Modelling the Yamnaya Expansion Through Radiocarbon Dates

Maisterintutkielma keskittyy pronssikautiseen Jamnaja-kulttuurin hautauksista kerättyjen radiohiiliajoitusten analysoimiseen erilaisilla menetelmillä. Muun muassa ajoituksia käsitellään OxCal 4.4, CalPal ja ArcGIS ohjelmissa. CalPal:in oiva Chronology composer-toiminto järjestää ajoitukset kronologiseen järjestykseen, kun taas OxCal 4.4.-ohjelmassa radiohiiliajoituksia käsitellään tilastollisesti seuraavaa tutkimusvaihetta varten. Jamnaja-kulttuurin määritelmä on ollut pitkään keskustelun alla. Tutkijat ovat pitkään olleet hyvin eri mieltä siitä, minkälaiset hautaukset kuuluvat Jamnaja-kulttuuriin ja millaisia ne ovat olleet tätä aikaisemmin. Hyvin usein kivikautisia hautauksia luokitellaan jamnajaksi, vaikka niillä ei näyttäisi olevan mitään yhteyksiä siihen. Tutkielmassa on tärkeää rajoittaa jamnaja-kulttuurin määritelmää niin, että tulisi selväksi, mitä hautauksia otetaan mukaan seuraaviin analyyseihin, ja mitä hautauksia jätetään tutkimuksen ulkopuolelle. Työtä varten hautauksia on jaettu neljään ryhmään niiden keskeisten piirteiden perusteella. Tutkielman varsinainen osuus keskittyy ArcGIS-ohjelman tarjoamaan Kriging interpolointitoimintoihin. Näistä analyysiä varten on valittu Empirical Bayesian Kriging-malli, jonka avulla pystytään seuraamaan muita tuloksia kuin lineaarista ekspansiota. Kyseisessä metodissa arvioidaan tunnettujen pisteiden perusteella, minkälaisia arvoja tuntemattomat pisteet tutkimusalueella saisivat. Metodia yleensä käytetään korkeusmallien rakentamiseen, mutta tässä tapauksessa korkeuden arvot on korvattu radiohiiliajoituksilla. Metodilla suoritetaan kahdenlaista tutkimusta: yhdessä aineistoa on käsitelty laadullisesti, kun taas toisessa ei. Koska radiohiiliajoitukset yleensä kalibroinnin jälkeen esitetään kahden arvon välinä, ne täytyy analysoida tilastollisesti. OxCal-ohjelman Tau_Boundary-funktio mahdollistaa välien pienentämisen, jotta ajoituksien painotettuja ja tavallisia keskiarvoja voidaan käyttää. Metodi perustuu oletettuihin Jamnaja-kulttuurin ilmestymiseen ja loppumiseen. Radiohiiliajoitukset aiheuttavat kyseisessä analyysissä paljon virhemarginaaleja, joten niiden laatua tulee käsitellä tarkasti. Samalla tavalla kuin hautauksien tilanteessa, ajoitukset on jaettu neljään ryhmään, joissa on huomioitu perinteisen ja AMS-ajoittamisten ero, ”vanhan puun vaikutus”, allaseffekti sekä erilaisten laboratorioiden tuottama tieto. Kiovan laboratorio on pitkään säännöllisesti tuottanut virheellisiä ajoituksia, joten niitä käsitellään tutkielmassa harkiten. Tulevaisuudessa tutkimusta voi yhdistää sekä isotooppeihin että genetiikkaan. Yhteisellä panoksella Jamnaja-ekspansiosta syntyy täydennetty kuva, jota voidaan käyttää tulkitsemaan 5000 vuoden takaisia tapahtumia. Lisäksi tutkimusta voi laajentaa sisällyttämällä lisää eroavia piirteitä. Kuitenkin kattavaa tietopankkia varten tarvitaan lisää hyvänlaatuisia radiohiiliajoituksia, etenkin Ukrainan alueelta

Transcriptomic Analysis of Gonadal Adispose Tissue in Male Mice Exposed Perinatally to 2,2\u27,4,4\u27-Tetrabromodiphenyl Ether (BDE-47)

For the majority of lipophilic compounds, adipose tissue is traditionally considered as a storage depot and only rarely as a target organ. Meanwhile, abnormalities in adipose tissue physiology induced by chemical exposure may contribute to the current epidemic of obesity and metabolic diseases. Polybrominated diphenyl ethers (PBDEs) are a group of lipophilic flame retardants found in the majority of human samples in North America. Their ability to alter the physiology of adipose tissue is unknown. We exposed pregnant mice to 0.2 mg/kg body weight/day of BDE-47 perinatally. Transcriptomic changes in gonadal adipose tissue were analyzed in male offspring using the RNA-seq approach with subsequent bioinformatic analysis. The expression of genes of coagulation and complement cascade, de novo lipogenesis, and xenobiotic metabolism was altered in response to BDE-47 exposure. The affected molecular network included the following hubs: PPARα, HNF1A, and HNF4. These findings suggest that adipose tissue should be considered a target tissue for BDE-47, in addition to its role as a storage depot. This study also builds a background for a targeted search of sensitive phenotypic endpoints of BDE-47 exposure, including lipid profile parameters and coagulation factors in circulation. Additional studies are needed to investigate the role of PBDEs as an obesogen

Transcriptomic Analysis of Gonadal Adipose Tissue in Male Mice Exposed Perinatally to 2,2′,4,4′-Tetrabromodiphenyl Ether (BDE-47)

For the majority of lipophilic compounds, adipose tissue is traditionally considered as a storage depot and only rarely as a target organ. Meanwhile, abnormalities in adipose tissue physiology induced by chemical exposure may contribute to the current epidemic of obesity and metabolic diseases. Polybrominated diphenyl ethers (PBDEs) are a group of lipophilic flame retardants found in the majority of human samples in North America. Their ability to alter the physiology of adipose tissue is unknown. We exposed pregnant mice to 0.2 mg/kg body weight/day of BDE-47 perinatally. Transcriptomic changes in gonadal adipose tissue were analyzed in male offspring using the RNA-seq approach with subsequent bioinformatic analysis. The expression of genes of coagulation and complement cascade, de novo lipogenesis, and xenobiotic metabolism was altered in response to BDE-47 exposure. The affected molecular network included the following hubs: PPARα, HNF1A, and HNF4. These findings suggest that adipose tissue should be considered a target tissue for BDE-47, in addition to its role as a storage depot. This study also builds a background for a targeted search of sensitive phenotypic endpoints of BDE-47 exposure, including lipid profile parameters and coagulation factors in circulation. Additional studies are needed to investigate the role of PBDEs as an obesogen

Chemical Exposures Affect Innate Immune Response to SARS-CoV-2

Severe outcomes of COVID-19 are associated with pathological response of the immune system to the SARS-CoV-2 infection. Emerging evidence suggests that an interaction may exist between COVID-19 pathogenesis and a broad range of xenobiotics, resulting in significant increases in death rates in highly exposed populations. Therefore, a better understanding of the molecular basis of the interaction between SARS-CoV-2 infection and chemical exposures may open opportunities for better preventive and therapeutic interventions. We attempted to gain mechanistic knowledge on the interaction between SARS-CoV-2 infection and chemical exposures using an in silico approach, where we identified genes and molecular pathways affected by both chemical exposures and SARS-CoV-2 in human immune cells (T-cells, B-cells, NK-cells, dendritic, and monocyte cells). Our findings demonstrate for the first time that overlapping molecular mechanisms affected by a broad range of chemical exposures and COVID-19 are linked to IFN type I/II signaling pathways and the process of antigen presentation. Based on our data, we also predict that exposures to various chemical compounds will predominantly impact the population of monocytes during the response against COVID-19

Transformation of group A streptococci by electroporation

The introduction, via electroporation, of free plasmid DNA into three strains of Streptococcus pyogenes is described. The method is very simple and rapid and efficiencies vary from 1 × 10^3 to 4 × 10^4 per µg of DNA. The method was also used to introduce an integrative plasmid and transformants were obtained, albeit at a somewhat lower frequency (2 × 10^2). Some of the plasmids used in this study are derivatives of the Lactococcus lactis subsp. cremoris Wg2 plasmid pWV01. These broad host range vectors replicate in Gram-positives as well as Gram-negatives (viz. Escherichia coli). Here we show that they also replicate in S. pyogenes and S. sanguis

Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3

We report here the draft genome sequence of the bacteriocin producer Enterococcus faecium strain L-3, isolated from a probiotic preparation, Laminolact, which is widely used in the Russian Federation. The draft genome sequence is composed of 74 contigs for a total of 2,643,001 bp, with 2,646 coding genes. Five clusters for bacteriocin production were found

Using Controlled Shunt Reactors for Voltage Stabilization on the Example of Real Electric Power System

The article is devoted to actual task of real-time simulation controlled shunt reactors to use in the appropriate electric power system. Such development allows fully and reliably reproducing the processes running in controlled shunt reactors and electric power systems as whole. As an example of such task solution the working results of controlled shunt reactors simulation and its application for voltage stabilization are presented

Data on chemical-gene interactions and biological categories enriched with genes sensitive to chemical exposures

A dataset of chemical-gene interactions was created by extracting data from the Comparative Toxicogenomics Database (CTD) with the following filtering criteria: data was extracted only from experiments that used human, rat, or mouse cells/tissues and used high-throughput approaches for gene expression analysis. Genes not present in genomes of all three species were filtered out. The resulting dataset included 591,084 chemical-gene interaction. All chemical compounds in the database were annotated for their major uses. For every gene in the database number of chemical-gene interactions was calculated and used as a metric of gene sensitivity to a variety of chemical exposures. The lists of genes with corresponding numbers of chemical-gene interactions were used in gene-set enrichment analysis (GSEA) to identify potential sensitivity to chemical exposures of molecular pathways in Hallmark, KEGG and Reactome collections. Thus, data presented here represent unbiased and searchable datasets of sensitivity of genes and molecular pathways to a broad range of chemical exposures. As such the data can be used for a diverse range of toxicological and regulatory applications. Approach for the identification of molecular mechanisms sensitive to chemical exposures may inform regulatory toxicology about best toxicity testing strategies. Analysis of sensitivity of genes and molecular pathways to chemical exposures based on these datasets was published in Chemosphere (Suvorov et al., 2021)

Approach to Creating an Information-Control System of Hybrid Power System Simulator

The results of development and experimental investigations of information and control hybrid simulator system of conventional and smart grids are considered in the paper. The fragments of the given system experimental investigation and its software tools are provided. Performed results illustrate the possibilities and features offered to a user and necessary for solution of complex power system design, research and exploitation tasks

Consolidating Russia and Eurasia Antibiotic Resistance Data for 1992–2014 Using Search Engine

Background: The World Health Organization recognizes the antibiotic resistance problem as a major health threat in the 21st century. The paper describes an effort to fight it undertaken at the verge of two industries - healthcare and Data Science. One of the major difficulties in monitoring antibiotic resistance is low availability of comprehensive research data. Our aim is to develop a nation-wide antibiotic resistance database using Internet search and data processing algorithms using Russian language publications. Materials and methods: An interdisciplinary team built an intelligent Internet search filter to locate all publicly available research data on antibiotic resistance in Russia and Eurasia countries, extracted it, and collated it for analysis. A database was constructed using data from 850 original studies conducted at 153 locations in 12 countries between 1992 and 2014. The studies contained susceptibility and resistance rates of 156 microorganisms to 157 antibiotic drugs. Results: The applied search methodology was highly robust in that it yielded search precision of 58% versus 20% in a typical Internet search. It allowed finding and collating within the database the following data items (among many others): publication details including title, source, date, authors, etc.; study details: time period, locations, research organization, therapy area, etc.; microorganisms and antibiotic drugs included in the study along with prevalence values of resistant and susceptible strains, and numbers of isolates.The next stage in project development will try to validate the data by matching it to major benchmark studies; in addition, a panel of experts will be convened to evaluate the outcomes.Conclusions: The work provides a supplementary tool to national surveillance systems in antibiotic resistance, and consolidates fragmented research data available for 12 countries for a period of more than 20 years