Different waves and directions of Neolithic migrations in the Armenian Highland

Background: The peopling of Europe and the nature of the Neolithic agricultural migration as a primary issue in the modern human colonization of the globe is still widely debated. At present, much uncertainty is associated with the reconstruction of the routes of migration for the first farmers from the Near East. In this context, hospitable climatic conditions and the key geographic position of the Armenian Highland suggest that it may have served as a conduit for several waves of expansion of the first agriculturalists from the Near East to Europe and the North Caucasus. Results: Here, we assess Y-chromosomal distribution in six geographically distinct populations of Armenians that roughly represent the extent of historical Armenia. Using the general haplogroup structure and the specific lineages representing putative genetic markers of the Neolithic Revolution, haplogroups R1b1a2, J2, and G, we identify distinct patterns of genetic affinity between the populations of the Armenian Highland and the neighboring ones north and west from this area. Conclusions: Based on the results obtained, we suggest a new insight on the different routes and waves of Neolithic expansion of the first farmers through the Armenian Highland. We detected at least two principle migratory directions: (1) westward alongside the coastline of the Mediterranean Sea and (2) northward to the North Caucasus. Electronic supplementary material The online version of this article (doi:10.1186/s13323-014-0015-6) contains supplementary material, which is available to authorized users

A curated dataset of modern and ancient high-coverage shotgun human genomes.

Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space

The prevalence of orodental trauma during epileptic seizures in terms of dental treatment – Survey study

Introduction Epilepsy is one of the most common neurological disorders. Seizures that occur during attacks may lead to head injuries. It is crucial to establish proper prophylactic management against trauma occurrence, as nowadays prevention is not sufficient. Aim Assessment of the frequency of head and intraoral trauma during epileptic seizures and to evaluate factors that may predispose to injuries. Material and Methods The questionnaire was carried out among 106 patients with epilepsy. Survey conducted questions regarding development of the disease and occurrence of orodental and head trauma. Results were statistically analyzed with the chi-square test (p<0.05). Results 52.4% of subjects admitted the occurrence of oral trauma during epileptic seizures. The most common were lips, tongue or cheeks injuries. 18% patients suffered from tooth crack and 17% from tooth fracture. 50% of respondents suffered from head trauma during seizures: 41% patients reported bruises, 39% burns, 37% wounds, 10% nose fractures, 7% eye socket trauma and 3% skull crack. 14.1% of respondents experienced dentist refusal to undertake treatment, while 4% of patients had epileptic attack during dental procedures. Conclusions Dental trauma is common result of epileptic seizures. It is necessary to implement prophylactic management to prevent hard and soft tissues injuries, for example by using custom-made mouthguards. Moreover, specially designed dental programs for this group of patients should be provided

Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning Approach

Background: During the last decades a number of genome-wide association studies (GWASs) has identified numerous single nucleotide polymorphisms (SNPs) associated with different complex diseases. However, associations reported in one population are often conflicting and did not replicate when studied in other populations. One of the reasons could be that most GWAS employ a case-control design in one or a limited number of populations, but little attention was paid to the global distribution of disease-associated alleles across different populations. Moreover, the majority of GWAS have been performed on selected European, African, and Chinese populations and the considerable number of populations remains understudied.Aim: We have investigated the global distribution of so far discovered disease-associated SNPs across worldwide populations of different ancestry and geographical regions with a special focus on the understudied population of Armenians.Data and Methods: We have used genotyping data from the Human Genome Diversity Project and of Armenian population and combined them with disease-associated SNP data taken from public repositories leading to a final dataset of 44,234 markers. Their frequency distribution across 1039 individuals from 53 populations was analyzed using self-organizing maps (SOM) machine learning. Our SOM portrayal approach reduces data dimensionality, clusters SNPs with similar frequency profiles and provides two-dimensional data images which enable visual evaluation of disease-associated SNPs landscapes among human populations.Results: We find that populations from Africa, Oceania, and America show specific patterns of minor allele frequencies of disease-associated SNPs, while populations from Europe, Middle East, Central South Asia, and Armenia mostly share similar patterns. Importantly, different sets of SNPs associated with common polygenic diseases, such as cancer, diabetes, neurodegeneration in populations from different geographic regions. Armenians are characterized by a set of SNPs that are distinct from other populations from the neighboring geographical regions.Conclusion: Genetic associations of diseases considerably vary across populations which necessitates health-related genotyping efforts especially for so far understudied populations. SOM portrayal represents novel promising methods in population genetic research with special strength in visualization-based comparison of SNP data

Transcriptional profiles of non-neuronal and immune cells in mouse trigeminal ganglia

Non-neuronal cells constitute 90%–95% of sensory ganglia. These cells, especially glial and immune cells, play critical roles in the modulation of sensory neurons. This study aimed to identify, profile, and summarize the types of trigeminal ganglion (TG) non-neuronal cells in naïve male mice using published and our own data generated by single-cell RNA sequencing, flow cytometry, and immunohistochemistry. TG has five types of non-neuronal cells, namely, glial, fibroblasts, smooth muscle, endothelial, and immune cells. There is an agreement among publications for glial, fibroblasts, smooth muscle, and endothelial cells. Based on gene profiles, glial cells were classified as myelinated and non-myelinated Schwann cells and satellite glial cells. Mpz has dominant expression in Schwann cells, and Fabp7 is specific for SCG. Two types of Col1a2+ fibroblasts located throughout TG were distinguished. TG smooth muscle and endothelial cells in the blood vessels were detected using well-defined markers. Our study reported three types of macrophages (Mph) and four types of neutrophils (Neu) in TG. Mph were located in the neuronal bodies and nerve fibers and were sub-grouped by unique transcriptomic profiles with Ccr2, Cx3cr1, and Iba1 as markers. A comparison of databases showed that type 1 Mph is similar to choroid plexus-low (CPlo) border-associated Mph (BAMs). Type 2 Mph has the highest prediction score with CPhi BAMs, while type 3 Mph is distinct. S100a8+ Neu were located in the dura surrounding TG and were sub-grouped by clustering and expressions of Csf3r, Ly6G, Ngp, Elane, and Mpo. Integrative analysis of published datasets indicated that Neu-1, Neu-2, and Neu-3 are similar to the brain Neu-1 group, while Neu-4 has a resemblance to the monocyte-derived cells. Overall, the generated and summarized datasets on non-neuronal TG cells showed a unique composition of myeloid cell types in TG and could provide essential and fundamental information for studies on cell plasticity, interactomic networks between neurons and non-neuronal cells, and function during a variety of pain conditions in the head and neck regions

Differential induction of total IgE by two Salmonella enterica serotypes

The main goal of this study was to establish how the inflammation caused by infection with two different Salmonella enterica serotypes, S. Typhimurium and S. Enteritidis, may lead to the predisposition to allergy as measured by total IgE level in the blood. Infection by S. Typhimurium did not affect the systemic IgE concentration while in S. Enteritidis-infected patients there was a significant 3.5-fold increase. This effect was especially profound in patients >4 years old, with up to the eight-fold increase above the norm. The degree of dysbiosis in these two infections measured with the comparative counts of cultivated bacteria showed an inverse relationship with the IgE concentration. Earlier we reported the elevated level of IL-17 in patients infected by S. Enteritidis. In the current study a significant correlation was found between the concentrations of IL-17 and IgE suggesting a possible role played by this cytokine in triggering the production of IgE in response to S. Enteritidis infection

The genetic history of the Southern Arc: a bridge between West Asia and Europe

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe

The Impact of Coronavirus on English Word-stock

In December 2019, the news of the coronavirus outbreak spread worldwide for the first time. At present, this historical event has already influenced merely all aspects of life. The language is one of the first that reflected the massive events occurring throughout the world.In the frame of this article, an attempt is made, firstly, to figure out dozens of new words, expressions and new definitions emerged in English due to global changes. Secondly, are considered the semantic changes some words have undergone as a result of extralinguistic processes i.e., narrowing of meaning, semantic broadening, etc. Thirdly, are emphasized the main word-formation means of coining new words and expressions: suffixation, compounding, abbreviation, etc

Structural Semantic Patterns with Negative Prefixes: A Case Study in English and Armenian

The aim of this article is to provide a general overview of the unique architecture of verb compounds in English and Armenian.It is well acknowledged that contrastive study can be used to get new insights into this or that linguistic phenomenon and the findings can prove to be useful both for the source and the target language. What is needed for cross-lingual comparison is structure perspectively, i.e., taking the meaning not the form as the starting point.Our research question is two-fold: How are semantically structured verb compounds in negative prefixes and How are these patternings rendered from English into Armenian

Auswirkungen der Jimpy Mutation auf retinale Morphologie und Funktion

Die Jimpy Maus hat eine Punktmutation im Proteolipid-Protein Gen (PLP1). Die resultierende Fehlfaltung des Proteins führt zum Zelltod von Oligodendrozyten, Zerstörung der Myelinscheide und nicht angemessen myelinisierten Neuronen im zentralen Nervensystem (ZNS). Es ist nicht bekannt, wie das Fehlen normaler Myelinisierung während der Entwicklung neuronale Funktionen beeinflusst. Aus diesem Grund charakterisierte ich die Netzhaut der Jimpy Maus, um herauszufinden, ob fehlende Myelinisierung im Sehnerv während der Entwicklung Einfluss hat auf die normale Funktion und Morphologie der Netzhaut. Messungen des optokinetischen Reflexes zeigten, dass Jimpy Mäuse im Allgemeinen ein funktionelles visuelles System besitzen. Sowohl PLP1 Antikörperfärbung als auch RT-PCR für PLP1 mRNA zeigten, dass PLP1 nicht in Wildtyp Retina exprimiert ist. Jedoch im Sehnerv, wo PLP1 normalerweise exprimiert wird, war folglich in Jimpy Mäusen die Myelinisierung von Axonen meistens nicht vorhanden. Dennoch waren weder die Anzahl der Axone noch deren Ultrastruktur im Sehnerv betroffen. Physiologische Aufzeichnungen von Ganglienzellaktivität mit Mikroelektroden-Arrays ergab eine Abnahme der vom Stimulus erzeugten Aktivität bei mesopischem Lichtpegel. Morphologische Analysen der Netzhaut zeigten keine signifikanten Unterschiede in der Gesamtmorphologie, wie Dicke der Netzhautschichten oder Zellzahl in der äußeren Körnerschicht. Die Zellkörper in den inneren und äußeren Körnerschichten waren jedoch in der Netzhaut der Jimpy Mäuse größer. Antikörperfärbung mittels Zelltyp-spezifischen Markern zeigte, daß die Anzahl von Stäbchenbipolaren und Horizontalzellen in Jimpy Mäusen erhöht ist. Während die Jimpy Mutation also dramatische Auswirkungen auf die Myelinisierung der Axone von retinalen Ganglienzellen hat, hat sie nur moderate Auswirkungen auf retinale Morphologie und Funktion