more compatible with network models, which depict the structure of intelligence as an interconnected network of cognitive processes sampled by a battery of tests. We emphasize the importance of compatibility between theories and models in scientific research on intelligence.
PMID: 33562895