Institutional Repositories, Open Access and Copyright: What Are the Practices and Implications?

A number of factors are driving open access to full-text journals: constantly rising prices of journal and database subscriptions, granting agencies requirements for recipients to submit their research publications into open access repositories, and pressure on libraries to create Institutional Repositories (IR) to promote the institutions’ reputations. Research proves that open access promotes the dissemination and use of scholarly works and citations for authors. This article examines the interactions among open access, institutional repositories, and copyright management. The research described herein investigates how institutional repositories are managing copyright and licensing issues that can interfere with open access

Institutional Repositories, Open Access and Copyright: What Are the Practices and Implications?

A number of factors are driving open access to full-text journals: constantly rising prices of journal and database subscriptions, granting agencies requirements for recipients to submit their research publications into open access repositories, and pressure on libraries to create Institutional Repositories (IR) to promote the institutions’ reputations. Research proves that open access promotes the dissemination and use of scholarly works and citations for authors. This article examines the interactions among open access, institutional repositories, and copyright management. The research described herein investigates how institutional repositories are managing copyright and licensing issues that can interfere with open access

Local Collections in Discovery Services: An Inquiry

Many libraries subscribed to discovery services in the hope of boosting the use of their local collections such as print materials, DVDs, or even subscribed ejournals and ebooks that are separate from licensed databases. However, anecdotal evidence shows that the implementation of a discovery service will increase the usage of the vendors’ electronic resources instead. This study aims to find out how well local collections are promoted through EBSCO Discovery Service (EDS), Primo, Summon, and WorldCat Discovery Services (WorldCat) by comparing results of queries in the discovery services versus the number of actual listings from these libraries’ traditional catalogs. Authors conducted three searches based on real-life student assignments in science, history, and sociology in each of the four discovery services. To offset the bias of location configuration, ten libraries with the same discovery tool were selected for each search and total results are averaged. ANOVA and Tukey Honest Significant Difference statistical analyses show differences among the four discovery services investigated. Discovery tools promote local collections in different ways. Some tools provide the possibility to list libraries’ local collections before listing the vendor’s database items, but others are less inclined to do so.

Linked data technologies and what libraries have accomplished so far

En els darrers deu anys, les biblioteques han de-dicat esforços en l’àmbit de les dades enllaçades i del web semàntic. Sovint costa entendre els detalls tècnics i el po-tencial que tenen per a la comunitat bibliotecària, a causa de la seva complexitat i ampli abast. Aquest article pretén aclarir alguns conceptes importants i explica quines són les tecnologies bàsiques de les dades enllaçades: l’RDF (marc de descripció de recursos), l’ontologia i el llenguatge de cer-ca. Es descriuen alguns dels assoliments obtinguts en bibli-oteques d’arreu del món pel que fa a la transformació de les seves dades en dades enllaçades, incloent-hi la tasca de la Library of Congress, de l’Online Computer Library Center (OCLC) i altres biblioteques nacionals. També s’analitzen alguns dels reptes i contratemps als quals s’han enfrontat les biblioteques a l’hora de desenvolupar aquestes tecno-logies. Tanmateix, no es pot tornar enrere: les biblioteques ho han d’aconseguir.En los últimos diez años, las bibliotecas han dedicado esfuer-zos en el ámbito de los datos enlazados y la web semántica. A menudo cuesta entender los detalles técnicos y el potencial que tienen para la comunidad bibliotecaria, debido a su complejidad y amplio alcance. Este artículo pretende aclarar algunos conceptos importantes y explica cuáles son las tecnologías básicas de los datos enlazados: RDF (marco de des-cripción de recursos), la ontología y el lenguaje de búsqueda. Se descri-ben algunos de los logros obtenidos en bibliotecas de todo el mundo en cuanto a la transformación de sus datos en datos enlazados, incluidas la tarea de la Library of Congress, del Online Computer Library Center (OCLC) y de otras bibliotecas nacionales. También se analizan algunos de los retos y contratiempos a los que se han enfrentado las bibliotecas a la hora de desarrollar estas tecnologías. Sin embargo, no se puede volver atrás: las bibliotecas lo deben conseguir.For the past ten years libraries have been working diligently towards Linked Data and the Seman-tic Web. Due to the complexity and vast scope of Linked Data, many people have a hard time to understand its technical details and its potential for the library commu-nity. This paper aims to help librarians better understand some important concepts by explaining the basic Linked Data technologies that consist of Resource Description Framework (RDF), the ontology, and the query language. It also includes an overview of the achievements by li-braries around the world in their efforts to turn library data into Linked Data including those by Library of Con-gress, Online Computer Library Center (OCLC), and some other national libraries. Some of the challenges and set-backs that libraries have encountered are analyzed and discussed. In spite of the difficulties, there is no way to turn back. Libraries will have to succeed

Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs. ChIP-seq analysis demonstrates direct recruitment of Chaf1a and Sumo2 to ERVs. Chaf1a reinforces transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrates the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study reports a genome-wide atlas of functional nodes that mediate proviral silencing in ESCs and illuminates the comprehensive, interconnected, and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome

Comparative effects of RRR-alpha- and RRR-gamma-tocopherol on proliferation and apoptosis in human colon cancer cell lines

BACKGROUND: Mediterranean societies, with diets rich in vitamin E isoforms, have a lower risk for colon cancer than those of northern Europe and the Americas. Vitamin E rich diets may neutralize free radicals generated by fecal bacteria in the gut and prevent DNA damage, but signal transduction activities can occur independent of the antioxidant function. The term vitamin E represents eight structurally related compounds, each differing in their potency and mechanisms of chemoprevention. The RRR-γ-tocopherol isoform is found primarily in the US diet, while RRR-α-tocopherol is highest in the plasma. METHODS: The effectiveness of RRR-α- and RRR-γ-tocopherol at inhibiting cell growth and inducing apoptosis in colon cancer cell lines with varying molecular characteristics (SW480, HCT-15, HCT-116 and HT-29) and primary colon cells (CCD-112CoN, nontransformed normal phenotype) was studied. Colon cells were treated with and without RRR-α- or RRR-γ-tocopherol using varying tocopherol concentrations and time intervals. Cell proliferation and apoptosis were measured using the trypan blue assay, annexin V staining, DNA laddering and caspase activation. RESULTS: Treatment with RRR-γ-tocopherol resulted in significant cell death for all cancer cell lines tested, while RRR-α-tocopherol did not. Further, RRR-γ-tocopherol treatment showed no cytotoxicity to normal colon cells CCD-112CoN at the highest concentration and time point tested. RRR-γ-tocopherol treatment resulted in cleavage of PARP, caspase 3, 7, and 8, but not caspase 9. Differences in the percentage cell death and apoptosis were observed in different cell lines suggesting that molecular differences in these cell lines may influence the ability of RRR-γ-tocopherol to induce cell death. CONCLUSION: This is the first study to demonstrate that multiple colon cancer cell lines containing varying genetic alterations will under go growth reduction and apoptosis in the presence of RRR-γ-tocopherol without damage to normal colon cells. The amount growth reduction was dependent upon the molecular signatures of the cell lines. Since RRR-γ-tocopherol is effective at inhibition of cell proliferation at both physiological and pharmacological concentrations dietary RRR-γ-tocopherol may be chemopreventive, while pharmacological concentrations of RRR-γ-tocopherol may aid chemotherapy without toxic effects to normal cells demonstrated by most chemotherapeutic agents

FrzS Regulates Social Motility in Myxococcus xanthus by Controlling Exopolysaccharide Production

Myxococcus xanthus Social (S) motility occurs at high cell densities and is powered by the extension and retraction of Type IV pili which bind ligands normally found in matrix exopolysaccharides (EPS). Previous studies showed that FrzS, a protein required for S-motility, is organized in polar clusters that show pole-to-pole translocation as cells reverse their direction of movement. Since the leading cell pole is the site of both the major FrzS cluster and type IV pilus extension/retraction, it was suggested that FrzS might regulate S-motility by activating pili at the leading cell pole. Here, we show that FrzS regulates EPS production, rather than type IV pilus function. We found that the frzS phenotype is distinct from that of Type IV pilus mutants such as pilA and pilT, but indistinguishable from EPS mutants, such as epsZ. Indeed, frzS mutants can be rescued by the addition of purified EPS, 1% methylcellulose, or co-culturing with wildtype cells. Our data also indicate that the cell density requirement in S-motility is likely a function of the ability of cells to construct functional multicellular clusters surrounding an EPS core

Adaptive Evolution of the Venom-Targeted vWF Protein in Opossums that Eat Pitvipers

The rapid evolution of venom toxin genes is often explained as the result of a biochemical arms race between venomous animals and their prey. However, it is not clear that an arms race analogy is appropriate in this context because there is no published evidence for rapid evolution in genes that might confer toxin resistance among routinely envenomed species. Here we report such evidence from an unusual predator-prey relationship between opossums (Marsupialia: Didelphidae) and pitvipers (Serpentes: Crotalinae). In particular, we found high ratios of replacement to silent substitutions in the gene encoding von Willebrand Factor (vWF), a venom-targeted hemostatic blood protein, in a clade of opossums known to eat pitvipers and to be resistant to their hemorrhagic venom. Observed amino-acid substitutions in venom-resistant opossums include changes in net charge and hydrophobicity that are hypothesized to weaken the bond between vWF and one of its toxic snake-venom ligands, the C-type lectin-like protein botrocetin. Our results provide the first example of rapid adaptive evolution in any venom-targeted molecule, and they support the notion that an evolutionary arms race might be driving the rapid evolution of snake venoms. However, in the arms race implied by our results, venomous snakes are prey, and their venom has a correspondingly defensive function in addition to its usual trophic role

Polyclonal rabbit anti-murine plasmacytoma cell globulins induce myeloma cells apoptosis and inhibit tumour growth in mice

Multiple myelomas (MMs) are etiologically heterogeneous and there are limited treatment options; indeed, current monoclonal antibody therapies have had limited success, so more effective antibodies are urgently needed. Polyclonal antibodies are a possible alternative because they target multiple antigens simultaneously. In this study, we produced polyclonal rabbit anti-murine plasmacytoma cell immunoglobulin (PAb) by immunizing rabbits with the murine plasmacytoma cell line MPC-11. The isolated PAb bound to plasma surface antigens in several MM cell lines, inhibited their proliferation as revealed by MTT assay, and induce apoptosis as indicated by flow cytometry, microscopic observation of apoptotic changes in morphology, and DNA fragmentation on agarose gels. The cytotoxicity of PAb on MPC-11 cell lines was both dose-dependent and time-dependent; PAb exerted a 50% inhibitory effect on MPC-11 cell viability at a concentration of 200 µg/ml in 48 h. Flow cytometry demonstrated that PAb treatment significantly increased the number of apoptotic cells (48.1%) compared with control IgG (8.3%). Apoptosis triggered by PAb was confirmed by activation of caspase-3, -8, and -9. Serial intravenous or intraperitoneal injections of PAb inhibited tumour growth and prolonged survival in mice bearing murine plasmacytoma, while TUNEL assay demonstrated that PAb induced statistically significant apoptosis (P < 0.05) compared to control treatments. We conclude that PAb is an effective agent for in vitro and in vivo induction of apoptosis in multiple myeloma and that exploratory clinical trials may be warranted