Spectral forecast: A general purpose prediction model as an alternative to classical neural networks.

Here, we describe a general-purpose prediction model. Our approach requires three matrices of equal size and uses two equations to determine the behavior against two possible outcomes. We use an example based on photon-pixel coupling data to show that in humans, this solution can indicate the predisposition to disease. An implementation of this model is made available in the supplementary material.

Gene promoters show chromosome-specificity and reveal chromosome territories in humans.

BACKGROUND: Gene promoters have guided evolution processes for millions of years. It seems that they were the main engine responsible for the integration of different mutations favorable for the environmental conditions. In cooperation with different transcription factors and other biochemical components, these regulatory regions dictate the synthesis frequency of RNA molecules. Predominantly in the last decade, it has become clear that nuclear organization impacts upon gene regulation. To fully understand the connections between Homo sapiens chromosomes and their gene promoters, we analyzed 1200 promoter sequences using our Kappa Index of Coincidence method. RESULTS: In order to measure the structural similarity of gene promoters, we used two-dimensional image-based patterns obtained through Kappa Index of Coincidence (Kappa IC) and (C+G)% values. The center of weight of each promoter pattern indicated a structure similarity between promoters of each chromosome. Furthermore, the proximity of chromosomes seems to be in accordance to the structural similarity of their gene promoters. The arrangement of chromosomes according to Kappa IC values of promoters, shows a striking symmetry between the chromosome length and the structure of promoters located on them. High Kappa IC and (C+G)% values of gene promoters were also directly associated with the most frequent genetic diseases. Taking into consideration these observations, a general hypothesis for the evolutionary dynamics of the genome has been proposed. In this hypothesis, heterochromatin and euchromatin domains exchange DNA sequences according to a difference in the rate of Slipped Strand Mispairing and point mutations. CONCLUSIONS: In this paper we showed that gene promoters appear to be specific to each chromosome. Furthermore, the proximity between chromosomes seems to be in accordance to the structural similarity of their gene promoters. Our findings are based on comprehensive data from Transcriptional Regulatory Element Database and a new computer model whose core is using Kappa index of coincidence.

Moonlighting genes harbor antisense ORFs that encode potential membrane proteins.

Moonlighting genes encode for single polypeptide molecules that perform multiple and often unrelated functions. These genes occur across all domains of life. Their ubiquity and functional diversity raise many questions as to their origins, evolution, and role in the cell cycle. In this study, we present a simple bioinformatics probe that allows us to rank genes by antisense translation potential, and we show that this probe enriches, reliably, for moonlighting genes across a variety of organisms. We find that moonlighting genes harbor putative antisense open reading frames (ORFs) rich in codons for non-polar amino acids. We also find that moonlighting genes tend to co-locate with genes involved in cell wall, cell membrane, or cell envelope production. On the basis of this and other findings, we offer a model in which we propose that moonlighting gene products are likely to escape the cell through gaps in the cell wall and membrane, at wall/membrane construction sites; and we propose that antisense ORFs produce "membrane-sticky" protein products, effectively binding moonlighting-gene DNA to the cell membrane in porous areas where intensive cell-wall/cell-membrane construction is underway. This leads to high potential for escape of moonlighting proteins to the cell surface. Evolutionary and other implications of these findings are discussed.

Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.

BACKGROUND: The main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. Generally, promoters have been classified in two major classes, namely TATA and CpG. Nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. Accordingly, we tried to ask ourselves some fundamental questions: Why certain genes have an overall predisposition for higher gene expression levels than others? What causes such a predisposition? Is there a structural relationship of these sequences in different tissues? Is there a strong phylogenetic relationship between promoters of closely related species? RESULTS: In order to gain valuable insights into different promoter regions, we obtained a series of image-based patterns which allowed us to identify 10 generic classes of promoters. A comprehensive analysis was undertaken for promoter sequences from Arabidopsis thaliana, Drosophila melanogaster, Homo sapiens and Oryza sativa, and a more extensive analysis of tissue-specific promoters in humans. We observed a clear preference for these species to use certain classes of promoters for specific biological processes. Moreover, in humans, we found that different tissues use distinct classes of promoters, reflecting an emerging promoter network. Depending on the tissue type, comparisons made between these classes of promoters reveal a complementarity between their patterns whereas some other classes of promoters have been observed to occur in competition. Furthermore, we also noticed the existence of some transitional states between these classes of promoters that may explain certain evolutionary mechanisms, which suggest a possible predisposition for specific levels of gene expression and perhaps for a different number of factors responsible for triggering gene expression. Our conclusions are based on comprehensive data from three different databases and a new computer model whose core is using Kappa index of coincidence. CONCLUSIONS: To fully understand the connections between gene promoters and gene expression, we analyzed thousands of promoter sequences using our Kappa Index of Coincidence method and a specialized Optical Character Recognition (OCR) neural network. Under our criteria, 10 classes of promoters were detected. In addition, the existence of "transitional" promoters suggests that there is an evolutionary weighted continuum between classes, depending perhaps upon changes in their gene products.

Photon-pixel coupling: A method for parallel acquisition of electrical signals in scientific investigations.

Here we describe a novel prototype method for parallel sampling of electrical signals from 200 sensors. The amplified signal from each sensor was remotely converted into a luminous signal on a LED matrix. A digital camera supported by a duralumin skeleton, was installed at 15 cm above an LED matrix inside an opaque box. Images were sampled at discrete time intervals of 5 s. A total of 25,920 images of the LED matrix have been recorded. Thus, 5.2 million measurements have been recorded as light intensities from the LED matrix. Light intensities of individual LEDs from the images were converted into 1 pixel value/LED. Each pixel value was then converted into percentages for evaluation. We used this methodology to measure the temporal variation of the electrical current on the skin of the torso on human volunteers, to assess the presence of a correlation between the electrical activity and diabetes (Ionescu-Tirgoviste et al., 2018). This method also allowed us to compile the first high resolution map of the electrical activity generated by the human skin (Ionescu-Tirgoviste et al., 2018). •A novel method for a parallel acquisition of electrical signals which can be applied in any related field.•It provides the ability to retrieve a large number of electrical channels simultaneously.•It provides for an inexpensive and reliable way to digitize hundreds to thousands of channels at video rate frequencies.

The electrical activity map of the human skin indicates strong differences between normal and diabetic individuals: A gateway to onset prevention.

The human skin is not only the largest organ, but also the most important candidate for novel non-invasive methods of investigation. Here we describe a large-scale prototype for determining the real-time distribution of the electrical activity from the surface of the human skin. A collection of 200 sensors have been placed across the entire trunk surface. The output of each sensor was remotely inserted into a 20 × 10 LED matrix for a parallel capture of the signals. Continuous observations of the electrical activity pattern were made above the LED matrix by a digital camera in an obscure environment. A total of 5.2 million measurements (25,920 maps) have been recorded as light intensities from the LED matrix and converted into percentages for evaluation. A total of 36 individuals were divided equally into two groups and subjected to a short glucose tolerance test for 1 h; one group with established Type 2 Diabetes (T2D) and the other group without diabetes. The electrical activity pattern and the average signal intensity of normal individuals (37% ±â€¯8.1) and diabetic individuals (58% ±â€¯7.8), showed a significant difference of 21%. The average signal intensity on the ventral side (VS) and dorsal side (DS) of the torso exhibited different behaviors in diabetics and non-diabetics. On average, diabetic individuals have shown an electrical activity of higher intensity on DS (DS = 60%, VS = 55%), while the normal group has shown a higher intensity on VS (DS = 36%, VS = 39%).

Maps of electrical activity in diabetic patients and normal individuals.

Here, data related to the electrical activity of the human skin are presented in detail. The 3D electrical activity maps in normal and diabetic individuals are shown and described using raw data obtained with Photon-Pixel coupling. Average electrical activity matrices are shown by subject, gender and group. Distributions of the electrical activity data are shown in connection with the ventral and dorsal side of the human torso. For a better understanding of the electrical activity data, critical parameters of the individuals that participated in the study are also presented.

Structural Properties of Gene Promoters Highlight More than Two Phenotypes of Diabetes.

Genome-wide association studies (GWAS) published in the last decade raised the number of loci associated with type 1 (T1D) and type 2 diabetes (T2D) to more than 50 for each of these diabetes phenotypes. The environmental factors seem to play an important role in the expression of these genes, acting through transcription factors that bind to promoters. Using the available databases we examined the promoters of various genes classically associated with the two main diabetes phenotypes. Our comparative analyses have revealed significant architectural differences between promoters of genes classically associated with T1D and T2D. Nevertheless, five gene promoters (about 16%) belonging to T1D and six gene promoters (over 19%) belonging to T2D have shown some intermediary structural properties, suggesting a direct relationship to either LADA (Latent Autoimmune Diabetes in Adults) phenotype or to non-autoimmune type 1 phenotype. The distribution of these promoters in at least three separate classes seems to indicate specific pathogenic pathways. The image-based patterns (DNA patterns) generated by promoters of genes associated with these three phenotypes support the clinical observation of a smooth link between specific cases of typical T1D and T2D. In addition, a global distribution of these DNA patterns suggests that promoters of genes associated with T1D appear to be evolutionary more conserved than those associated with T2D. Though, the image based patterns obtained by our method might be a new useful parameter for understanding the pathogenetic mechanism and the diabetogenic gene networks.

A 3D map of the islet routes throughout the healthy human pancreas.

Islets of Langerhans are fundamental in understanding diabetes. A healthy human pancreas from a donor has been used to asses various islet parameters and their three-dimensional distribution. Here we show that islets are spread gradually from the head up to the tail section of the pancreas in the form of contracted or dilated islet routes. We also report a particular anatomical structure, namely the cluster of islets. Our observations revealed a total of 11 islet clusters which comprise of small islets that surround large blood vessels. Additional observations in the peripancreatic adipose tissue have shown lymphoid-like nodes and blood vessels captured in a local inflammatory process. Our observations are based on regional slice maps of the pancreas, comprising of 5,423 islets. We also devised an index of sphericity which briefly indicates various islet shapes that are dominant throughout the pancreas.

Free Radicals Scavenging Capacity, Antidiabetic and Antihypertensive Activities of Flavonoid-Rich Fractions from Leaves of Trichilia emetica and Opilia amentacea in an Animal Model of Type 2 Diabetes Mellitus.

Trichilia emetica and Opilia amentacea traditional Burkinabe medicinal plants were investigated to determine their therapeutic potential to inhibit key enzymes in carbohydrate metabolism, which has relevance to the management of type 2 diabetes. In vitro and in vivo antioxidant and antihypertensive potential and antilipidemia and antihyperglycemia activities in an animal model of type 2 diabetes mellitus have been studied. The antioxidant activity of the flavonoids from leaves of Trichilia emetica and Opilia amentacea has been evaluated using ß -carotene-linoleic acid system, 1,1-diphenyl-2-picrylhydrazyl inhibitory activity, chelation of iron (II) ions, and lipid peroxidation which showed more pronounced antioxidant capacities of Trichilia emetica. Total cholesterol concentrations decreased in an animal model of type 2 diabetes mellitus under effects of flavonoid-rich fractions from leaves of Trichilia emetica and Opilia amentacea has been observed. Extract of flavonoid-rich fractions from Trichilia emetica shown maximum radical scavenging activity and possessed marked antiamylase activity which may be due to the presence of certain secondary metabolites. Suggested better antihyperglycemia, antilipidemia, and antihypertensive properties of flavonoid-rich fractions from Trichilia emetica compared to the extract of Opilia amentacea are demonstrating antidiabetic potential of Trichilia emetica as therapeutic targets for the management of type 2 diabetes.