Family tree and or map-like approaches to Slavic languages?

The file consists of the presenters' raw notes and the PowerPoint presentation delivered at the "Slavic Languages: Time and Contingency” conference, UC Berkeley 12–13 Feb. 2010.Lexicostatistics is decades old, but newer techniques for computational approaches to historical linguistics have gained new attention with the rise of more sophisticated methods of data handling. Thus, for example, Gray and Atkinson (2003) claim to have established, using lexicostatistics and a Bayesian (MCMC) model, an authoritative Stammbaum for the Indo-European language family, including absolute chronologies of its branching. Others have argued that such methods, while valid for biology, cannot yield authoritative dates for language data (Atkinson 2009: 128). The present paper examines a smaller subset of languages—Slavic—using new lexicostatistical methods in attempt to compare the computational results with received analyses that are closer to the present. We assume that examining a group of languages closer in time to the present, where the splits are more easily verifiable, allows testing of quantifiable methods. If a close fit can be found between a lexicostatistical approach and traditional analysis in Slavic, it should allow extension to greater time depths and larger families such as Indo-European. The present paper applies several methods to two corpora, one the Slavic subset of Indo-European in Dyen, Kruskal and Black (1992) and the Slavic text-token set in Mańczak 2004. References Atkinson, Quentin D. 2009. Review of Language Classification by Numbers. By April McMahon and Robert McMahon. Oxford: Oxford University Press, 2005. Pp xvii, 265. Diachonica 26/1: 125–133. Dyen, Isidore, Joseph B. Kruskal, and Paul Black. 1992. An Indoeuropean Classification: A Lexicostatistical Experiment. Philadelphia: American Philosophical Society. Gray, Russell D. and Quentin D. Atkinson. 2003. Language-Tree Divergence Times Support the Anatolian Theory of Indo-European Origin. Nature 426: 435–439. Mańczak, Witold. 2004. Przedhistoryczne migracje słowian i pochodzenie języka staro-cerkiewno-słowianskiego. Cracow: PAU

Open Access 101: Access to Your Work and the Works You Need to Build on

This event is an RSVP pizza lunch for graduate student to learn more about the benefits of open access for them and for academe in general. Presenters: Lorraine Haricombe, Dean of KU Libraries; A. Townsend Peterson, Distinguished Professor of Ecology and Evolutionary Biology; Marc L. Greenberg, chair of KU's Slavic Languages & Literatures department; Marko Snoj, director of the Fran Ramovš Institute for Slovene Language of the Scientific Research Center of the Slovenian Academy of Sciences and Arts in Ljubljana, Slovenia; and Ada Emmett, Scholarly Communications program head, KU Libraries

Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli

Proper maintenance of the genome is of great importance. Consequently, damaged nucleotides are repaired through redundant pathways. We considered whether the genome is protected from formamidopyrimidine nucleosides (Fapy•dA, Fapy•dG) via a pathway distinct from the Escherichia coli guanine oxidation system. The formamidopyrimidines are produced in significant quantities in DNA as a result of oxidative stress and are efficiently excised by formamidopyrimidine DNA glycosylase. Previous reports suggest that the formamidopyrimidine nucleosides are substrates for endonucleases III and VIII, enzymes that are typically associated with pyrimidine lesion repair in E.coli. We investigated the possibility that Endo III and/or Endo VIII play a role in formamidopyrimidine nucleoside repair by examining Fapy•dA and Fapy•dG excision opposite all four native 2′-deoxyribonucleotides. Endo VIII excises both lesions more efficiently than does Endo III, but the enzymes exhibit similar selectivity with respect to their action on duplexes containing the formamidopyrimidines opposite native deoxyribonucleotides. Fapy•dA is removed more rapidly than Fapy•dG, and duplexes containing purine nucleotides opposite the lesions are superior substrates compared with those containing formamidopyrimidine–pyrimidine base pairs. This dependence upon opposing nucleotide indicates that Endo III and Endo VIII do not serve as back up enzymes to formamidopyrimidine DNA glycosylase in the repair of formamidopyrimidines. When considered in conjunction with cellular studies [J. O. Blaisdell, Z. Hatahet and S. S. Wallace (1999) J. Bacteriol., 181, 6396–6402], these results also suggest that Endo III and Endo VIII do not protect E.coli against possible mutations attributable to formamidopyrimidine lesions

The Saito-Kurokawa lifting and Darmon points

Let E_{/_\Q} be an elliptic curve of conductor $Np$ with $p\nmid N$ and let $f$ be its associated newform of weight 2. Denote by $f_\infty$ the $p$-adic Hida family passing though $f$, and by $F_\infty$ its $\Lambda$-adic Saito-Kurokawa lift. The $p$-adic family $F_\infty$ of Siegel modular forms admits a formal Fourier expansion, from which we can define a family of normalized Fourier coefficients $\{\widetilde A_T(k)\}_T$ indexed by positive definite symmetric half-integral matrices $T$ of size $2\times 2$. We relate explicitly certain global points on $E$ (coming from the theory of Stark-Heegner points) with the values of these Fourier coefficients and of their $p$-adic derivatives, evaluated at weight $k=2$.Comment: 14 pages. Title change

Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids

A broad scientific community is involved in investigations aimed at delineating the mechanisms of formation and cellular processing of oxidatively generated damage to nucleic acids. Perhaps as a consequence of this breadth of research expertise, there are nomenclature problems for several of the oxidized bases including 8-oxo-7,8-dihydroguanine (8-oxoGua), a ubiquitous marker of almost every type of oxidative stress in cells. Efforts to standardize the nomenclature and abbreviations of the main DNA degradation products that arise from oxidative pathways are reported. Information is also provided on the main oxidative radicals, non-radical oxygen species, one-electron agents and enzymes involved in DNA degradation pathways as well in their targets and reactivity. A brief classification of oxidatively generated damage to DNA that may involve single modifications, tandem base modifications, intrastrand and interstrand cross-links together with DNA-protein cross-links and base adducts arising from the addition of lipid peroxides breakdown products is also included

Development of the Pediatric Quality of Life Inventory™ Eosinophilic Esophagitis Module items: qualitative methods

BACKGROUND: Currently there is no disease-specific outcome measure to assess the health-related quality of life (HRQOL) of pediatric patients with Eosinophilic Esophagitis (EoE). Therefore, the objective of this qualitative study was to further develop and finalize the items and support the content validity for the new Pediatric Quality of Life Inventory™ (PedsQL™) Eosinophilic Esophagitis Module. METHODS: Multiphase qualitative methodology was utilized in the development of the PedsQL™ EoE Module conceptual model. Focus interview transcripts of pediatric patients with EoE and their parents and expert review were previously used to develop the initial items and domains for the PedsQL™ EoE Module. In the current investigation, utilizing the respondent debriefing methodology, cognitive interviewing was conducted individually with pediatric patients with EoE and their parents on each newly developed item. RESULTS: Information from a total of 86 participants was obtained in combination from the previous investigation and the current study. From the previous 42 focus interviews, items were developed around the domain themes of symptoms, difficulties with eating food, treatment adherence, worry about symptoms and illness, feelings of being different than family and peers, and problems discussing EoE with others. In the current study’s cognitive interviewing phase, a separate cohort of 44 participants systematically reviewed and provided feedback on each item. Items were added, modified or deleted based on this feedback. Items were finalized after this feedback from patients and parents. CONCLUSIONS: Using well-established qualitative methods, the content validity of the new PedsQL™ Eosinophilic Esophagitis Module items was supported in the current investigation. In the next iterative instrument development phase, the PedsQL™ Eosinophilic Esophagitis Module is now undergoing multisite national field testing

Passive sampling methods for contaminated sediments: Risk assessment and management

This paper details how activity-based passive sampling methods (PSMs), which provide information on bioavailability in terms of freely dissolved contaminant concentrations (Cfree), can be used to better inform risk management decision making at multiple points in the process of assessing and managing contaminated sediment sites. PSMs can increase certainty in site investigation and management, because Cfree is a better predictor of bioavailability than total bulk sediment concentration (Ctotal) for 4 key endpoints included in conceptual site models (benthic organism toxicity, bioaccumulation, sediment flux, and water column exposures). The use of passive sampling devices (PSDs) presents challenges with respect to representative sampling for estimating average concentrations and other metrics relevant for exposure and risk assessment. These challenges can be addressed by designing studies that account for sources of variation associated with PSMs and considering appropriate spatial scales to meet study objectives. Possible applications of PSMs include: quantifying spatial and temporal trends in bioavailable contaminants, identifying and evaluating contaminant source contributions, calibrating site-specific models, and, improving weight-of-evidence based decision frameworks. PSM data can be used to assist in delineating sediment management zones based on likelihood of exposure effects, monitor remedy effectiveness, and, evaluate risk reduction after sediment treatment, disposal, or beneficial reuse after management actions. Examples are provided illustrating why PSMs and freely dissolved contaminant concentrations (Cfree) should be incorporated into contaminated sediment investigations and study designs to better focus on and understand contaminant bioavailability, more accurately estimate exposure to sediment-associated contaminants, and better inform risk management decisions. Research and communication needs for encouraging broader use are discussed. Integr Environ Assess Manag 2014;10:224–236. © 2014 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of SETAC

Diets containing sea cucumber (Isostichopus badionotus) meals are hypocholesterolemic in young rats

Peer reviewedPublisher PD

A Functional Nuclear Localization Sequence in the C. elegans TRPV Channel OCR-2

The ability to modulate gene expression in response to sensory experience is critical to the normal development and function of the nervous system. Calcium is a key activator of the signal transduction cascades that mediate the process of translating a cellular stimulus into transcriptional changes. With the recent discovery that the mammalian Cav1.2 calcium channel can be cleaved, enter the nucleus and act as a transcription factor to control neuronal gene expression, a more direct role for the calcium channels themselves in regulating transcription has begun to be appreciated. Here we report the identification of a nuclear localization sequence (NLS) in the C. elegans transient receptor potential vanilloid (TRPV) cation channel OCR-2. TRPV channels have previously been implicated in transcriptional regulation of neuronal genes in the nematode, although the precise mechanism remains unclear. We show that the NLS in OCR-2 is functional, being able to direct nuclear accumulation of a synthetic cargo protein as well as the carboxy-terminal cytosolic tail of OCR-2 where it is endogenously found. Furthermore, we discovered that a carboxy-terminal portion of the full-length channel can localize to the nucleus of neuronal cells. These results suggest that the OCR-2 TRPV cation channel may have a direct nuclear function in neuronal cells that was not previously appreciated

Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids. Free Radic. Res

Abstract A broad scientific community is involved in investigations aimed at delineating the mechanisms of formation and cellular processing of oxidatively generated damage to nucleic acids. Perhaps as a consequence of this breadth of research expertise, there are nomenclature problems for several of the oxidized bases including 8-oxo-7,8-dihydroguanine (8-oxoGua), a ubiquitous marker of almost every type of oxidative stress in cells. Efforts to standardize the nomenclature and abbreviations of the main DNA degradation products that arise from oxidative pathways are reported. Information is also provided on the main oxidative radicals, non-radical oxygen species, one-electron agents and enzymes involved in DNA degradation pathways as well in their targets and reactivity. A brief classification of oxidatively generated damage to DNA that may involve single modifications, tandem base modifications, intrastrand and interstrand cross-links together with DNA-protein cross-links and base adducts arising from the addition of lipid peroxides breakdown products is also included