A. Bernadotte - Academia.edu (original) (raw)
Papers by A. Bernadotte
Brain Pathology, 2010
Parkinson's disease (PD) is the second most common neurodegenerative illness after Alzheimer's di... more Parkinson's disease (PD) is the second most common neurodegenerative illness after Alzheimer's disease (AD). Cognitive impairment and dementia are common features in PD and characterized by a wide range of cognitive deficits distinct from those seen in AD. Mild cognitive impairment occurs even early in PD and is associated with shorter time to dementia. The purpose of this review is to present recent findings on clinical aspects of dementia in PD and to elucidate underlying clinical and neurobiological risk factors.
Mathematics
The article formulates the Dictionary Recognition problem, which is relevant for a wide range of ... more The article formulates the Dictionary Recognition problem, which is relevant for a wide range of applied problems: word recognition in a noisy audio signal for natural language processing tasks or in a noisy electromagnetic signal, recognition of visual patterns in limited visibility, and much more. A Dictionary Recognition problem is finding a set of words from a given set to maximize the classification accuracy of the words in the dictionary without losing semantic representation. The idea of solving the problem is to represent a set of objects (encoded as a sequence of symbols or visual sequences) in the form of a k-partite graph, where each partite of the graph corresponds to a group of objects with a certain common feature (equivalence class). The task is to find such a set of representatives of the k equivalence classes on which the k-classification accuracy by the classifier H meets certain criteria: (1) maximum classification accuracy; (2) maximin accuracy—the binary classif...
Programmnaya Ingeneria
In many modern applications, such as intrusion detection and prevention systems, expert knowledge... more In many modern applications, such as intrusion detection and prevention systems, expert knowledge can be formalized in the form of regular expressions. After this formalization, a finite automaton checks whether a word belongs to a regular language. Deterministic finite automata have an optimal time complexity, but the number of automaton states (space complexity) can grow exponentially with the length of the regular expression. At the same time, the time complexity is the main disadvantage of non-deterministic finite automata. Therefore, reducing spatial complexity while maintaining low time complexity is highly relevant. In applied problems of regular language recognition, a significant problem is the problem of the exponentially growing number of states of the recognizing deterministic finite automaton depending on the length of regular expressions of the recognized language — the exponential explosion problem. There are the following three main approaches to solving this proble...
Aging, 2016
The cellular senescence definition comes to the fact of cells irreversible proliferation disabili... more The cellular senescence definition comes to the fact of cells irreversible proliferation disability. Besides the cell cycle arrest, senescent cells go through some morphological, biochemical, and functional changes which are the signs of cellular senescence. The senescent cells (including replicative senescence and stress-induced premature senescence) of all the tissues look alike. They are metabolically active and possess the set of characteristics in vitro and in vivo, which are known as biomarkers of aging and cellular senescence. Among biomarkers of cellular senescence telomere shortening is a rather elegant frequently used biomarker. Validity of telomere shortening as a marker for cellular senescence is based on theoretical and experimental data.
Bioorganic & Medicinal Chemistry Letters, 2006
From in silico docking and COMPARE analysis, novel inhibitors of human NAD(P)H quinone oxidoreduc... more From in silico docking and COMPARE analysis, novel inhibitors of human NAD(P)H quinone oxidoreductase (NQO1) have been identified from the NCI compound database, the most potent of which has an observed IC 50 of 0.7 lM. The inhibitors exhibit a diverse range of scaffolds. The ability of docking calculations to predict experimentally determined binding affinities for NQO1 is discussed, considering the influence of target flexibility and scoring function.
Sensors, 2021
In this work, we focus on silent speech recognition in electroencephalography (EEG) data of healt... more In this work, we focus on silent speech recognition in electroencephalography (EEG) data of healthy individuals to advance brain–computer interface (BCI) development to include people with neurodegeneration and movement and communication difficulties in society. Our dataset was recorded from 270 healthy subjects during silent speech of eight different Russia words (commands): `forward’, `backward’, `up’, `down’, `help’, `take’, `stop’, and `release’, and one pseudoword. We began by demonstrating that silent word distributions can be very close statistically and that there are words describing directed movements that share similar patterns of brain activity. However, after training one individual, we achieved 85% accuracy performing 9 words (including pseudoword) classification and 88% accuracy on binary classification on average. We show that a smaller dataset collected on one participant allows for building a more accurate classifier for a given subject than a larger dataset collec...
Advances in gerontology = Uspekhi gerontologii, 2013
Old and young donors cells show different ability to homologous recombination (shown on the first... more Old and young donors cells show different ability to homologous recombination (shown on the first stage--the chromosome transference) in vitro, that we suppose could be the reasons of the genome instability in aging. Homologous recombination, induced by X-radiation, is limited in cells taken from donors older than 70 years. Alpha-amanitin, the RNA-polymerize II repressor, in toxic doze, could induce the chromosome transference in the cells from all studied groups: from old and young donors and donors with repair process defect (with BRCA 1, 2 mutations). Summarized effect of X-radiation and alpha-amanitin does not increase the induction of the chromosome transference.
Advances in gerontology = Uspekhi gerontologii, 2013
Old and young donors cells show different ability to homologous recombination (shown on the first... more Old and young donors cells show different ability to homologous recombination (shown on the first stage--the chromosome transference) in vitro, that we suppose could be the reasons of the genome instability in aging. Homologous recombination, induced by X-radiation, is limited in cells taken from donors older than 70 years. Alpha-amanitin, the RNA-polymerize II repressor, in toxic doze, could induce the chromosome transference in the cells from all studied groups: from old and young donors and donors with repair process defect (with BRCA 1, 2 mutations). Summarized effect of X-radiation and alpha-amanitin does not increase the induction of the chromosome transference.
Discoveries, 2017
In many origin-of-life scenarios, first a kit of elements and simple compounds emerges, then a pr... more In many origin-of-life scenarios, first a kit of elements and simple compounds emerges, then a primitive membrane and then a nanocell with a minimal genome is self-assembled, which then proceeds to multiply by copying itself while mutating. Testing this scenario, we selected Deinococcus Radiodurans known for its exceptional self-repair properties as a model system, separated its bacterial lysis into DNA, RNA and protein fractions, while lipids were used for liposome formation. The fractions were sealed in glass tubes individually and in combinations and stored for three weeks. Upon seeding on Petri dishes, the fractions containing liposomes together with nucleic acid and/or proteins gave in total 19 colonies of Deinococcus radiodurans (confirmed by proteomics), while liposome-free fractions as well as liposome-only fractions gave no colonies. The self-assembly of viable cells from essentially dead mixtures validates the lyposome-based origin-of-life scenario.
The Lewy body dementias comprise disorders characterized by parkinsonism and a dementia syndrome ... more The Lewy body dementias comprise disorders characterized by parkinsonism and a dementia syndrome with a predominant attentional, executive and visuospatial component, and with the Lewy body as the core pathological marker. Dementia with Lewy bodies (DLB) and Parkinson’s disease with dementia (PDD) are two conditions that meet this definition and are only differentiated by the duration of parkinsonism prior to dementia onset. The standardized clinical criteria for DLB establish an arbitrary 1-year cutoff between symptoms: if dementia begins at the same time or within 1 year of parkinsonism, the patient is presumed to suffer from DLB; if dementia onset occurs more than 1 year after parkinsonism, PDD is assumed. The third report of the DLB consortium [1] highlighted the unresolved boundary issues between DLB and PDD but maintained this arbitrary cut point. The appropriateness of such an artificial cut point for differentiating two similar clinical syndromes has been debated. Indeed, DL...
Any violation of the homologous chromosome DNA repair leads to the genome instability, characteri... more Any violation of the homologous chromosome DNA repair leads to the genome instability, characteristic for hereditary syndromes and for aging cells. Using low doses of ionizing radiation (3-10 cGy) we have found any transference of the homologous centromere loci of the chromosome 1 (1q12) from the periphery to the cen- tre of the nucleus in the lymphocytes of young healthy donors. The same effect was found after any influence of RNA-polymerase inhibitor a-amanitine. Some changes in the chromatin structure during aging (70-80 years old patients) result in the difficulties in chromosome displacement, accompanied with any trouble in the appro- achement of the homologous chromosome loci as an answer to low doses of radiation.
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cellular Immunology, 2018
Several parameters representing the clinical diversity of Parkinson's disease (PD), including sev... more Several parameters representing the clinical diversity of Parkinson's disease (PD), including severity, phenotypes, cognitive decline, anxiety and depression were analyzed to examine the link with interleukin-1β (IL-1β), the interleukin-1 receptor antagonist (IL-1RA), IL-6, IL-10, and tumor necrosis factor-α (TNFα) and also to determine the relationship between levels of these factors in serum and cerebrospinal fluid (CSF). Significantly elevated serum IL-1β and IL-6 and reduced IL- 1RA levels were found in the PD group. In CSF and serum, inflammatory factors behaved differently, with increased CSF TNFα indicating rapid PD progression, while IL-1β was found to be increased in serum. A low level of IL-6 was associated with a longer duration of PD. Anxiety, depression, non-tremor phenotype and late-onset PD correlated with a high serum level of IL-10. The serum TNFα level was lower in PD patients with mild cognitive impairment compared to controls. Serum IL-1β, IL-6 and IL-10 levels correlated with these markers in CSF.
Methods in Molecular Biology
Tsitologiia, 2013
Any violation of the homologous chromosome DNA repair leads to the genome instability, characteri... more Any violation of the homologous chromosome DNA repair leads to the genome instability, characteristic for hereditary syndromes and for aging cells. Using low doses of ionizing radiation (3-10 cGy) we have found any transference of the homologous centromere loci of the chromosome 1 (1q12) from the periphery to the cen- tre of the nucleus in the lymphocytes of young healthy donors. The same effect was found after any influence of RNA-polymerase inhibitor a-amanitine. Some changes in the chromatin structure during aging (70-80 years old patients) result in the difficulties in chromosome displacement, accompanied with any trouble in the appro- achement of the homologous chromosome loci as an answer to low doses of radiation.
Advances in Gerontology, 2014
Lung, 2014
Some studies have shown that peptides have high treatment potential due to their biological activ... more Some studies have shown that peptides have high treatment potential due to their biological activity, harmlessness, and tissue-specific action. Tetrapeptide Ala-Asp-Glu-Leu (ADEL) was effective on models of acute bacterial lung inflammation, fibrosis, and toxic lung damage in several studies. We measured Ki67, Mcl-1, p53, CD79, and NOS-3 protein levels in the 1st, 7th, and 14th passages of bronchoepithelial human embryonic cell cultures. Gene expression of NKX2-1, SCGB1A1, SCGB3A2, FOXA1, FOXA2, MUC4, MUC5AC, and SFTPA1 was measured by real-time polymerase chain reaction. Using the methods of spectrophotometry, viscometry, and circular dichroism, we studied the ADEL-DNA interaction in vitro. Peptide ADEL regulates the levels of Ki67, Mcl-1, p53, CD79, and NOS-3 proteins in cell cultures of human bronchial epithelium in various passages. The strongest activating effect of peptide ADEL on bronchial epithelial cell proliferation through Ki67 and Mcl-1 was observed in "old" cell cultures. ADEL regulates the expression of genes involved in bronchial epithelium differentiation: NKX2-1, SCGB1A1, SCGB3A2, FOXA1, and FOXA2. ADEL also activates several genes, which reduced expression correlated with pathological lung development: MUC4, MUC5AC, and SFTPA1. Spectrophotometry, viscometry, and circular dichroism showed ADEL-DNA interaction, with a binding region in the major groove (N7 guanine). ADEL can bind to specific DNA regions and regulate gene expression and synthesis of proteins involved in the differentiation and maintenance of functional activity of the bronchial epithelium. Through activation of some specific gene expression, peptide ADEL may protect the bronchial epithelium from pulmonary pathology. ADEL also may have a geroprotective effect on bronchial tissue.
Brain Pathology, 2010
Parkinson's disease (PD) is the second most common neurodegenerative illness after Alzheimer's di... more Parkinson's disease (PD) is the second most common neurodegenerative illness after Alzheimer's disease (AD). Cognitive impairment and dementia are common features in PD and characterized by a wide range of cognitive deficits distinct from those seen in AD. Mild cognitive impairment occurs even early in PD and is associated with shorter time to dementia. The purpose of this review is to present recent findings on clinical aspects of dementia in PD and to elucidate underlying clinical and neurobiological risk factors.
Mathematics
The article formulates the Dictionary Recognition problem, which is relevant for a wide range of ... more The article formulates the Dictionary Recognition problem, which is relevant for a wide range of applied problems: word recognition in a noisy audio signal for natural language processing tasks or in a noisy electromagnetic signal, recognition of visual patterns in limited visibility, and much more. A Dictionary Recognition problem is finding a set of words from a given set to maximize the classification accuracy of the words in the dictionary without losing semantic representation. The idea of solving the problem is to represent a set of objects (encoded as a sequence of symbols or visual sequences) in the form of a k-partite graph, where each partite of the graph corresponds to a group of objects with a certain common feature (equivalence class). The task is to find such a set of representatives of the k equivalence classes on which the k-classification accuracy by the classifier H meets certain criteria: (1) maximum classification accuracy; (2) maximin accuracy—the binary classif...
Programmnaya Ingeneria
In many modern applications, such as intrusion detection and prevention systems, expert knowledge... more In many modern applications, such as intrusion detection and prevention systems, expert knowledge can be formalized in the form of regular expressions. After this formalization, a finite automaton checks whether a word belongs to a regular language. Deterministic finite automata have an optimal time complexity, but the number of automaton states (space complexity) can grow exponentially with the length of the regular expression. At the same time, the time complexity is the main disadvantage of non-deterministic finite automata. Therefore, reducing spatial complexity while maintaining low time complexity is highly relevant. In applied problems of regular language recognition, a significant problem is the problem of the exponentially growing number of states of the recognizing deterministic finite automaton depending on the length of regular expressions of the recognized language — the exponential explosion problem. There are the following three main approaches to solving this proble...
Aging, 2016
The cellular senescence definition comes to the fact of cells irreversible proliferation disabili... more The cellular senescence definition comes to the fact of cells irreversible proliferation disability. Besides the cell cycle arrest, senescent cells go through some morphological, biochemical, and functional changes which are the signs of cellular senescence. The senescent cells (including replicative senescence and stress-induced premature senescence) of all the tissues look alike. They are metabolically active and possess the set of characteristics in vitro and in vivo, which are known as biomarkers of aging and cellular senescence. Among biomarkers of cellular senescence telomere shortening is a rather elegant frequently used biomarker. Validity of telomere shortening as a marker for cellular senescence is based on theoretical and experimental data.
Bioorganic & Medicinal Chemistry Letters, 2006
From in silico docking and COMPARE analysis, novel inhibitors of human NAD(P)H quinone oxidoreduc... more From in silico docking and COMPARE analysis, novel inhibitors of human NAD(P)H quinone oxidoreductase (NQO1) have been identified from the NCI compound database, the most potent of which has an observed IC 50 of 0.7 lM. The inhibitors exhibit a diverse range of scaffolds. The ability of docking calculations to predict experimentally determined binding affinities for NQO1 is discussed, considering the influence of target flexibility and scoring function.
Sensors, 2021
In this work, we focus on silent speech recognition in electroencephalography (EEG) data of healt... more In this work, we focus on silent speech recognition in electroencephalography (EEG) data of healthy individuals to advance brain–computer interface (BCI) development to include people with neurodegeneration and movement and communication difficulties in society. Our dataset was recorded from 270 healthy subjects during silent speech of eight different Russia words (commands): `forward’, `backward’, `up’, `down’, `help’, `take’, `stop’, and `release’, and one pseudoword. We began by demonstrating that silent word distributions can be very close statistically and that there are words describing directed movements that share similar patterns of brain activity. However, after training one individual, we achieved 85% accuracy performing 9 words (including pseudoword) classification and 88% accuracy on binary classification on average. We show that a smaller dataset collected on one participant allows for building a more accurate classifier for a given subject than a larger dataset collec...
Advances in gerontology = Uspekhi gerontologii, 2013
Old and young donors cells show different ability to homologous recombination (shown on the first... more Old and young donors cells show different ability to homologous recombination (shown on the first stage--the chromosome transference) in vitro, that we suppose could be the reasons of the genome instability in aging. Homologous recombination, induced by X-radiation, is limited in cells taken from donors older than 70 years. Alpha-amanitin, the RNA-polymerize II repressor, in toxic doze, could induce the chromosome transference in the cells from all studied groups: from old and young donors and donors with repair process defect (with BRCA 1, 2 mutations). Summarized effect of X-radiation and alpha-amanitin does not increase the induction of the chromosome transference.
Advances in gerontology = Uspekhi gerontologii, 2013
Old and young donors cells show different ability to homologous recombination (shown on the first... more Old and young donors cells show different ability to homologous recombination (shown on the first stage--the chromosome transference) in vitro, that we suppose could be the reasons of the genome instability in aging. Homologous recombination, induced by X-radiation, is limited in cells taken from donors older than 70 years. Alpha-amanitin, the RNA-polymerize II repressor, in toxic doze, could induce the chromosome transference in the cells from all studied groups: from old and young donors and donors with repair process defect (with BRCA 1, 2 mutations). Summarized effect of X-radiation and alpha-amanitin does not increase the induction of the chromosome transference.
Discoveries, 2017
In many origin-of-life scenarios, first a kit of elements and simple compounds emerges, then a pr... more In many origin-of-life scenarios, first a kit of elements and simple compounds emerges, then a primitive membrane and then a nanocell with a minimal genome is self-assembled, which then proceeds to multiply by copying itself while mutating. Testing this scenario, we selected Deinococcus Radiodurans known for its exceptional self-repair properties as a model system, separated its bacterial lysis into DNA, RNA and protein fractions, while lipids were used for liposome formation. The fractions were sealed in glass tubes individually and in combinations and stored for three weeks. Upon seeding on Petri dishes, the fractions containing liposomes together with nucleic acid and/or proteins gave in total 19 colonies of Deinococcus radiodurans (confirmed by proteomics), while liposome-free fractions as well as liposome-only fractions gave no colonies. The self-assembly of viable cells from essentially dead mixtures validates the lyposome-based origin-of-life scenario.
The Lewy body dementias comprise disorders characterized by parkinsonism and a dementia syndrome ... more The Lewy body dementias comprise disorders characterized by parkinsonism and a dementia syndrome with a predominant attentional, executive and visuospatial component, and with the Lewy body as the core pathological marker. Dementia with Lewy bodies (DLB) and Parkinson’s disease with dementia (PDD) are two conditions that meet this definition and are only differentiated by the duration of parkinsonism prior to dementia onset. The standardized clinical criteria for DLB establish an arbitrary 1-year cutoff between symptoms: if dementia begins at the same time or within 1 year of parkinsonism, the patient is presumed to suffer from DLB; if dementia onset occurs more than 1 year after parkinsonism, PDD is assumed. The third report of the DLB consortium [1] highlighted the unresolved boundary issues between DLB and PDD but maintained this arbitrary cut point. The appropriateness of such an artificial cut point for differentiating two similar clinical syndromes has been debated. Indeed, DL...
Any violation of the homologous chromosome DNA repair leads to the genome instability, characteri... more Any violation of the homologous chromosome DNA repair leads to the genome instability, characteristic for hereditary syndromes and for aging cells. Using low doses of ionizing radiation (3-10 cGy) we have found any transference of the homologous centromere loci of the chromosome 1 (1q12) from the periphery to the cen- tre of the nucleus in the lymphocytes of young healthy donors. The same effect was found after any influence of RNA-polymerase inhibitor a-amanitine. Some changes in the chromatin structure during aging (70-80 years old patients) result in the difficulties in chromosome displacement, accompanied with any trouble in the appro- achement of the homologous chromosome loci as an answer to low doses of radiation.
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cellular Immunology, 2018
Several parameters representing the clinical diversity of Parkinson's disease (PD), including sev... more Several parameters representing the clinical diversity of Parkinson's disease (PD), including severity, phenotypes, cognitive decline, anxiety and depression were analyzed to examine the link with interleukin-1β (IL-1β), the interleukin-1 receptor antagonist (IL-1RA), IL-6, IL-10, and tumor necrosis factor-α (TNFα) and also to determine the relationship between levels of these factors in serum and cerebrospinal fluid (CSF). Significantly elevated serum IL-1β and IL-6 and reduced IL- 1RA levels were found in the PD group. In CSF and serum, inflammatory factors behaved differently, with increased CSF TNFα indicating rapid PD progression, while IL-1β was found to be increased in serum. A low level of IL-6 was associated with a longer duration of PD. Anxiety, depression, non-tremor phenotype and late-onset PD correlated with a high serum level of IL-10. The serum TNFα level was lower in PD patients with mild cognitive impairment compared to controls. Serum IL-1β, IL-6 and IL-10 levels correlated with these markers in CSF.
Methods in Molecular Biology
Tsitologiia, 2013
Any violation of the homologous chromosome DNA repair leads to the genome instability, characteri... more Any violation of the homologous chromosome DNA repair leads to the genome instability, characteristic for hereditary syndromes and for aging cells. Using low doses of ionizing radiation (3-10 cGy) we have found any transference of the homologous centromere loci of the chromosome 1 (1q12) from the periphery to the cen- tre of the nucleus in the lymphocytes of young healthy donors. The same effect was found after any influence of RNA-polymerase inhibitor a-amanitine. Some changes in the chromatin structure during aging (70-80 years old patients) result in the difficulties in chromosome displacement, accompanied with any trouble in the appro- achement of the homologous chromosome loci as an answer to low doses of radiation.
Advances in Gerontology, 2014
Lung, 2014
Some studies have shown that peptides have high treatment potential due to their biological activ... more Some studies have shown that peptides have high treatment potential due to their biological activity, harmlessness, and tissue-specific action. Tetrapeptide Ala-Asp-Glu-Leu (ADEL) was effective on models of acute bacterial lung inflammation, fibrosis, and toxic lung damage in several studies. We measured Ki67, Mcl-1, p53, CD79, and NOS-3 protein levels in the 1st, 7th, and 14th passages of bronchoepithelial human embryonic cell cultures. Gene expression of NKX2-1, SCGB1A1, SCGB3A2, FOXA1, FOXA2, MUC4, MUC5AC, and SFTPA1 was measured by real-time polymerase chain reaction. Using the methods of spectrophotometry, viscometry, and circular dichroism, we studied the ADEL-DNA interaction in vitro. Peptide ADEL regulates the levels of Ki67, Mcl-1, p53, CD79, and NOS-3 proteins in cell cultures of human bronchial epithelium in various passages. The strongest activating effect of peptide ADEL on bronchial epithelial cell proliferation through Ki67 and Mcl-1 was observed in "old" cell cultures. ADEL regulates the expression of genes involved in bronchial epithelium differentiation: NKX2-1, SCGB1A1, SCGB3A2, FOXA1, and FOXA2. ADEL also activates several genes, which reduced expression correlated with pathological lung development: MUC4, MUC5AC, and SFTPA1. Spectrophotometry, viscometry, and circular dichroism showed ADEL-DNA interaction, with a binding region in the major groove (N7 guanine). ADEL can bind to specific DNA regions and regulate gene expression and synthesis of proteins involved in the differentiation and maintenance of functional activity of the bronchial epithelium. Through activation of some specific gene expression, peptide ADEL may protect the bronchial epithelium from pulmonary pathology. ADEL also may have a geroprotective effect on bronchial tissue.