Gene regulatory networks modelling using a dynamic evolutionary hybrid

<p>Abstract</p> <p>Background</p> <p>Inference of gene regulatory networks is a key goal in the quest for understanding fundamental cellular processes and revealing underlying relations among genes. With the availability of gene expression data, computational methods aiming at regulatory networks reconstruction are facing challenges posed by the data's high dimensionality, temporal dynamics or measurement noise. We propose an approach based on a novel multi-layer evolutionary trained neuro-fuzzy recurrent network (ENFRN) that is able to select potential regulators of target genes and describe their regulation type.</p> <p>Results</p> <p>The recurrent, self-organizing structure and evolutionary training of our network yield an optimized pool of regulatory relations, while its fuzzy nature avoids noise-related problems. Furthermore, we are able to assign scores for each regulation, highlighting the confidence in the retrieved relations. The approach was tested by applying it to several benchmark datasets of yeast, managing to acquire biologically validated relations among genes.</p> <p>Conclusions</p> <p>The results demonstrate the effectiveness of the ENFRN in retrieving biologically valid regulatory relations and providing meaningful insights for better understanding the dynamics of gene regulatory networks.</p> <p>The algorithms and methods described in this paper have been implemented in a Matlab toolbox and are available from: <url>http://bioserver-1.bioacademy.gr/DataRepository/Project_ENFRN_GRN/</url>.</p

THE IMPACT OF COMMUNITY ACTIVITIES ON TRANSPORT IN THE DOWNTOWN AREA OF TOMOHON IN THE NEW NORMAL ERA

Society cannot be separated from activities in order to meet important needs. Activities to meet this need require a tool for moving places, namely modes of transportation. Movements of transportation modes must be well planned so that people can feel safe and comfortable. Since the city center of Tomohon is a diverse land use area, activities to meet the needs of the area are concentrated. This has generated interest in conducting research on the impact of community activities on transportation, especially in the context of the COVID-19 pandemic. This study aims to identify the characteristics and patterns of community activity, the factors that influence it, the extent and model of Tomohon's downtown traffic impact in the new normal era. This study uses a quantitative approach using methods of factor analysis and path analysis. The sample for this survey consisted of 400 respondents randomly selected from a target audience of people active in downtown Tomohon. The results of this survey are (1) the characteristics and patterns of community activities based on the main forms of activities carried out, the timing of activities, and the types of activities. (2) There are three community activity factors that influence before the new normal era, and there are two community activity factors that influence during the new normal era. (3) Social activity factors (F3) have the greatest impact on the traffic attraction before the new normal era, while economic, educational and religious activity factors (K1) have the greatest influence on traffic attraction during the new normal era. Keywords: factors, community activities, traffic, path analysi

Effects of relative submergence on flow and sediment patterns around clasts

River morphodynamics and sediment transportMechanics of sediment transpor

SOM Loss and Soil Quality in the Clear Creek, IA

The Clear Creek, IA Experimental Watershed (CCEW), which drains to the Iowa River, experiences severe surface erosion due to a combination of high slopes, erodible soils, and extensive agriculture. Concurrent with soil loss is the removal of Soil Organic Matter (SOM). High values of SOM have been related to soil quality; therefore, excessive SOM loss corresponds to degrading soil health. Soil quality assessments are important tools for evaluating management practices in agricultural systems; however, it is difficult to measure soil quality directly at the watershed scale because it varies with a number of site-specific soil characteristics. The coupling of soil surveys with GIS and Non-Point Source computer simulation models will effectively forecast the impacts of ever-changing management practices on soil quality at the watershed scale in less time. NPS models can be extended to evaluate the movement of additional particle-bound constituents like SOM, by incorporating erosion rates and enrichment ratios. The ANNualized AGricultural Non-Point Source pollution modeling system (AnnAGNPS) was used to evaluate upland erosion, enrichment ratios, and SOM loss at the watershed scale in the headwaters of the CCEW using current crop rotations. Gross erosion rates averaged 7.73 MT/ha/yr for individual cells within the watershed. In addition, enrichment ratios, which were determined using gross and net erosion values from AnnAGNPS, were coupled with an organic matter coverage map of the watershed to determine an SOM loss of0.41 MT/ha/yr, which was similar to the loss rates determined by AnnAGNPS (0.29 MT/ ha/yr). To understand the state of soil health in this watershed, the NRCS Soil Conditioning Index (SCI) was determined for the watershed. The average SCI for the watershed was 0.38, which suggests improving soil health conditions. This improvement is most probably due to conservation practices like reduced tillage

A Role for cAMP in Long-Term Depression at Hippocampal Mossy Fiber Synapses

AbstractMossy fiber synapses on hippocampal CA3 pyramidal cells, in addition to expressing an NMDA receptor–independent form of long-term potentiation (LTP), have recently been shown to express a novel presynaptic form of long-term depression (LTD). We have studied the mechanisms underlying mossy fiber LTD and present evidence that it is triggered, at least in part, by a metabotropic glutamate receptor–mediated decrease in adenylyl cyclase activity, which leads to a decrease in the activity of the cAMP-dependent protein kinase (PKA) and a reversal of the presynaptic processes responsible for mossy fiber LTP. The bidirectional control of synaptic strength at mossy fiber synapses by activity therefore appears to be due to modulation of the cAMP-PKA signaling pathway in mossy fiber boutons

The volume-mortality relation for radical cystectomy in England: retrospective analysis of hospital episode statistics

Objectives To investigate the relation between volume and mortality after adjustment for case mix for radical cystectomy in the English healthcare setting using improved statistical methodology, taking into account the institutional and surgeon volume effects and institutional structural and process of care factors

Introduction to the Special Section on Complex Posttraumatic Stress Disorder (CPTSD): The Evolution of a Disorder

The inclusion of complex posttraumatic stress disorder (CPTSD) in the 11th revision of the International Classification of Diseases is an important development in the field of psychotraumatology. Complex PTSD was developed as a response to a clinical need to describe difficulties commonly associated with exposure to traumatic stressors that are predominantly of an interpersonal nature. With this special section, we bring attention to this common condition following exposure to traumatic stressors that only recently has been designated an official diagnosis. In this introduction, we review the history of CPTSD as a new condition and we briefly introduce the papers for the special section in the present issue of the Journal of Traumatic Stress. It is our hope that the work presented in the special section will add to an ever?expanding evidence base. We also hope that this work inspires further research on the cultural validity of CPTSD, its assessment, and treatment

Takotsubo cardiomyopathy and sepsis: a systematic review

Takotsubo cardiomyopathy (TTC) is characterized by a systolic dysfunction localized in the apical and medial aspect of the left ventricle. It is usually related to physical or emotional stress. Recent evidence highlighting the role of infection led us to analyze the links between TTC and sepsis. A systematic review of the literature was undertaken to assess any trends in clinical findings, diagnosis, and outcomes in such patients. We identified 23 selected papers reporting a total of 26 patients, having sepsis, in whom TTC occurred. For each case, we collected data identifying population characteristics, source of sepsis, clinical disease description, and the results of cardiovascular investigations. The majority of patients were females (n = 16), mean age was 62.8 (14.0 standard deviation) years, and clinical outcome was favorable in 92.3% of the cases once the management of sepsis was initiated. A better understanding of the mechanisms of sepsis-associated TTC may generate novel strategies to treat the complications of this cardiomyopathy and may even help predict and prevent its occurrence

Surgeons produce innovative ideas which are frequently lost in the labyrinth of patents

Thoracic and cardiovascular surgery are innovative specialties that regularly recruit the latest technological developments into their armoury of devices and equipment. The introduction of new technology is dependant on patents; an important but single component of intellectual property. Patents enable the attribution of rights to concepts, ideas and inventions and this facilitates ownership, subsequent licensing and overall management of innovation and its outcome. It is not just thoracic and cardiovascular surgery, but the healthcare world in general that experiences ongoing technological evolution; so to remain contemporary, it is important that those in positions of responsibility are familiar with the relevant processes. This requires basic medico-legal knowledge and may be entwined with significant financial responsibility. Penetrating clinical, academic and industrial environments, informed awareness of patents also contributes to important leadership skills, encouraging the incorporation of innovation into the professional milieu. We aim to present through this manuscript an overview of these issues in order to promote awareness of patents within thoracic and cardiovascular surgery using a descriptive and practical approac

Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment

Background: Biopsies taken from individual tumours exhibit extensive differences in their cellular composition due to the inherent heterogeneity of cancers and vagaries of sample collection. As a result genes expressed in specific cell types, or associated with certain biological processes are detected at widely variable levels across samples in transcriptomic analyses. This heterogeneity also means that the level of expression of genes expressed specifically in a given cell type or process, will vary in line with the number of those cells within samples or activity of the pathway, and will therefore be correlated in their expression.Results: Using a novel 3D network-based approach we have analysed six large human cancer microarray datasets derived from more than 1,000 individuals. Based upon this analysis, and without needing to isolate the individual cells, we have defined a broad spectrum of cell-type and pathway-specific gene signatures present in cancer expression data which were also found to be largely conserved in a number of independent datasets.Conclusions: The conserved signature of the tumour-associated macrophage is shown to be largely-independent of tumour cell type. All stromal cell signatures have some degree of correlation with each other, since they must all be inversely correlated with the tumour component. However, viewed in the context of established tumours, the interactions between stromal components appear to be multifactorial given the level of one component e.g. vasculature, does not correlate tightly with another, such as the macrophage