bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Behavior of Nuclei during Mitosis of Lilium Hybrids
Authors: Sixiang Zheng , Feihu Liu , Chaojun Zhang , Zhilin Chen , Yuhua Ma , Pinghong Meng , Yan Zhao 
Published: October 2010

AbstractMitosis is nuclear division plus cytokinesis,and produces two identical daughter cells during prophase, prometaphase, metaphase, anaphase, and telophase. However, a new nucleus behavior in interspecific hybrid progenies of Lilium was observed in our experiment. Very unusual behaviors of nuclei surprisingly presented during the mitosis, such as sprouting or germination, tube-like elongation, penetrating cell membrane into a neighbor cell, the top of nuclei tube expanding, intruding and splitting of the tube-like nucleus, and micronucleus formation, and so on. Furthermore, the tetrad of meiosis was founded in mitosis of root.Routine of the unusual nucleus behaviors observed in our experiment may be summarized as nucleus germination¬— tube-like elongation— penetrating cell membrane— entering a neighbor cell—the top of nuclei tube expanding—tube ingression and splitting— formation of a new nucleus or micronucleus.Many kinds of abnormal mitosis caused by chemical and physical induction such as unequal division, chromosome bridges, lagging chromosomes, and multiple nuclei have resulted in variations of chromosome number and structure. However, this new nucleus behavior is firstly reported, these phenomena implied that the DNA maybe easily emigrates from one cell to another. Therefore, the unusual behaviors of nuclei in hybrid progenies of Lilium not only create mutations for breeding of new cultivars, also produce possibly ideal materials for exotic DNA or gene transfication with simple method in meristem. This mode of nuclei behaviors is a new addition to cytogenetics of plant of vegetative propagation and provide a new genetic mechanism of species evolution from interspecific hybridization.
11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2
Authors: Baker Michael 
Published: October 2010

Abstract11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish. Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively. Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs. Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known. An opportunity to understand their evolution is presented by the recent sequencing of genomes from sea urchin, a basal deuterostome, and amphioxus, a basal chordate, and the availability of substantial sequence for acorn worm and elephant shark, which together provide a more complete dataset for analysis of the origins of 11[beta]-HSD2 and 17[beta]-HSD2. BLAST searches find an ancestral sequence of 17[beta]-HSD2 in sea urchin, acorn worm and amphioxus, while an ancestral sequence of 11[beta]-HSD2 first appears in sharks. Sequence analyses indicate that 17[beta]-HSD2 in sea urchin may have a non-enzymatic activity. Evolutionary analyses indicate that if acorn worm 17[beta]-HSD2 is catalytically active, then it metabolizes novel substrate(s).
ADP-ribose polymer - a novel and general biomarker of human cancers of head & neck, breast, and cervix
Authors: Lakadong Rennie , Kataki Amal , Sharan Rajeshwar 
Published: October 2010

Abstract
Background:
Poly-ADP-ribosylation (PAR), a reversible post-translational modification of cellular proteins, is involved in various cellular and molecular processes including carcinogenesis (Althaus & Richter, 1987; Jacobson & Jacobson, 1989; Poirier & Moreau, 1992; Boulikas, 1993; Sharan, 2009). ADP-ribose polymer adducts are added onto target cellular proteins by this metabolic process. We hypothesize that a decrease in the concentration of total poly-ADP-ribose adducts of peripheral blood lymphocyte (PBL) proteins strongly correlates with incidence of human cancer. Methods: A novel, sensitive and convenient immunoprobe assay of poly-ADP-ribose adducts of cellular proteins has been employed using slot blots of total PBL lysate (Sharan et al, 1998; 2005; Sharan, 2009). This assay quantifies the metabolic concentration of poly-ADP-ribose adducts of cellular proteins.

Results:
Using the immunoprobe assay, we show a statistically significant (P ≤ 0.001) reduction (~ 42 to 49%) in the level of poly-ADP-ribose adducts of PBL proteins of patients with advanced cancers of head & neck (H & N) region (comprising fourteen distinct types of cancers at different sites), breast and cervix in comparison to healthy controls. Conclusion: These preliminary findings may imply potential utility of the poly-ADP-ribose adducts of PBL proteins as a novel and general biomarker of human cancers with potentials of clinical and epidemiological applications.
Toward a Complete Phyloreferencing Language
Authors: Keesey T. Michael 
Published: October 2010

AbstractA phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few “standard” forms (node, branch, and perhaps apomorphybased clades) without the capacity to represent more “exotic” forms (e.g., ancestorbased clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic graph, wherein nodes model taxonomic units and directed edges model immediate descent. Higher taxa are modeled as unions of nodes. A phyloreferencing language must minimally allow for certain classes of entity: Boolean values, sets (including taxa, relations, and the empty set), and lists (including graphs and functions). It must also minimally allow for basic operations related to logic, set theory, and graph theory. Higher structures such as declarations and piecewise constructs must also be possible. With these as a basis, functions related to phylogeny can be defined: maximal, minimal, predecessor union/intersection, successor union/intersection, exclusive predecessors, synapomorphic predecessors, clade, crown clade, and total clade. I show how such a language may be used to represent various types of phyloreference, both “standard” and “exotic”.
Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
Authors: Keesey T. Michael 
Published: October 2010

AbstractNames on Nodes^1^ is an opensource^2^ Flex application which utilizes a mathematical approach to automate the application of phylogeneticallydefined names to phylogenetic hypotheses. Phylogenetic hypotheses are modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (NEXUS, NexML, Newick, and GraphML) or created de novo. Hypotheses may also be merged from multiple sources. Names on Nodes stores hypotheses as MathML, an XMLbased language for representing mathematical content and presentation. Phylogenetic definitions may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and automatically apply them to phylogenetic hypotheses. In the current version of the application, such dictionaries exist only as MathML files, but in future versions definitions may also be loaded from databases (e.g., RegNum).Additional functionality in Names on Nodes includes the ability to coarsen a phylogenetic graph (thereby simplifying it while still reflecting the overall structure) or to export it as an image file (raster or vector, potentially with semantic annotations).1. Source code available at: "http://bitbucket.org/keesey/namesonnodes-sa/":http://bitbucket.org/keesey/namesonnodes‐sa/2. MIT license
Lethal and sublethal effects of polybrominated diphenyl ethers (PBDEs) for turbot (Psetta maxima) early life stage (ELS)
Authors: Mhadhbi Lazhar , Fumega Jose , Boumaiza Moncef , Beiras Ricardo 
Published: October 2010

AbstractA new toxic menace, polybrominated diphenyl ethers (PBDEs), is being detected in the aquatic environment all over the world. The environmental presence of PBDEs and its entry into the environment as BDE-47 and -99 make quality aquatic toxicity data necessary to assess the aquatic hazard risk of PBDs. This study examines the effects of three PBDE-47 and -99 on embryo and larval stages of the marine flatfish turbot (Psetta maxima). The acute toxicity of the three PBDEs was examined and NOEC, LOEC, LC10 and LC50 were calculated. All tested compounds caused lethal as well as nonlethal malformations during embryo development. The effects of PBDEs in the different life stages of turbot were analysed. PBDEs seemed to be teratogenic at concentrations higher than 8.14 and 16.12 µgL-1 for BDE-47 and -99 respectively, leading to prolonged delays in embryo development and consequent death (at 48 h), as well as severe malformations and mortality of larvae. PBDEs showed a higher acute toxicity for embryo-larvae (LC50 for lethal endpoints to embryos 27.35 µg BDE-47 L-1 and 38.28 µg BDE-99 L-1, and 14.13 and 29.64 µg L-1 for BDE-47 and -99, respectively for larvae). Generally, the BDE-47 seemed to cause adverse effects at comparatively low dose rates, whereas much higher doses were needed to cause the same effects with BDE-99. The results of the present study show that the acute toxicity of PBDEs decreases as the degree of bromination increases, since the order of toxicity was BDE-47 BDE-99. The major isomers also exhibited a clear toxic potential for turbot ELS although at high concentrations, above solubility saturation, pointing at particulate matter as the main via of uptake for those hydrophobic molecules.
Acute Toxicity of Perfluorooctane Sulfonic Acid on Early Life Stages of Daphnia Magna, Siriella Armata, Paracentrotus Lividus Sea Urchin, and Turbot (Scophthalmus Maximus L.).
Authors: Mhadhbi Lazhar , Pérez Fernandez Sara , Real Conde Diego , Boumaiza Moncef , Beiras Ricardo 
Published: October 2010

AbstractPerfluorooctane sulfonate (PFOS) is a persistent organic pollutant whose potential toxicity is causing great concern. In the present study, we used two crustaceans (Daphnia magna, Siriella armata), echinoid embryos (Paracentrotus lividus) and turbot (Scophthalmus maximus L.) embryos and larvae to investigate the acute toxicity of this compound. The marine species S. armata exhibited greater sensitivity than the freshwater species D. magna. In the 48-h acute toxicity test the median lethal concentration was 10.96 mg/L for S. armata and 87.46 mg/L for D. magna. In the 96h toxicity test, turbot showed the lowest EC50 (0.155 mgL-1), whilst the EC50 for S. armata was 7.92 mgL-1 which was approximately three times lower than that for sea urchin (24.12 mgL-1). The EC10 values were estimated as 0.032 mgL-1, 4.23 mgL-1 and 45.21 mgL-1 for turbot, Siriella and daphnia, respectively. The LOEC values were 75 µgL-1, 2.5 mgL-1 and 75 mgL-1 (p< 0.05) for turbot, daphnia, and Siriella, respectively. The NOEC values were estimated at 37.5 µgL-1, 1.25 mgL-1 and 50 mgL-1 (p< 0.05) for turbot, Siriella and daphnia, respectively. The order of acute toxicity was: turbot > S. armata > sea urchin > Daphnia magna. This result highlights the importance of including a marine fish in the battery of species to describe the toxicity of these compounds. Considering the persistent nature of PFOS, more research is required to determine potential consequences of long-term exposure to these compounds in aquatic ecosystems.
Cognitive Sciences and Child Poverty: Facts and Challenges
Authors: D'Angiulli Amedeo , Lipina Sebastian 
Published: October 2010

AbstractIn the context of cognitive neuroscience, the study of poverty and social gradients is a very young area of research where a core consensus of basic results is quickly emerging. However, as any emerging scientific discipline, the approaches used are influenced by epistemological stances inherited from other disciplines, and potentially implicit ideological systems as well. Explicitly or inadvertently, such influences can lead this critically important new area of research to methodological and ethical foundational challenges and to issues that are in need of debate (e.g., poverty definition criteria, lack of specificity when considering child poverty in terms of how children experience different type of deprivations, or lack of critics regarding social exclusion in different countries). Debate on these issues goes beyond consensus on interventions aiming at attenuating the effects of poverty on children’s development. Without an analysis of the emerging issues, scientist may dangerously risk the tendency to simplify the complexity that characterizes both phenomena of development and social inequality. The aim of the present paper is to contribute to a debate on the implicit and explicit conceptual and methodological assumptions underlying the current neurocognitive research on social inequality.
The Synthesis of Resveratrol (Thesis)
Authors: Sprouse Dustin 
Published: October 2010

AbstractThe purpose of this research experiment was to perform and improve the synthesis of resveratrol (CAS: 501-36-0). Resveratrol (trans-3,4',5-trihydroxystilbene), a natural polyphenolic, non-flavonoid antioxidant, is a phytoalexin found naturally in many plants. The compound was synthesized using the decarbonylative Heck reaction. The modified four-step reaction generated poor yields but the spectra indicate that the overall resveratrol compound was obtained. Several improvements were made to help increase yield.
Urban Creek flow, re-aeration and ecological health
Authors: Pollard Peter , Bagraith Sam 
Published: October 2010

AbstractFor two years we studied the health of a lowland freshwater ecosystem, Moggill Creek, flowing through the western suburbs of Brisbane Qld, Australia. We found: Terrestrial organic carbon was most likely driving very high bacterial growth and respiration rates that removed dissolved oxygen from the water. The diversity of fish and invertebrates was high and the overhanging riparian vegetation cover limited algal and cyanobacterial production. Overall the creek was in fair to good health—Report Grade“D”. Conclusion: Water column dissolved oxygen concentrations and Creek health relied on environmental flow during rain to physically re-aerate the water to counter the high bacterial consumption of oxygen that resulted from the respiration of the organic carbon loads that were entering the ecosystem.
A normalization technique for next generation sequencing experiments
Authors: Klambauer Günter , Schwarzbauer Karin , Mayr Andreas , Hochreiter Sepp 
Published: October 2010

AbstractNext generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of read counts from the estimated mean Poisson distribution indicate CNVs.
cn.FARMS: a probabilistic model to detect DNA copy numbers
Authors: Clevert Djork-Arné , Mitterecker Andreas , Mayr Andreas , Burger Robert , De Bondt An , Tuefferd Marianne , Talloen Willem , Göhlmann Hinrich , Hochreiter Sepp 
Published: October 2010

AbstractMotivation: Existing pre-processing methods for DNA microarrays designed to detect copy number variations (CNVs) lead to high false discovery rates (FDRs). High FDRs misguide researchers especially in the medical context where CNVs are wrongly associated with diseases. We propose a probabilistic latent variable model, cn.FARMS, for array-based CNV analysis which controls the FDR without loss of sensitivity. At a DNA region, cn.FARMS constructs a model by a Bayesian maximum a posteriori estimation where the unobserved, latent variable represents the copy number that is measured by observed genetic markers (probes). The latent variable’s prior prefers parameters which represent the null hypothesis, (same copy number for all samples), from which the posterior can only deviate by a high information content in the data. The more probes agree on the region’s copy number, the less is the uncertainty about the latent variable’s value, the higher is the information content. Results: We compared cn.FARMS on a HapMap Mapping250K_Nsp and SNP6.0 benchmark data set to CRMAv2 and dChip. The comparison is based on the sex determination based on the data from the X chromosome, where males possess one copy and females two. The ROC curve serves to compare the FDR for different true positive rates. In both experiments cn.FARMS yielded the best classification results.Availability: This approach is publicly available in R at http://www.bioinf.jku.at/software
Porous Chitsan-Gelatin Scaffolds Embedded with PLGA Nanoparticles for Bone Repair
Authors: Nandagiri Vijay Kumar , Gentile Piergiergio , Chiono Valeria , Muttu Clara , Ciardelli Gianluca , Montevecchi Franco Maria , Ramtoola Ziebun 
Published: October 2010

AbstractBone regeneration can be accelerated by localized delivery of appropriate growth factors/bio active molecules. Localized delivery can be achieved by incorporating bioactive molecules within biodegradable particulate carrier system followed by embed them in a suitable porous scaffolds. These carrier system facilitates the impregnated growth factor(s) to release at a desirable rate and concentration, and to linger at injury sites for a sufficient time to recruit progenitors and stimulate tissue healing processes. In this study, an attempt has been made to engraft the porous chitosan-gelatin scaffolds with PLGA nanoparticles for localized delivery of bioactive components. Scaffolds loaded with PLGA nanoparticles were subjected to physical and mechanical characterizations such as microarchitecture analysis, swelling, porosity, mechanical properties, dissolution studies.
The Synthesis and Characterization of New, Robust Titanium (IV) Scorpionate Complexes
Authors: Gerschler-Zia Jared , Dunne James , Sadow Aaron 
Published: October 2010

AbstractTitanium complexes possessing sterically encumbered ligands have allowed for the preparation of reactive moieties (imido, alkylidene and alkylidyne species) relevant to reactions such as olefin polymerization and alkyne hydroamination. For this reason, we have targeted robust scorpionate ancillary ligands to support reactive titanium centers. Thus, a series of titanium complexes were synthesized using an achiral oxazoline-based scorpionate ligand, tris(4,4-dimethyl-2-oxazolinyl)phenyl borate [To^M^]^-^ as well as the related chiral ligand, tris(4-isopropyl-2-oxazolinyl)phenyl borate [To^P^]^-^. The complex [Ti(κ^3^- To^M^)Cl~3~] was prepared in moderate yield (43%) by the rapid (<1 min at room temperature) reaction of Li[To^M^] and TiCl~4~ in methylene chloride; this new compound was characterized by ^1^H NMR spectroscopy as the expected C~3v~-symmetric species. One route to Ti (IV) alkyls involves salt metathesis; accordingly, syntheses of [To^M^]Ti alkyl complexes by interaction of [Ti(κ^3^-To^M^)Cl~3~] and one or three equivalents of alkylating agents, such as benzyl potassium (KCH~2~C~6~H~5~), trimethylsilylmethyllithium (LiCH~2~Si(CH~3~) ~3~), or neopentyl lithium (LiCH~2~C(CH~3~)~3~) are currently under investigation. The complexes [Ti(=NBut) (κ~3~-To^M^)(Cl)(Bu^t^py)] (Bu^t^py=4 tert-butylpyridine) and [Ti(=NBu^t^) (κ~3~-To^P^)(Cl)(Bu^t^py)] were synthesized by reaction of the known Ti imido [Ti(=NBu^t^)(Cl)~2~(Bu^t^py)~2~] with Li[To^M^] or Li[To^P^], respectively, by stirring overnight in methylene chloride at ambient temperature. The complexes were identified using ^1^H NMR spectroscopy, ^1^H-^13^C HMQC and ^1^H-^15^N HMBC correlation experiments.
The human genome is composed of viral DNA: Viral homologues of the protein products cause Alzheimer&apos;s disease and others via autoimmune mechanisms.
Authors: Carter Christopher 
Published: October 2010

AbstractThe human genome is composed of millions of fragmented contiguous viral DNA sequences, dating from the dawn of evolution and reflecting retroviral insertions over millions of years of coexistence. Herpes and other viral insertion points correspond to the locations of over 120 Alzheimer&apos;s disease susceptibility genes and to linkage hotspots. The greater the number of pathogen matches, the more important the gene. These DNA sequences are translated into short contiguous 5-12 amino acid stretches (vatches), identical in viruses and man, and in other pathogens implicated in Alzheimer&apos;s disease (Borrelia, Chlamydia, Helicobacter, C. Neoformans , P. Gingivalis). C. Neoformans, which has been associated with a rare but curable form of dementia, expresses the most number of hits to Alzheimer&apos;s disease proteins. Vatches are often immunogenic and antibodies to viral proteins may knock down their human counterparts or activate immune responses killing the cells containing their human homologues. This is supported by the presence of the complement membrane attack complex in Alzheimer&apos;s disease neurones and by the ability of tau antigens (homologous to pathogen proteins) to promote the formation of neurofibrillary tangles and Alzheimer&apos;s disease pathology in mice. Vatches may act as dummy ligands or decoy receptors and interfere with the interactome of their human counterparts. Alzheimer&apos;s disease is thus a &quot;pathogenetic&quot; disorder caused by pathogens but dependent on the genes that create these matching sequences. This scenario is relevant to many other, and perhaps most human disorders, given the massive genomic extent of viral coverage. The vatches in the human proteome, dictated by polymorphisms and mutations, may predict, from birth, the spectrum of pathogens that match our proteins and which pathogenetic disease we are likely to develop. These may all be preventable by vaccination, pathogen detection and elimination and curable by immunosuppressant approaches, perhaps with a unique, safe, and effective immunosuppressant panacea.
Dicroidium: no more a Triassic Gondwana index fossil
Authors: Srivastava Ashwini , Srivastava Rashmi , Agnihotri Deepa 
Published: October 2010

AbstractA large number of Dicroidium-frond, considered as the marker of Early Triassic Gondwana flora, are discovered for the first time with well preserved cuticle from Early Permian (Lower Gondwana) sequence of Barakar Formation, Satpura Gondwana Basin, India. The presence of Dicroidium in Late Permian mixed floral zone of Jordan has been viewed as its possible origin in paleotropics but the evidence in hand exhibits its Gondwanic derivation and threatens the recognition of Dicroidium flora for Middle Gondwana in association with Lower Gondwana Glossopteris and Upper Gondwana Ptilophyllun flora.