Network analyses reveal the role of large snakes in connecting feeding guilds in a species‐rich Amazonian snake community

Abstract P75 neurotrophic receptor (p75NTR) is an important receptor for the role of neurotrophins in modulating brain plasticity and apoptosis. The current understanding of the role of p75NTR in cellular adaptation following pathological insults remains blurred, which makes p75NTR’s related signaling networks an interesting and challenging initial point of investigation. We identified p75NTR and related genes through extensive data mining of a PubMed literature search including published works related to p75NTR from the past 20 years. Bioinformatic network and pathway analyses of identified genes (n = 235) were performed using ReactomeFIViz in Cytoscape based on the highly reliable Reactome functional interaction network algorithm. This approach merges interactions extracted from human curated pathways with predicted interactions from machine learning. Genome-wide pathway analysis showed total of 16 enriched hierarchical clusters. A total of 278 enriched single pathways were also identified (p < 0.05, false discovery rate corrected). Gene network analyses showed multiple known and new targets in the p75NTR gene network. This study provides a comprehensive analysis and investigation into the current knowledge of p75NTR signaling networks and pathways. These results also identify several genes and their respective protein products as involved in the p75NTR network, which have not previously been clearly studied in this pathway. These results can be used to generate novel hypotheses to gain a greater understanding of p75NTR in acute brain injuries, neurodegenerative diseases and general response to cellular damage.

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Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00290.2016 ◽

2016 ◽

Vol 311 (5) ◽

pp. G964-G973 ◽

Cited By ~ 12

Author(s):

Jagmohan Singh ◽

Ettickan Boopathi ◽

Sankar Addya ◽

Benjamin Phillips ◽

Isidore Rigoutsos ◽

...

Keyword(s):

Smooth Muscle ◽

Anal Sphincter ◽

Internal Anal Sphincter ◽

Smooth Muscles ◽

Smooth Muscle Contractility ◽

Network Analyses ◽

Rhoa Signaling

A comprehensive genomic and proteomic, computational, and physiological approach was employed to examine the (previously unexplored) role of microRNAs (miRNAs) as regulators of internal anal sphincter (IAS) smooth muscle contractile phenotype and basal tone. miRNA profiling, genome-wide expression, validation, and network analyses were employed to assess changes in mRNA and miRNA expression in IAS smooth muscles from young vs. aging rats. Multiple miRNAs, including rno-miR-1, rno-miR-340-5p, rno-miR-185, rno-miR-199a-3p, rno-miR-200c, rno-miR-200b, rno-miR-31, rno-miR-133a, and rno-miR-206, were found to be upregulated in aging IAS. qPCR confirmed the upregulated expression of these miRNAs and downregulation of multiple, predicted targets ( Eln, Col3a1, Col1a1, Zeb2, Myocd, Srf, Smad1, Smad2, Rhoa/Rock2, Fn1, Tagln v2, Klf4, and Acta2) involved in regulation of smooth muscle contractility. Subsequent studies demonstrated an aging-associated increase in the expression of miR-133a, corresponding decreases in RhoA, ROCK2, MYOCD, SRF, and SM22α protein expression, RhoA-signaling, and a decrease in basal and agonist [U-46619 (thromboxane A2analog)]-induced increase in the IAS tone. Moreover, in vitro transfection of miR-133a caused a dose-dependent increase of IAS tone in strips, which was reversed by anti-miR-133a. Last, in vivo perianal injection of anti-miR-133a reversed the loss of IAS tone associated with age. This work establishes the important regulatory effect of miRNA-133a on basal and agonist-stimulated IAS tone. Moreover, reversal of age-associated loss of tone via anti-miR delivery strongly implicates miR dysregulation as a causal factor in the aging-associated decrease in IAS tone and suggests that miR-133a is a feasible therapeutic target in aging-associated rectoanal incontinence.

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Assessment of Different Dimensions of Shame Proneness: Validation of the SHAME

Assessment ◽

10.1177/1073191118820130 ◽

2018 ◽

Vol 27 (8) ◽

pp. 1699-1717 ◽

Cited By ~ 1

Author(s):

Corinna N. Scheel ◽

Hedwig Eisenbarth ◽

Katrin Rentzsch

Keyword(s):

Clinical Sample ◽

Large Body ◽

Factor Analyses ◽

Confirmatory Factor Analyses ◽

Invariance Testing ◽

Network Analyses ◽

Shame Proneness ◽

Confirmatory Factor ◽

Different Dimensions

A large body of research revealed that shame is associated with adaptive and maladaptive correlates. The aim of this work was to validate a new dimensional instrument (SHAME), which was developed to disentangle adaptive and maladaptive dimensions of shame proneness. Confirmatory factor analyses supported the three-factorial structure (bodily, cognitive, and existential shame) in American ( n = 502) and German ( n = 496) community samples, using invariance testing. Bifactor model analyses exhibited distinct associations of adaptive (bodily and cognitive shame) and maladaptive (existential shame) dimensions of shame with psychopathology and social functioning. Network analyses highlighted the role of existential shame in psychopathology, especially for a clinical sample of patients with Borderline Personality Disorder ( n = 92). By placing shame pronenesss into a network of similar and dissimilar constructs, the current findings serve as a foundation for drawing conclusions about the adaptive and maladaptive nature of shame.

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Strange fruit: The rise of Brazils new right-wing and the Non-Partisan School Movement

Journal of Alternative & Community Media ◽

10.1386/joacm_00040_1 ◽

2019 ◽

Vol 4 (1) ◽

pp. 7-22 ◽

Cited By ~ 1

Author(s):

Richard Romancini ◽

Fernanda Castilho

Keyword(s):

Public Sphere ◽

Communication Style ◽

New Right ◽

Right Wing ◽

Left Wing ◽

Network Analyses ◽

Official Discourse ◽

President Elect ◽

School Movement

The new right-wing Brazilian Non-Partisan School Movement (in Portuguese, Escola Sem Partido, or ESP) was created in 2004 to denounce indoctrination in schools. It has, however, had greater repercussions via a strong presence on social media. The objective of this article is to analyse these discussions on Twitter. ESPs official discourse and theoretical discussions about the role of social networks supported this study. The content and network analyses of the tweets reveal the following relevant conclusions: the dissemination of content is much stronger than any discussion, on the part of both the new right wing and the left-wing partisans; there is a predominance of ESP supporters in a discussion that has characteristics of an anti-public sphere; communication between these two groups is weak; and the tone of the content spread by ESP supporters resonates with many features of president-elect Jair Bolsonaros communication style.

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The Contrasting Role of Water and Acid Within Organic Phase Amphiphile Aggregation

10.33774/chemrxiv-2021-cd724-v2 ◽

2021 ◽

Author(s):

Biswajit Sadhu ◽

Aurora E. Clark

Keyword(s):

Self Assembly ◽

Dynamics Simulation ◽

Test Bed ◽

Network Analyses ◽

Liquid Liquid Extraction ◽

Polar Media ◽

Polar Solutes ◽

Local Aggregation ◽

The Individual

Hypothesis: Amphiphile self-assembly in non-polar media is often enhanced by polar co-solutes, as observed upon amphiphile mediated transport of water and acid into organic solution. Such co-extraction precludes understanding the individual roles of polar solutes upon self-assembly. Using this liquid-liquid extraction (LLE) system as a test-bed, we hypothesize that co-solute competition and hydrogen bond (HB) characteristics cause different size/shape distributions of assembled amphiphiles and alter self-assembly mechanisms in non-polar solvents. Experiments: Concentration dependent classical molecular dynamics simulation and intermolecular network analyses identified the correlating relationships between HB properties of H2O and HNO3 upon the aggregation of N,N,N,N-tetraoctyl-3-oxapentanediamide (TODGA), a prevalent LLE amphiphile extractant. Findings: Concentration dependent competition of hydrogen bonding fundamentally impacts amphiphile self-assembly in non-polar media. H2O bridges TODGA and enhances self-assembly, however as [H2O]org increases, preferential self-solvation leads to large (H2O)n clusters that cause TODGA clusters to sorb to the (H2O)n periphery and form extended aggregation. HNO3 restricts the (H2O)n size by disrupting the HB network. At large [H2O]org, HNO3 modulates TODGA self-assembly from extended to local aggregation. We attribute prior experimental observations to the role of water rather than co-extracted HNO3, thus providing valuable new insight into the means by which extractant aggregation can be tuned.

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The cytosolic invertase NI6 affects vegetative growth, flowering, fruit set and yield in tomato

Journal of Experimental Botany ◽

10.1093/jxb/eraa594 ◽

2020 ◽

Author(s):

Carla Coluccio Leskow ◽

Mariana Conte ◽

Talia del Pozo ◽

Luisa Bermúdez ◽

Bruno Silvestre Lira ◽

...

Keyword(s):

Fruit Set ◽

Expression Patterns ◽

Sugar Metabolism ◽

Global Gene Expression ◽

Metabolite Profile ◽

Mesophyll Cells ◽

Network Analyses ◽

Encoding Gene ◽

Delayed Flowering

Abstract Sucrose metabolism is of high importance for most plant species, both as the main source of carbon and via signaling mechanisms that have been proposed for this molecule. Two cleaving enzymes channel sucrose into sink metabolism; sucrose synthases (SUS) and invertases (INV), which are localized in different subcellular compartments. Although acid soluble and insoluble invertases have been largely investigated, studies on the role of neutral invertases (A/N-INV) have lagged behind. Here, we identified a tomato A/N-INV encoding gene (NI6) co-localizing with a previously reported pathway QTL largely affecting primary carbon metabolism in tomato. Of the eight A/N-INV genes identified in the tomato genome, NI6 mRNA is present in all organs, but its expression was higher in sink tissues (mainly roots and fruits). A NI6-GFP fusion protein was found in the cytosol of mesophyll cells. Tomato NI6-silenced plants showed impaired growth phenotypes, delayed flowering and dramatic reduction in the fruit set. Global gene expression and metabolite profile analyses of these plants revealed that NI6 is not only essential for sugar metabolism but also plays a signaling role in stress adaptation. Gene-metabolite network analyses allowed identification of major hubs, whose expression patterns were greatly affected by NI6 silencing, within the signaling cascade that coordinates carbohydrate metabolism with growth and development in tomato.

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“Would You Be My Friend?”: Friendship Selection and Contagion Processes of Early Adolescents Who Experience Victimization

The Journal of Early Adolescence ◽

10.1177/0272431618824753 ◽

2019 ◽

Vol 39 (9) ◽

pp. 1286-1310 ◽

Cited By ~ 2

Author(s):

Christian Berger ◽

Mariola Claudia Gremmen ◽

Diego Palacios ◽

Eduardo Franco

Keyword(s):

Peer Relations ◽

Early Adolescents ◽

Negative Consequences ◽

Network Analyses ◽

Time Period ◽

Prosocial Peers ◽

Social Network Analyses ◽

Over Time ◽

Friendship Selection

Victimization in early adolescence can have severe negative consequences later in life. Friendships are especially important in this time period. The present study investigated friendship selection and influence (contagion) processes with regard to victimization, as well as prosocial and aggressive characteristics of victims’ friends. Using social network analyses (RSiena), we longitudinally analyzed data of five fourth-grade classrooms, including 185 students (56.8% girls; [Formula: see text] age at Time 1 = 10 years old). Results showed that early adolescents who experience peer victimization were not likely to select peers with similar levels of victimization as friends but selected prosocial peers as friends. Moreover, friends did not become more similar over time in their victimization levels. Prosocial students selected similar peers as friends. The discussion highlights the relevance of fostering positive peer relations for targeting victimization and discusses the defending role of friends in victimization situations.

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Comparative Genomics and Functional Studies of Wheat BED-NLR Loci

Genes ◽

10.3390/genes11121406 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1406

Author(s):

Clemence Marchal ◽

Georg Haberer ◽

Manuel Spannagl ◽

Cristobal Uauy ◽

Keyword(s):

Cell Death ◽

Fungal Pathogens ◽

Plant Pathogens ◽

Functional Studies ◽

Network Analyses ◽

Binding Factor ◽

Localization Signal ◽

Integrated Domains ◽

Genomic Regions

Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signal (NLS) in Yr7, Yr5, and the other characterized BED-NLRs. We thus propose that this is a feature of BED-NLRs that confer resistance to plant pathogens. We show that the NLS was functional in truncated versions of the Yr7 protein when expressed in N. benthamiana. We did not observe cell-death upon the overexpression of Yr7 full-length, truncated, and ‘MHD’ variants in N. benthamiana. This suggests that either this system is not suitable to study BED-NLR signaling or that BED-NLRs require additional components to trigger cell death. These results define novel future directions to further understand the role of BED domains in BED-NLR mediated resistance.

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Networked Justice: Judges, the Diffusion of Ideas, and Legal Reform Movements in Mexico

Journal of Latin American Studies ◽

10.1017/s0022216x16001486 ◽

2016 ◽

Vol 48 (4) ◽

pp. 739-768 ◽

Cited By ~ 5

Author(s):

MATTHEW C. INGRAM

Keyword(s):

Rule Of Law ◽

Original Data ◽

Reform Movements ◽

Mixed Methods Design ◽

Causal Inferences ◽

The Rule Of Law ◽

Network Analyses ◽

Mexican State ◽

The Social

AbstractExisting research shows that the ideas of judges shape their behaviour. A natural next question to ask is, where do these ideas come from? Yet, there is little empirical evidence regarding the content and distribution of these ideas and even less evidence regarding the sources of these ideas, especially how ideas transfer or diffuse among judges. In this article, a survey of judges in the Mexican state of Michoacán generates original data on the attitudes and professional ties among these legal elites, and a mixed-methods design examines the diffusion of these attitudes along these ties, sequencing quantitative network analyses and interviews with judges to strengthen causal inferences. The core finding that the social structure of judges influences the attitudes judges hold contributes a valuable analytic complement to scholarship on comparative judicial behaviour, and clarifies our understanding of the role of judicial networks in strengthening democracy and the rule of law.

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Translational profiling of mouse dopaminoceptive neurons reveals a role of PGE2 in dorsal striatum

10.1101/2020.09.02.279240 ◽

2020 ◽

Author(s):

Enrica Montalban ◽

Albert Giralt ◽

Lieng Taing ◽

Yuki Nakamura ◽

Claire Martin ◽

...

Keyword(s):

Prostaglandin E2 ◽

Dopamine Receptor ◽

Expression Patterns ◽

Dorsal Striatum ◽

D1 Receptor ◽

D2 Dopamine Receptor ◽

Neuronal Populations ◽

Network Analyses ◽

Upstream Regulator

ABSTRACTForebrain dopaminoceptive neurons play a key role in movement, action selection, motivation, and working memory. Their activity is dysregulated in addiction, Parkinson’s disease and other conditions. To characterize the diverse dopamine target neuronal populations, we compare translating mRNAs in neurons of dorsal striatum and nucleus accumbens expressing D1 or D2 dopamine receptor and prefrontal cortex expressing D1 receptor. We identify D1/D2 and striatal dorso-ventral differences in the translational and splicing landscapes, which establish the characteristics of dopaminoceptive neurons. Expression differences and network analyses identify novel transcription factors with presumptive roles in these differences. Prostaglandin E2 appears as a candidate upstream regulator in the dorsal striatum, a hypothesis supported by converging functional evidence indicating its role in enhancing D2 dopamine receptor action. Our study provides powerful resources for characterizing dopamine target neurons, new information about striatal gene expression patterns, and reveals the unforeseen role of prostaglandin E2 in the dorsal striatum.

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