cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.103854
title: Poster: Flying non-LTR retrotransposons.

description: Poster presented at Frontiers of Retrovirology'09 Flying non-LTR retrotransposons: DNA transposons as freely available “wings”? Olga Novikova, Alexander Blinov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Horizontal transmission (HT) can be defined as the process by which genes move between reproductively isolated species. Many examples of HT of transposable elements have been identified in eukaryotes. The mechanisms of HT are still unknown since it is not possible experimentally to show how the HT can occur. The frequencies of HT events are not equal among diverse types of transposable elements. Majority cases of putative HT are known for DNA transposons and LTR retrotransposons. According to the rough estimation, approximately 96% of HT events described for Drosophila account for LTR retrotransposons and DNA transposons, and only 4% - for non-LTR retrotransposons [1]. It seems to be that HT of non-LTR retrotransposons is relatively rare event. Previously, we provided strong evidences for the recent horizontal transmission of CR1 non-LTR retrotransposons between silkmoth (Bombycidae) and large blue butterflies, genus Maculinea (Lycaenidae) [2]. The further investigations showed that the multiple HT events of DNA transposons took place between the same groups (Bombycidae and Lycaenidae) recently. At the same time, HTs among other groups of lepidopterans appeared to be relatively rare. Moreover, we identified number of chimeric DNA transposons in genomes of Bombyx and Maculinea which carry insertions of non-LTR retrotransposons (including CR1) and capable for transposition since insertions did not disrupt coding regions of DNA transposons. Thus we can suppose that non-LTR retrotransposons have ridden DNA transposons and used them as the “wings” for their transmission. We also suppose that the features of life cycles of large blue butterflies and silkmoth played important roles in increasing of HT frequency. Large blue butterflies are living in ant nests during the third larvae stage where they are fed by ants or eat up ant’s larvae. Silkmoth characterized by periodical massive outbreaks and can represent main course in ants menu during such years. The ant nest can be the crucial point of tangency between donor of chimeric DNA transposons (silkmoth) and recipient (common ancestor of large blue butterflies). References 1. Loreto EL, Carareto CM, Capy P: Revisiting horizontal transfer of transposable elements in Drosophila. Heredity 2008, 100:545-554. 2. Novikova O., Sliwińska E., Fet V., Settele J., Blinov A., Woyciechowski M: CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol 2007, 7:93.
DOI: 10.6084/m9.figshare.103868
title: Transmission electron microscopy of an arf1 mutant in yeast

description: Electron micrographs of <em>arf1</em> mutant yeast cells.
DOI: 10.6084/m9.figshare.103868.v1
title: Transmission electron microscopy of an arf1 mutant in yeast

description: Electron micrographs of <em>arf1</em> mutant yeast cells.
DOI: 10.6084/m9.figshare.103854.v1
title: Poster: Flying non-LTR retrotransposons.

description: Poster presented at Frontiers of Retrovirology'09 Flying non-LTR retrotransposons: DNA transposons as freely available “wings”? Olga Novikova, Alexander Blinov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Horizontal transmission (HT) can be defined as the process by which genes move between reproductively isolated species. Many examples of HT of transposable elements have been identified in eukaryotes. The mechanisms of HT are still unknown since it is not possible experimentally to show how the HT can occur. The frequencies of HT events are not equal among diverse types of transposable elements. Majority cases of putative HT are known for DNA transposons and LTR retrotransposons. According to the rough estimation, approximately 96% of HT events described for Drosophila account for LTR retrotransposons and DNA transposons, and only 4% - for non-LTR retrotransposons [1]. It seems to be that HT of non-LTR retrotransposons is relatively rare event. Previously, we provided strong evidences for the recent horizontal transmission of CR1 non-LTR retrotransposons between silkmoth (Bombycidae) and large blue butterflies, genus Maculinea (Lycaenidae) [2]. The further investigations showed that the multiple HT events of DNA transposons took place between the same groups (Bombycidae and Lycaenidae) recently. At the same time, HTs among other groups of lepidopterans appeared to be relatively rare. Moreover, we identified number of chimeric DNA transposons in genomes of Bombyx and Maculinea which carry insertions of non-LTR retrotransposons (including CR1) and capable for transposition since insertions did not disrupt coding regions of DNA transposons. Thus we can suppose that non-LTR retrotransposons have ridden DNA transposons and used them as the “wings” for their transmission. We also suppose that the features of life cycles of large blue butterflies and silkmoth played important roles in increasing of HT frequency. Large blue butterflies are living in ant nests during the third larvae stage where they are fed by ants or eat up ant’s larvae. Silkmoth characterized by periodical massive outbreaks and can represent main course in ants menu during such years. The ant nest can be the crucial point of tangency between donor of chimeric DNA transposons (silkmoth) and recipient (common ancestor of large blue butterflies). References 1. Loreto EL, Carareto CM, Capy P: Revisiting horizontal transfer of transposable elements in Drosophila. Heredity 2008, 100:545-554. 2. Novikova O., Sliwińska E., Fet V., Settele J., Blinov A., Woyciechowski M: CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol 2007, 7:93.
DOI: 10.6084/m9.figshare.103784
title: Database - Research grant NN113181739

description: Computation databases for the reserach on dividend policy and share buybacks outcomes on WSE.
DOI: 10.6084/m9.figshare.103898.v1
title: chc1 steady Pb cytrate-20zoom4.tif

description: Electron micrographs of chc1 (clathrin heavy chain) mutant yeast cells.
DOI: 10.6084/m9.figshare.103784.v2
title: Database - Research grant NN113181739

description: Computation databases for the reserach on dividend policy and share buybacks outcomes on WSE.
DOI: 10.6084/m9.figshare.103785.v1
title: Statistical analysis on colorectal adenomas. Role of the lynphocitary inflammatory infiltrateGA 1995 - PII0016508595261575.pdf

description: INTRODUCTION<br>The colon and rectum carcinoma is an heterogeneous disease. Clinical, biological, histopathological and experimental evidences back up the theory of the adenoma-carcinoma sequence evidences.<br>Among the histopathologlcal characteristics,the variables studied are subjective, although we have recently started. Using quantifying techniques in the morphological study (9), in order to obtain more objective parameters. As far as we know, these techniques have not yet been used in this pathobiology.<br>The present work aims to introduce the information of conventional histopathological techniques, AgNORs and morphometric (glandular and nuclear types) in order to put in relation these variables in the pathology of the adenoma-carcinoma sequence.<br>MATERIAL AND METHOD<br>We selected 100 consecutive patients, 50 with adenoma (33 with low-grade -LGA- dysplasia and 17 with high-grade -HGA- and 50 with adenocarcinoma-(ACA)- who were studied in the conventional way. From these patients we obtained representative surgical and endoscopic samples that we stained with H-E for histopathological diagnostic and morphometric study purposes (Zeiss-KontronMOP-Videoplan image analyzer) as well as for argentic techniques for the AgNORs quantifying.<br>We studied glandular and nuclear variables(area, perimeter, maximum diameter and shape factor) and the cellular proliferation (mitotic index, nuclear organising antigen -AgNORs-) in both neoplasia types and with regard to the nuclear atypia grade (dysplasia) in the adenomas (Kruskal-Wallis tests and by-steps discrimination).<br>RESULTS<br>In the one variant statistical and stepwise discriminant survey, the variables that showed significant differences (p&lt;0.05), were as follows: mitotic index (LGA 10,8; HGA 11,0; ACA 22,5), nuclear perimeter (media) (LGA 10,6; HGA 11,3; ACA 14,4), nuclear area (standard deviation, DT) (LGA 6,9; HGA 9,4; ACA 10,0) maximum nuclear diameter (DT) (LGA 2,6; HGA 3,0; ACA 3,8), maximum glandular diameter (media) (LGA 0,2; HGA 0,1; ACA0,09), glandular shape factor (media) (LGA 0,7; HGA0,7; ACA 0,6), glandular shape factor (DT) (LGA 0,1; HGA0,1; ACA 0,2), luminal nucleus~edge distance (media) (LGA 17,1; HGA 16,1; ACA 12,0). We noticed a progressive increase of the area, maximum diameter and nuclear perimeter, mitotic index along with a gradual decrease of the glandular shape and luminal nucleus-edge distance.<br>CONCLUSION<br>Therefore, the development of adenocarcinomas in colon and rectum adenomas happens over increasing dysplasia grades: higher nuclear size and mitosis index, smaller and more abnormal glands together with loss of the nucleus basal polarity.
DOI: 10.6084/m9.figshare.103784.v1
title: Dividend - Database

description: Computation database for the reserach on dividend policy outcomes on WSE. Research grant NN113181739
DOI: 10.6084/m9.figshare.103775
title: Repeated PCR reactions of reciprocal crosses between svt2 and Col-0 wild-type lines

description: Numbers correspond to gel lanes above. Letters C and H indicate Col or heterozygous genotype, respectively. n.d., not detected
DOI: 10.6084/m9.figshare.103774
title: Reciprocal crosses between svt2 and Col-0 wild-type lines

description: Molecular analysis of the InDel polymorphism markers showed evidence of cryptic but persistent homozygosity, irrespective of the direction of the sexual cross (L1). However, heterozygosity was expected at all loci. n.d., not detected. * indicates that a PCR product failed to generate for these reactions
DOI: 10.6084/m9.figshare.103785.v2
title: Statistical analysis on colorectal adenomas. Role of the lynphocitary inflammatory infiltrate

description: INTRODUCTION<br>The colon and rectum carcinoma is an heterogeneous disease. Clinical, biological, histopathological and experimental evidences back up the theory of the adenoma-carcinoma sequence evidences.<br>Among the histopathologlcal characteristics,the variables studied are subjective, although we have recently started. Using quantifying techniques in the morphological study (9), in order to obtain more objective parameters. As far as we know, these techniques have not yet been used in this pathobiology.<br>The present work aims to introduce the information of conventional histopathological techniques, AgNORs and morphometric (glandular and nuclear types) in order to put in relation these variables in the pathology of the adenoma-carcinoma sequence.<br>MATERIAL AND METHOD<br>We selected 100 consecutive patients, 50 with adenoma (33 with low-grade -LGA- dysplasia and 17 with high-grade -HGA- and 50 with adenocarcinoma-(ACA)- who were studied in the conventional way. From these patients we obtained representative surgical and endoscopic samples that we stained with H-E for histopathological diagnostic and morphometric study purposes (Zeiss-KontronMOP-Videoplan image analyzer) as well as for argentic techniques for the AgNORs quantifying.<br>We studied glandular and nuclear variables(area, perimeter, maximum diameter and shape factor) and the cellular proliferation (mitotic index, nuclear organising antigen -AgNORs-) in both neoplasia types and with regard to the nuclear atypia grade (dysplasia) in the adenomas (Kruskal-Wallis tests and by-steps discrimination).<br>RESULTS<br>In the one variant statistical and stepwise discriminant survey, the variables that showed significant differences (p&lt;0.05), were as follows: mitotic index (LGA 10,8; HGA 11,0; ACA 22,5), nuclear perimeter (media) (LGA 10,6; HGA 11,3; ACA 14,4), nuclear area (standard deviation, DT) (LGA 6,9; HGA 9,4; ACA 10,0) maximum nuclear diameter (DT) (LGA 2,6; HGA 3,0; ACA 3,8), maximum glandular diameter (media) (LGA 0,2; HGA 0,1; ACA0,09), glandular shape factor (media) (LGA 0,7; HGA0,7; ACA 0,6), glandular shape factor (DT) (LGA 0,1; HGA0,1; ACA 0,2), luminal nucleus~edge distance (media) (LGA 17,1; HGA 16,1; ACA 12,0). We noticed a progressive increase of the area, maximum diameter and nuclear perimeter, mitotic index along with a gradual decrease of the glandular shape and luminal nucleus-edge distance.<br>CONCLUSION<br>Therefore, the development of adenocarcinomas in colon and rectum adenomas happens over increasing dysplasia grades: higher nuclear size and mitosis index, smaller and more abnormal glands together with loss of the nucleus basal polarity.
DOI: 10.6084/m9.figshare.103774.v1
title: Reciprocal crosses between svt2 and Col-0 wild-type lines

description: Molecular analysis of the InDel polymorphism markers showed evidence of cryptic but persistent homozygosity, irrespective of the direction of the sexual cross (L1). However, heterozygosity was expected at all loci. n.d., not detected. * indicates that a PCR product failed to generate for these reactions
DOI: 10.6084/m9.figshare.103775.v1
title: Repeated PCR reactions of reciprocal crosses between svt2 and Col-0 wild-type lines

description: Numbers correspond to gel lanes above. Letters C and H indicate Col or heterozygous genotype, respectively. n.d., not detected
DOI: 10.6084/m9.figshare.103771
title: Quantitative PCR to verify that VTC1 is a single copy gene in Col-0 and Ler-0 wild types and vtc1-1 and svt2 mutants

description: Quantitative PCR was performed as described in Materials and Methods. The PAD4 gene is a known single copy gene. Therefore, an RQ/RQ ratio of approximately 1 indicates that VTC1 is present in similar quantity as PAD4, and therefore a single-copy gene
DOI: 10.6084/m9.figshare.103772
title: Summary of PCR-based molecular genotypes

description: With the exception of svt2 Col R1 M2, where Col and Ler markers and one heterozygous marker were found (svt2 M2 Col-0 rev.1), phenotype matched genotype. That is, a Col-like phenotype correlated with the presence of Col polymorphisms, while a Ler-like phenotype correlated with Ler polymorphisms. C, L, and H refer to Col, Ler, or heterozygous, respectively
DOI: 10.6084/m9.figshare.103767
title: Primary inflorescence length of Col-0 WT, vtc1-1, svt2 (M1) and Ler-0 WT (cm)

description: Primary inflorescence length when plants were four weeks old
DOI: 10.6084/m9.figshare.103771.v1
title: Quantitative PCR to verify that VTC1 is a single copy gene in Col-0 and Ler-0 wild types and vtc1-1 and svt2 mutants

description: Quantitative PCR was performed as described in Materials and Methods. The PAD4 gene is a known single copy gene. Therefore, an RQ/RQ ratio of approximately 1 indicates that VTC1 is present in similar quantity as PAD4, and therefore a single-copy gene
DOI: 10.6084/m9.figshare.103766
title: Total ascorbic acid of Col-0 WT, vtc1-1, and D3 suppressor mutants (μmol gFW-1)

description: Total ascorbic acid content per gram fresh weight in whole rosettes of three-week-old plants
DOI: 10.6084/m9.figshare.103767.v1
title: Primary inflorescence length of Col-0 WT, vtc1-1, svt2 (M1) and Ler-0 WT (cm)

description: Primary inflorescence length when plants were four weeks old
DOI: 10.6084/m9.figshare.103768
title: Total ascorbic acid of Col-0 WT, vtc1-1, svt2 (M1) and Ler-0 WT (μmol gFW-1)

description: Total ascorbic acid content per gram fresh weight in whole rosettes of three-week-old plants
DOI: 10.6084/m9.figshare.103769
title: Root lengths of Col-0 WT, vtc1-1, svt2 (M1) and Ler-0 WT (mm)

description: Root length in seven-day-old seedlings grown on 1x MS
DOI: 10.6084/m9.figshare.103768.v1
title: Total ascorbic acid of Col-0 WT, vtc1-1, svt2 (M1) and Ler-0 WT (μmol gFW-1)

description: Total ascorbic acid content per gram fresh weight in whole rosettes of three-week-old plants
DOI: 10.6084/m9.figshare.103764
title: Gaussian Job Archive for C12H9NO2S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.103765
title: Root lengths of Col-0 WT, vtc1-1, and D3 suppressor mutants (mm)

description: Root length in seven-day-old seedlings grown on 1x MS
DOI: 10.6084/m9.figshare.103764.v1
title: Gaussian Job Archive for C12H9NO2S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.103765.v1
title: Root lengths of Col-0 WT, vtc1-1, and D3 suppressor mutants (mm)

description: Root length in seven-day-old seedlings grown on 1x MS
DOI: 10.6084/m9.figshare.103766.v1
title: Total ascorbic acid of Col-0 WT, vtc1-1, and D3 suppressor mutants (μmol gFW-1)

description: Total ascorbic acid content per gram fresh weight in whole rosettes of three-week-old plants
DOI: 10.6084/m9.figshare.103745
title: Nephrology On-Demand 90-day blog metrics

description: Data showing the number of pageviews and reading time of 20 blog posts covering either local/regional or national/international nephrology conferences by readers from different regions. ‘Entrances’ refers to the number of visits to Nephrology On-Demand that occurred through a particular blog; this data was not used in the preparation of the manuscript.
DOI: 10.6084/m9.figshare.103707
title: Pan Matrix data

description: The file pan_matrix.txt is a huge table (tab-separated columns) where each row corresponds to a genome and each column to a domain sequences family. The rows are named by the BIOID-code, see map_ecoli.txt to look up the strain names. The columns are named Cluster 1, Cluster 2,...etc. The corresponding Pfam-A domain sequence is given in the file cluster_info.txt (see below). In cell (i,j) in this table you find the number of occurrences that domain sequence j has in genome number i.
DOI: 10.6084/m9.figshare.103707.v1
title: Pan Matrix data

description: The file pan_matrix.txt is a huge table (tab-separated columns) where each row corresponds to a genome and each column to a domain sequences family. The rows are named by the BIOID-code, see map_ecoli.txt to look up the strain names. The columns are named Cluster 1, Cluster 2,...etc. The corresponding Pfam-A domain sequence is given in the file cluster_info.txt (see below). In cell (i,j) in this table you find the number of occurrences that domain sequence j has in genome number i.
DOI: 10.6084/m9.figshare.103745.v1
title: Nephrology On-Demand 90-day blog metrics

description: Data showing the number of pageviews and reading time of 20 blog posts covering either local/regional or national/international nephrology conferences by readers from different regions. ‘Entrances’ refers to the number of visits to Nephrology On-Demand that occurred through a particular blog; this data was not used in the preparation of the manuscript.
DOI: 10.6084/m9.figshare.103706
title: Cluster information

description: The file cluster_info.txt is a table with two columns. Each row corresponds to a domain sequence family. These are named Cluster 1, Cluster 2,...etc. In the second column is listed the ordered occurrence of Pfam-A domains for each domain sequence family.
DOI: 10.6084/m9.figshare.103706.v1
title: Cluster information

description: The file cluster_info.txt is a table with two columns. Each row corresponds to a domain sequence family. These are named Cluster 1, Cluster 2,...etc. In the second column is listed the ordered occurrence of Pfam-A domains for each domain sequence family.
DOI: 10.6084/m9.figshare.103740.v1
title: JensWilting_Synchronisation_with_Delays_Poster.pdf

description: I investigate a population of N limit-cycle oscillators coupled on a network structure with time delays introduced by finite signal propagation speed and embedding on a ring. By numerical simulation I find that in complete graphs velocity waves arise that were unknown before. I present attempts to understand these as perturbations of the frequency-locked phase waves which are well-understood. In regular rings and small-world networks frequency synchronisation occurs with a large variety of phase patterns. While all these patterns seem to be almost equally probable in regular rings, small-world topology sometimes prefers one pattern to form for a large number of initial conditions. I propose implications of this for the creation and storage of firing patterns in the context of the temporal coding hypothesis for information processing in the brain. The presented results suggest future analysis in order to improve theoretical understanding of the new phenomena observed and to conclude the work begun here.
DOI: 10.6084/m9.figshare.103690.v1
title: [Morphological and biological features of neoplasms: Integration of molecular findings]

description: Integration of morphologic and molecular findings in neoplasms (for details, please refer to Histopathology 2008; 53(1):1-19). Molecular definition of neoplasm and precursor lesions. Intraepithelial lesions and topographic heterogeneity. Biological bases of neoplasm natural history. - Clonality and loss of heterozygosity (LOH) in neoplasms. Fractional allelic loss. - Genetic control of initiation and promotion. Tumor progression. - Topographic heterogeneity and tumor cell segregation. Accumulation of genetic alterations. - Molecular pathways pleiotropism and redundancy.
DOI: 10.6084/m9.figshare.103740.v2
title: JensWilting_Synchronisation_with_Delays_Poster.pdf

description: I investigate a population of N limit-cycle oscillators coupled on a network structure with time delays introduced by finite signal propagation speed and embedding on a ring. By numerical simulation I find that in complete graphs velocity waves arise that were unknown before. I present attempts to understand these as perturbations of the frequency-locked phase waves which are well-understood. In regular rings and small-world networks frequency synchronisation occurs with a large variety of phase patterns. While all these patterns seem to be almost equally probable in regular rings, small-world topology sometimes prefers one pattern to form for a large number of initial conditions. I propose implications of this for the creation and storage of firing patterns in the context of the temporal coding hypothesis for information processing in the brain. The presented results suggest future analysis in order to improve theoretical understanding of the new phenomena observed and to conclude the work begun here.
DOI: 10.6084/m9.figshare.103685
title: Sequence File (3)

description: Illumina filtered sequence file from swab sampling of surfaces inside a university classroom.
DOI: 10.6084/m9.figshare.103686
title: Metadata for swab sequences

description: Metadata for analyzing 16S sequence files from indoor surfaces.
DOI: 10.6084/m9.figshare.103688.v1
title: C-cell pathology: from pathology to molecular diagnostic

description: Lecture Objectives: - Clinical features - Gross pathology - Histopathology - Morphological features - Immunohistochemical profile - Precursor lesions/early neoplams - Differential diagnosis - Molecular pathway - Prognosis
DOI: 10.6084/m9.figshare.103683
title: Sequence file (1)

description: First of three fasta sequence files for indoor surfaces in a university classroom. All sequences are 16S ribosomal segements. Primers used were F515-R806. Reverse 806 reads are in this file.
DOI: 10.6084/m9.figshare.103684
title: Sequence file (2)

description: Second of 3 parts of the sequence file for indoor surfaces.
DOI: 10.6084/m9.figshare.103686.v1
title: Metadata for swab sequences

description: Metadata for analyzing 16S sequence files from indoor surfaces.