bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unique and Shared Functions of Nuclear Lamina LEM Domain Proteins in Drosophila
Authors: Barton Lacy J , Wilmington Shameika R , Martin Melinda J , Skopec Hannah M , Lovander Kaylee E , Pinto Belinda S , Geyer Pamela K 
Published: April 2014

Abstract
The nuclear lamina is an extensive protein network that contributes to nuclear structure and function. LEM domain (LAP2, emerin, MAN1 domain, LEM-D) proteins are components of the nuclear lamina, identified by a shared ∼45-amino-acid motif that binds Barrier-to-autointegration factor (BAF), a chromatin-interacting protein. Drosophila melanogaster has three nuclear lamina LEM-D proteins, named Otefin (Ote), Bocksbeutel (Bocks), and dMAN1. Although these LEM-D proteins are globally expressed, loss of either Ote or dMAN1 causes tissue-specific defects in adult flies that differ from each other. The reason for such distinct tissue-restricted defects is unknown. Here, we generated null alleles of bocks, finding that loss of Bocks causes no overt adult phenotypes. Next, we defined phenotypes associated with lem-d double mutants. Although the absence of individual LEM-D proteins does not affect viability, loss of any two proteins causes lethality. Mutant phenotypes displayed by lem-d double mutants differ from baf mutants, suggesting that BAF function is retained in animals with a single nuclear lamina LEM-D protein. Interestingly, lem-d double mutants displayed distinct developmental and cellular mutant phenotypes, suggesting that Drosophila LEM-D proteins have developmental functions that are differentially shared with other LEM-D family members. This conclusion is supported by studies showing that ectopically produced LEM-D proteins have distinct capacities to rescue the tissue-specific phenotypes found in single lem-d mutants. Our findings predict that cell-specific mutant phenotypes caused by loss of LEM-D proteins reflect both the constellation of LEM-D proteins within the nuclear lamina and the capacity of functional compensation of the remaining LEM-D proteins.
A RAD-Tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish
Authors: Amores Angel , Catchen Julian , Nanda Indrajit , Warren Wesley , Walter Ron , Schartl Manfred , Postlethwait John H 
Published: April 2014

AbstractMammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3–40 among deer alone); in contrast, teleost fish genomes are stable (24–25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years.
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
Authors: Raj Anil , Stephens Matthew , Pritchard Jonathan K 
Published: April 2014

Abstract
Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH–Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford.edu/structure.html.
Plant remains from the Polish Triassic. Present knowledge and future prospects
Authors: Pacyna Grzegorz 
Published: April 2014

ABSTRACT
The Triassic plant macrofossils of Poland are very poorly known. There are few Triassic rock exposures here, they contain very few plant specimens, there is little scientific interest in the subject, and the rare plant remains found in drill cores are of low stratigraphical significance. The Lower Triassic macroflora is surprisingly poorer taxonomically than coeval European floras, and only single specimens have been found. The flora of the Middle Triassic is even poorer as a result of the Muschelkalk sea transgression. Only the Upper Triassic floras contain many specimens and taxa. The Upper Triassic macrofloras from Polish territory are well known since the early 19th century. Pioneering descriptions of these floras were given by Goeppert and Raciborski. From the Polish Triassic, the seed fern Lepidopteris ottonis (index species for the Rhaetian stage) and Neocalamites lehmannianus (sphenopsid species typical of almost all European Upper Triassic and Lower Jurassic floras) were described for the first time ever. In the 20th century only single specimens were described from outcrops and drill cores. Barbacka revised Lepidopteris ottonis specimens from old collections and described some new material. Palynological research on Triassic strata in Poland intensified from the 1970s on. That work has produced spore-pollen and megaspore zonations for Triassic strata in Poland, but the correlation of the dispersed spores and pollen grains with their parent plants is low. The Polish Triassic flora is comprised of ferns, lycopsids, sphenopsids, cycads, bennettitaleans, ginkgoaleans and conifers. This flora is taxonomically poorer than equally old and geographically close European floras. All available data about Polish Triassic plants fossils are critically summarised in this paper for the first time. The biostratigraphical and lithostratigraphical correlations of Polish Triassic floras with other European Triassic floras are outlined. New macrofloral assemblages for the Lower and Middle Triassic and macrofloral assemblage zones for the Upper Triassic are proposed for Poland. Recent new finds of taxonomically rich, abundant and well-preserved floras accompanying vertebrate remains in Silesia provide an opportunity for comprehensive research on Polish Triassic floras. This should improve our perception of their taxonomy and allow them to be described in evolutionary and palaeoecological contexts
Observations Concerning the Thickness of Rocks Eroded Between the Cambrian and Bolsovian (= Westphalian C) in Central and Western Bohemia
Authors: Pešek Jiří , Martínek Karel 
Published: April 2014

Abstract
Carboniferous outliers are found west of the late Carboniferous West Bohemian basins and also south of the West and Central Bohemian basins. The West Bohemian group is Asturian (= Westphalian D) or younger and is notably coal-bearing, the other group of outliers consists mostly of coal-bearing upper Carboniferous volcaniclastic rocks of Bolsovian (= Westphalian C) and/or Asturian age. They form a discontinuous belt extending through the area between and around the towns of Merklín and Beroun. These rocks are underlain chiefly by rocks of ages varying from the Neoproterozoic or Cambrian up to the Ordovician. If the nappe structure of the Barrandian Lower Paleozoic proposed by Melichar and Hladil (e.g. 1999) is not widely present, then it can be assumed that as much as 1850 m of Lower Paleozoic sediments and volcanics could have been eroded prior to the onset of sedimentation of the Bolsovian rocks. In the upper Carboniferous outliers near Mirošov, Skořice and Kamenný Újezd, where sedimentation began as late as in the Asturian, the thickness of eroded deposits might have been even greater, reaching as much as 3150 m.
Historical Influence of Man on the Vegetation Record in the Prášilské Lake Sediments (Bohemian Forest, Czech Republic)
Authors: Břízová Eva 
Published: April 2014

Abstract
The Prášilské Lake is the glacial lake in the Bohemian Forest (Šumava Mts) located on the Czech side in the elevation of 1,079 m above sea level. The lake area is 4 ha, the maximal depth is 15.5 m. The lake catchment area is situated in the sub-alpine zone. The studied area has never been the object of forest or agricultural farming in the history because of its inaccessibility. The sediment dating was carried out by means of lead isotope 210Pb. The oldest layer established by this isotope in the Prášilské Lake was in the depth of 0.47 m. This dating was used for the deepest layer of sediment and its age was dated to the year of 1843 (depth 0.11 m) and a base of this profile to the medieval age (depth 0.47 m), which corresponds to about the 12th-13th century A.D. The analysed profile (0-0.47 m) can be divided into the local pollen assemblage zones PRI-1 (depth 0.37-0.47 m), PRI-2 (depth 0.25-0.37 m), PRI-3 (depth 0.12- 0.25 m), PRI-4 (depth 0.06-0.12 m), PRI-5 (depth 0.02-0.06 m), PRI-6 (depth 0-0.02 m). On the basis of dating by the 210Pb method the age of sediment (0-0.11 m) is established into the range of 1843 to 1994. It is noticeable in the pollen spectrum that it concerns a locality situated already above the forest border, the pollen curves of stratigraphical important taxons (mainly woody species) do not change markedly. The rich woody component is formed mainly by pollen grains of Picea and Fagus. The herbaceous component (NAP) is very diverse; however, in a general way the pollen grains of woody species (AP) predominate due to the above mentioned deciduous forests. A representation of the herbaceous component (NAP) is very varied as far as species are concerned, human influence is very visible here (e.g. occurrence of cereals Cerealia, Zea mays, Fagopyrum-type, weed: Centaurea cyanus, Agrostemma githago etc.). The dating of this part also corresponds to the results of the pollen analysis. Of the plants producing spores the findings of lesser clubmoss (Selaginella-type cf. Selaginella selaginoides) and water plant quillwort (Isoëtes), whose nearest contemporary place of the finding in our territory is in the Černé and Plešné Lake and Wielki Staw (the Giant Mts), were quite interesting. The most of spores were recorded at the family Polypodiaceae and green alga Botryococcus, which indicate cold and humid conditions of the occurrence.
Revision of the Pennsylvanian Flora from Val Sanagra in Western Part of the Southern Alps (Italy)
Authors: Pšenička Josef , Opluštil Stanislav , Ronchi Ausonio , Šimůnek Zbyněk 
Published: April 2014

Abstract
The Pennsylvanian flora from the Alpe Logone/Val Sanagra locality in the Western Lombardy (Southern Alps, Italy) last underwent a taxonomic study in the mid 20th century. The main problem is generally poor preservation of the plant remains, which makes their identification problematic. Despite this, the authors have identified 43 fossil species from this locality. Based on the sedimentary context of this paleoflora, we assume that the Val Sanagra sediments were deposited in a continental setting, in a fluvial environment with a well-developed and vegetated floodplain where where clastic substrates would locally and occasionally change into peat swamp. The common presence of rhytidolepis and sub-rhytidolepis sigillarias, as well of Eusphenopteris neuropteroides, Lobatopteris miltonii, Mariopteris latifolia, Paripteris linguaefolia, Pecopteris microphylla, Alethopteris sp. (cf. grandinii) indicates that the flora from the Val Sanagra locality spans the interval between the Duckmantian and Bolsovian (middle Moscovian), and thus represents one of the oldest Pennsylvanian floras of the Southern Alps.
Determination of chlorogenic and gallic acids by UPLC-MS/MS
Authors: Gryszczyńska Agnieszka , Opala Bogna , Łowicki Zdzisław , Krajewska-Patan Anna , Buchwald Waldemar , Czerny Bogusław , Mielcarek Sebastian , Boroń Dariusz , Bogacz Anna , Mrozikiewicz Przemysław M. 
Published: April 2014

Summary
The aim of our study were qualitative and quantitative analyses of two polyphenolic acids: chlorogenic and gallic acids. These compounds were determined in two species of Rhodiola: R. kirilowii and R. rosea. After collecting plants, aqueous and hydroalcoholic extracts were prepared. In order to identify analysed polyphenolic compounds ultra performance liquid chromatography - tandem mass spectrometry (UPLC-MS/MS, Waters) was used. Gallic acid is commonly found in the roots of these plants. Aqueous extract in both species is a rich source of gallic acid. The UPLC-MS/MS studies allow to use this analytical method for determination of polyphenolic acids accordance with the requirements of ICH. Chromatographic method developed by our team is more precise then previously published.
Chemical composition of Scaligeria meifolia Boiss. essential oil from Iran
Authors: Rowshan Vahid , Tarakemeh Ameneh 
Published: April 2014

Summary
Scaligeria meifolia Boiss., belonging to the Apiaceae family, grows wild in Iran. The essential oil from aerial parts of S. meifolia were obtained by hydrodistillation and analyzed by GC and GC/MS. Thirty-one constituents representing 99.98% of total oil components were identified. The main constituents of the essential oil were germacrene-D, (24.2%), germacrene-B (14.8%), limonene (14.2%), γ-elemene (11.6 %) and β-elemene (5.2%).
Determination of lotaustralin in Rhodiola species
Authors: Gryszczyńska Agnieszka , Łowicki Zdzisław , Opala Bogna , Krajewska-Patan Anna , Buchwald Waldemar , Czerny Bogusław , Mielcarek Sebastian , Mrozikiewicz Przemysław M. 
Published: April 2014

Summary
In our research, the concentration of lotaustralin in the roots of two species Rhodiola kirilowii and Rhodiola rosea were compared. Aqueous and hydroalcoholic extracts from those plants were analyzed too. To determine the content of this compound the ultra performance liquid chromatography - tandem mass spectrometry (UPLC-MS/MS, Waters) was used. The obtained results showed that the content of measured lotaustralin depends on the species of Rhodiola. R. rosea roots are the richer source of lotaustralin then R. kirilowii. The same situation was observed in the extracts. A hydroalcoholic extract from R. rosea contains up to 135.276 mg of lotaustralin in 100 g of dry powdered material. In the case of R. kirilowii extracts, an aqueous extract contained more lotaustralin (74.791 mg/100 g of dry powdered material) then a hydroalcoholic extract.
Permeation-enhancing properties of Nepeta cataria var. citriodora dry extract
Authors: Winnicki Andrzej M. , Śmieszek Jakub M. , Partyka Danuta , Modnicki Daniel 
Published: April 2014

Abstract
This paper presents the research on permeation enhancing properties of Nepeta cataria var. citriodora (catnip) dry extract in comparison to oleanolic acid and ursolic acid. Progesterone was chosen as a model substance for permeation test. The hydrogels made of hydroxypropylmethylcellulose with progesterone, enhancers and ethanol were applied in the study. The in vitro progesterone penetration test was based on the method proposed by Fürst, using artificial lipophilic membranes which were made of colloxylin and dodecanol. Statistical analyses showed an increase in penetration of progesterone caused by catnip dry extract in comparison to ursolic acid and blank sample. HPLC assay was applied to study the effect of enhancers on progesterone physicochemical properties. The solubility of progesterone was tested in solvent systems corresponding to liquid phases of gels. The statistical increase in progesterone solubility was observed in the presence of dry extract in comparison to the result from ursolic acid-containing sample. The partition coefficient of progesterone was evaluated by standard procedures. The statistically significant reduction of log P values for progesterone was determined in the presence of catnip dry extract
Antioxidant activities and polyphenolics content of Flammulina velutipes mushroom extracts
Authors: Sławińska Aneta , Radzki Wojciech , Kalbarczyk Janusz 
Published: April 2014

Abstract
A study was conducted in order to determine the content of phenolic compounds and antioxidative activity of extracts from Flammulina velutipes. Water and ethanolic, methanolic, acetone (70% v/v) extracts were prepared from lyophilized fruiting bodies of mushrooms. Different extraction techniques were used: ultrasonication and stirring by a rotary shaker at ambient temperature and at 50oC, and at boiling point for each solvent. Next, total phenolics by Folin-Ciocalteu method, antioxidant capacity (EC) by ferric reducing antioxidant power assay (FRAP) and scavenging ability on 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals were analysed in these extracts. It was observed that the extraction method and the kind of solvent influenced the antioxidant activity and concentration of total phenolics in the extracts. The highest concentration of phenolic compounds (7.58±0.17 mg GAE/g extract) were observed for water extract prepared with use of ultrasonification method (at 50oC for 1h). Results showed that water extracts possessed high equivalent capacity (EC) for all applied extraction methods. The highest EC value (9.2±0.18 mM Fe2+/g extract) was observed in water extract prepared by stirring at ambient temperature for 1 h. This extract was characterized by high level of total phenolics. The acetone extracts, prepared by ultrasonic extraction at 50oC for 1 h, at 10 mg/ml showed the highest scavenging activity (57.53±1.18%), although, the value was lower than that of ascorbic acid at 10 mg/ml (60.50±1.32%)
Antioxidant activity, total phenolic and flavonoids contents of three herbs used as condiments and additives in pickles products
Authors: Pirbalouti Abdollah Ghasemi , Setayesh Milad , Siahpoosh Amir , Mashayekhi Hamid 
Published: April 2014

Abstract
Heracleum lasiopetalum Boiss, Kelussia odoratissima Mozaff., and Echinophora platyloba DC. belong the Apiaceae family. They are Iranian endemic plants. These three herbs have been used as food additives in traditional preparations such as pickles. Antioxidant activity (AA) of methanol extracts (ME) of the plants was evaluated by three assays, including DPPH, FRAP, and TEAC. From all three assays, comparing all the MEs for their IC50 and EC1 values, E. platyloba had the highest AA. Total phenolic content (TPC) of the extracts ranged from 74 to 120 mg TAE/g. The extract of H. lasiopetalum exhibited the highest TPC. The flavonoids content (FC) of the extracts ranged from 7.63 to 14.52 mg RE/g, from which the extract of E. platyloba had the highest flavonoids concentration. A positive correlation between the FC and AA in DPPH assay was found. A significant correlation was also found between the TPC and AA in FRAP assay. These results suggested that the level of AA in these plants varied in a great extent. Our results indicated that extract of E. platyloba could be an important dietary source of flavonoids compounds with high antioxidant capacity. In addition, E. platyloba can be used as an alternative preservative and natural flavor instead of synthetic ones in food industry (especially pickles)
Effect of flavonoids content on antioxidant activity of commercial cosmetic plant extracts
Authors: Malinowska Paulina 
Published: April 2014

Abstract
The aim of this work was to evaluate the antioxidant capacity and flavonoids content in 10 commercial cosmetic plant extracts used in cosmetics industry. Antioxidant activity of plant extracts were measured using two methods: FRAP (Ferric Reducing Antioxidant Power) and TEAC (Trolox Equivalent Antioxidant Capacity). The relationship between flavonoids content and antioxidant capacity of plant extracts were checked. As a result of this research it was found that FRAP and TEAC values of plant extracts significantly depend on the flavonoids content. The highest antioxidant activity, both in FRAP and TEAC assays, was observed for arnica flowers, hawthorn flowers and lungwort herb extracts. These extracts can be used as source of natural antioxidants for the prolongation of the oxidative stability of cosmetic products. Additionally, they can replace synthetic antioxidants
Modest XML for Corpora: Not a standard, but a suggestion
Authors: Hardie Andrew 
Published: April 2014

Abstract
This paper argues for, and presents, a modest approach to XML encoding for use by the majority of contemporary linguists who need to engage in corpus construction. While extensive standards for corpus encoding exist - most notably, the Text Encoding Initiative’s Guidelines and the Corpus Encoding Standard based on them - these are rather heavyweight approaches, implicitly intended for major corpus-building projects, which are rather different from the increasingly common efforts in corpus construction undertaken by individual researchers in support of their personal research goals. Therefore, there is a clear benefit to be had from a set of recommendations (not a standard) that outlines general best practices in the use of XML in corpora without going into any of the more technical aspects of XML or the full weight of TEI encoding. This paper presents such a set of suggestions, dubbed Modest XML for Corpora, and posits that such a set of pointers to a limited level of XML knowledge could work as part of the normal, general training of corpus linguists.
The Modest XML recommendations cover the following set of things, which, according to the foregoing argument, are sufficient knowledge about XML for most corpus linguists’ day-to-day needs: use of tags; adding attribute value pairs; recommended use of attributes; nesting of tags; encoding of special characters; XML well-formedness; a collection of de facto standard tags and attributes; going beyond the basic de facto standard tags; and text headers.