scholarly journals DDN2.0: R and Python packages for differential dependency network analysis of biological systems

2021 ◽  
Author(s):  
Bai Zhang ◽  
Yi Fu ◽  
Yingzhou Lu ◽  
Zhen Zhang ◽  
Robert Clarke ◽  
...  
Keyword(s):  
Network Analysis ◽  
Software Tool ◽  
Data Driven ◽  
Experimental Conditions ◽  
Dependency Networks ◽  
Disease Biology ◽  
Dependency Network ◽  
The Common ◽  
Key Pathways ◽  
Molecular Circuitry

Data-driven differential dependency network analysis identifies in a complex and often unknown overall molecular circuitry a network of differentially connected molecular entities (pairwise selective coupling or uncoupling depending on the specific phenotypes or experimental conditions). Such differential dependency networks are typically used to assist in the inference of potential key pathways. Based on our previously developed Differential Dependency Network (DDN) method, we report here the fully implemented R and Python software tool packages for public use. The DDN algorithm uses a fused Lasso model and block-wise coordinate descent to estimate both the common and differential edges of dependency networks. The identified DDN can help to provide plausible interpretation of data, gain new insight of disease biology, and generate novel hypotheses for further validation and investigations.

scholarly journals The hourglass effect in hierarchical dependency networks

2017 ◽  
Vol 5 (4) ◽  
pp. 490-528 ◽  
Author(s):  
KAESER M. SABRIN ◽  
CONSTANTINE DOVROLIS
Keyword(s):  
Low Complexity ◽  
Core Size ◽  
Original Network ◽  
Hierarchical Network ◽  
Modular Systems ◽  
The Core ◽  
Dependency Networks ◽  
Dependency Network ◽  
Hierarchical Dependency ◽  
Almost All

AbstractMany hierarchically modular systems are structured in a way that resembles an hourglass. This “hourglass effect” means that the system generates many outputs from many inputs through a relatively small number of intermediate modules that are critical for the operation of the entire system, referred to as the waist of the hourglass. We investigate the hourglass effect in general, not necessarily layered, hierarchical dependency networks. Our analysis focuses on the number of source-to-target dependency paths that traverse each vertex, and it identifies the core of a dependency network as the smallest set of vertices that collectively cover almost all dependency paths. We then examine if a given network exhibits the hourglass property or not, comparing its core size with a “flat” (i.e., non-hierarchical) network that preserves the source dependencies of each target in the original network. As a possible explanation for the hourglass effect, we propose the Reuse Preference model that captures the bias of new modules to reuse intermediate modules of similar complexity instead of connecting directly to sources or low complexity modules. We have applied the proposed framework in a diverse set of dependency networks from technological, natural, and information systems, showing that all these networks exhibit the general hourglass property but to a varying degree and with different waist characteristics.

Regulation of matrix turnover: fibroblasts, forces, factors and fibrosis

2007 ◽  
Vol 35 (4) ◽  
pp. 647-651 ◽  
Author(s):  
G.J. Laurent ◽  
R.C. Chambers ◽  
M.R. Hill ◽  
R.J. McAnulty
Keyword(s):  
Cell Phenotype ◽  
Gene Interactions ◽  
Internal Organs ◽  
Matrix Deposition ◽  
Molecular Events ◽  
The Common ◽  
Extracellular Molecules ◽  
Altered Cell ◽  
Key Pathways ◽  
Circulating Fibrocytes

Fibroblasts are multifunctional cells that are responsible for matrix homoeostasis, continuously synthesizing and degrading a diverse group of extracellular molecules and their receptors. Rates of turnover of matrix molecules and the proteases that degrade them are normally under the control of diverse chemical and mechanical cues, with cytokines, growth factors, proteases, lipid mediators and mechanical forces playing roles. The maintenance of this homoeostasis is vital to the preservation of normal tissue function and is clearly lost in chronic diseases of the joints, skin and internal organs where destruction and excessive deposition is seen. Current research is focusing on defining the key pathways of activation either in resident fibroblasts, matrix-producing cells derived from circulating fibrocytes, or from transdifferentiation of resident cells. The common downstream signalling pathways are also being defined, as well as the gene interactions leading to altered cell phenotype. The present article reviews these findings and our current concepts of the key molecular events leading to tissue damage and excessive matrix deposition in tissue fibrosis. These studies are leading to an appreciation of the complexity of events with multiple pathways involved, but, as the facts emerge, we are finding promising new ways to treat fibrosis and halt the inexorable progression that is a feature of so many fibrotic and remodelling disorders.

scholarly journals The life history of Hepatozoon leptodactyli (Lesage, 1908) Pessoa, 1970: a parasite of the common laboratory animal: the frog of the genus Leptodactylus

1973 ◽  
Vol 71 (1-2) ◽  
pp. 1-8 ◽  
Author(s):  
Sylvio Celso Goncalves da Costa ◽  
Samuel B. Pessoa ◽  
Neize de Moura Pereira ◽  
Tania Colombo
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Life History ◽  
Laboratory Animal ◽  
Peripheral Circulation ◽  
Experimental Conditions ◽  
History Of ◽  
The Central Nervous System ◽  
The Common ◽  
Common Laboratory

The main object of the present paper is to furnish a brief account to the knowledgement of Protozoa parasitic in common Brazilian frog of the genus Leptodactylus for general students in Zoology and for investigators that use this frog as a laboratory animal. Hepatozoon leptodactyli (Haemogregarina leptodactyli) was found in two species of frogs - Leptodactylus ocellatus and L. pentadactylus - in which develop schizogony whereas sporogony occurs in the leech Haementeria lutzi as was obtainded in experimental conditions. Intracellular forms have been found in peripheral circulation, chiefly in erythrocytes, but we have found them in leukocytes too. Tissue stages were found in frog, liver, lungs, spleen, gut, brain and heart. The occurence of hemogregarine in the Central Nervous System was recorded by Costa & al,(13) and Ball (2). Some cytochemical methods were employed in attempt to differentiate gametocytes from trophozoites in the peripheral blood and to characterize the cystic membrane as well. The speorogonic cycle was developed in only one specie of leech. A brief description of the parasite is given.

scholarly journals Influence of saprophages (Isopoda, Diplopoda) on leaf litter decomposition under different levels of humidification and chemical loading

2020 ◽  
Vol 28 (4) ◽  
pp. 384-389
Author(s):  
A. P. Pokhylenko ◽  
O. O. Didur ◽  
Y. L. Kulbachko ◽  
L. P. Bandura ◽  
S. A. Chernykh
Keyword(s):  
Leaf Litter ◽  
Litter Decomposition ◽  
Zinc Content ◽  
Leaf Litter Decomposition ◽  
Absolute Difference ◽  
Average Weight ◽  
Chemical Stress ◽  
Experimental Conditions ◽  
The Common ◽  
Different Levels

The paper presents a study about the influence of two saprophage groups (Isopoda, Diplopoda) on leaf litter decomposition under different levels of humidification and chemical stress. Because of their worldwide distribution, we focused on the common pillbug Armadillidium vulgare (Latreille, 1804) (Isopoda, Armadillidiidae), and the common millipede species Rossiulus kessleri (Lohmander, 1927) (Julida, Julidae). The function of environment creation by the given saprophages, as destructors of dead plant matter, supporting such ecosystem services as soil fertility improvement and nutrients’ turnover, is highlighted. To conduct the experiment, the animals were collected manually and using pitfall trapping. In order to bring the experimental conditions closer to the natural, the individuals were not sexed. The maximum consumption of leaf litter by woodlice was recorded in the conditions with adequate moisture (0.5 mL of distilled water per box) and amounted to 2.52 mg/10 individuals per day, which exceeds its consumption with low and increased moisture, respectively, by 1.82 and 1.24 times. As for the effect of interaction, the consumption of maple litter with optimal moisture (4.77 mg/10 individuals per day) was the greatest. The largest absolute difference between broad-leaved tree species in the average weight of leaf litter consumed by woodlice was between maple leaf litter and oak leaf litter, the minimum – between robinia leaf litter and oak leaf litter. According to the results of the obtained data (Diplopoda), it can be stated that there is a statistically significant effect of chemical stress and discrepancy of the average zinc content in the object of study (in Diplopoda and their faecal pellets). We found that the diet provided did not affect the distribution of zinc in Diplopoda under conditions of chemical stress. According to the results of pairwise comparisons, we determined that the zinc content in the Diplopoda clearly differs for control and almost every concentration of zinc sulfate solution – 0.03 and 0.15 g/L, the samples of which do not form a homogeneous group. The species composition, abundance and distribution in space of soil invertebrates are informative indicators which reflect the ecological state of soils, intensity in development of soil horizons as well as intensity of processes occurring in them.

Contralateral coordination and retargeting of limb movements during scratching in the locust

1998 ◽  
Vol 201 (13) ◽  
pp. 2021-2032 ◽  
Author(s):  
T Matheson
Keyword(s):  
Nerve Cord ◽  
Tactile Stimulation ◽  
Schistocerca Gregaria ◽  
Limb Movements ◽  
Single Cycle ◽  
Experimental Conditions ◽  
The Subject ◽  
The Common ◽  
Peripheral Sensory ◽  
Stimulus Site

Locusts, Schistocerca gregaria, in common with many limbed vertebrates, can make directed scratching movements in response to tactile stimulation. For instance, stimulation of different sites on a wing elicits different movements that are accurately targeted so that the hindleg tarsus passes across the stimulus site. I have analysed these limb movements to define the ability of a locust to target stimulus sites correctly under a range of experimental conditions. In particular, I describe aspects of the behaviour that reveal possible neuronal pathways underlying the responses. These neuronal pathways will be the subject of further physiological analyses. Limb targeting during scratching is continuously graded in form; different patterns of movement are not separated by sharp transitions. The computation of limb trajectory takes into account the starting posture of the hindleg, so that different trajectories can be used to reach a common stimulus site from different starting postures. Moreover, the trajectories of the two hindlegs moving simultaneously from different starting postures in response to a single stimulus can be different, so that their tarsi converge onto the common stimulus site. Different trajectories can be used to reach a common stimulus site from the same start posture. Targeting information from a forewing is passed not only down the nerve cord to the ipsilateral hindleg but also across the nerve cord, so that the contralateral hindleg can also make directed movements. This contralateral transmission does not rely on peripheral sensory feedback. When the stimulus site moves during a rhythmical scratch, the targeting of subsequent cycles reflects this change. Both ipsilateral and contralateral hindlegs can retarget their movements. The trajectory of a single cycle of scratching directed towards a particular stimulus site can be modified after it has begun, so that the tarsus is redirected towards a new stimulus site.

Network analysis of Dengue NS1 interacting core human proteins driving dengue pathogenesis

2021 ◽  
Vol 16 ◽  
Author(s):  
Elakkiya Elumalai ◽  
Suresh Kumar Muthuvel
Keyword(s):  
Network Analysis ◽  
Cathepsin L ◽  
Dengue Infection ◽  
Protein Translation ◽  
Ras Signaling ◽  
Protein Drug ◽  
Core Proteins ◽  
Interaction Partners ◽  
Human Proteins ◽  
The Common

Aim: We aimed to identify critical human proteins involved in cathepsin L regulation Background: It has been shown that Dengue Virus (DENV) NS1 activates cathepsin L (CTSL). The CTSL activates heparanase, which cleaves heparan sulfate proteoglycans and causes dengue pathogenesis. NS1 directly interacts with PTBP1 and Gab proteins. Gab protein activates the Ras signaling pathway. Still, no known direct interaction partners are linking GAB1 to cathepsin L. Objective: Our objective includes three main points.1-Network analysis of NS1 interacting human proteins 2- Identification of protein-drug and protein-disease interactions 3- Identification of core proteins involved in cathepsin L regulation. Method: We collected NS1 interacting Human proteins from DenHunt, Int-Act Molecular Interaction Database, Virus Mentha, Virus Pathogen Database and Analysis Resource (ViPR), and Virus MINT. We employed Pesca, cytohubba, and centiscape as the significant plug-ins in Cytoscape for network analysis. To study protein-diseases and protein-drugs interaction, we used NetworkAnalyst. Result: Based on the prior knowledge on the interaction of NS1 with GAB1 and PTBP1 human proteins, we found several core proteins that drive dengue pathogenesis. The proteins EED, NXF1, and MOV10, are the mediators between PTBP1 and CTSL. Similarly, DNM2, GRB2, PXN, PTPRC, and NTRK1 mediate GAB1 and PTBP1. The common first neighbors of MOV10, NXF1, and EED were identified, and the common primary pathways in all three subnetworks were mRNA processing and protein translation. The common interaction partners were considered for drug and disease network analysis. These proteins were; PARP1, NFKB2, HDAC2, SLC25A4, ATP5A1, EPN1, CTSL, UBR4, CLK3, and ARPC4. PARP1 was the highly connected node in the protein-drug network. The highest degree protein, LMNA, was associated with many diseases. The NXF1 is connected with LMNA. Here, we reported one essential protein, namely, NXF1 protein, which links PTBP1 with CTSL. The NXF1 is also connected with TPM3, which is connected to CTSL. Conclusion: We listed functionally important proteins which are involved in cathepsin L activation. Based on network properties, we proposed, NXF1 and TPM3 are the important high centrality proteins in dengue infection.

Knowledge Discovery Process Models

2012 ◽  
pp. 72-100 ◽  
Author(s):  
Mouhib Alnoukari ◽  
Asim El Sheikh
Keyword(s):  
Life Cycle ◽  
Knowledge Discovery ◽  
Process Model ◽  
Common Factor ◽  
Final Outcome ◽  
Process Models ◽  
Data Driven ◽  
Discovery Process ◽  
The Common ◽  
Discovery Process Models

Knowledge Discovery (KD) process model was first discussed in 1989. Different models were suggested starting with Fayyad’s et al (1996) process model. The common factor of all data-driven discovery process is that knowledge is the final outcome of this process. In this chapter, the authors will analyze most of the KD process models suggested in the literature. The chapter will have a detailed discussion on the KD process models that have innovative life cycle steps. It will propose a categorization of the existing KD models. The chapter deeply analyzes the strengths and weaknesses of the leading KD process models, with the supported commercial systems and reported applications, and their matrix characteristics.

scholarly journals Evaluation of the Common Molecular Basis in Alzheimer’s and Parkinson’s Diseases

2019 ◽  
Vol 20 (15) ◽  
pp. 3730 ◽  
Author(s):  
Pratip Rana ◽  
Edian F. Franco ◽  
Yug Rao ◽  
Khajamoinuddin Syed ◽  
Debmalya Barh ◽  
...  
Keyword(s):  
Network Analysis ◽  
Literature Mining ◽  
Extensive Literature ◽  
Genome Wide ◽  
Parkinson’S Diseases ◽  
Epigenetic Regulator ◽  
Major Genome ◽  
The Common ◽  
Exact Relationship ◽  
Subsequent Literature

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are the most common neurodegenerative disorders related to aging. Though several risk factors are shared between these two diseases, the exact relationship between them is still unknown. In this paper, we analyzed how these two diseases relate to each other from the genomic, epigenomic, and transcriptomic viewpoints. Using an extensive literature mining, we first accumulated the list of genes from major genome-wide association (GWAS) studies. Based on these GWAS studies, we observed that only one gene (HLA-DRB5) was shared between AD and PD. A subsequent literature search identified a few other genes involved in these two diseases, among which SIRT1 seemed to be the most prominent one. While we listed all the miRNAs that have been previously reported for AD and PD separately, we found only 15 different miRNAs that were reported in both diseases. In order to get better insights, we predicted the gene co-expression network for both AD and PD using network analysis algorithms applied to two GEO datasets. The network analysis revealed six clusters of genes related to AD and four clusters of genes related to PD; however, there was very low functional similarity between these clusters, pointing to insignificant similarity between AD and PD even at the level of affected biological processes. Finally, we postulated the putative epigenetic regulator modules that are common to AD and PD.

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