Tumor markers in breast cancer - European Group on Tumor Markers recommendations

Recommendations are presented for the routine clinical use of serum and tissue-based markers in the diagnosis and management of patients with breast cancer. Their low sensitivity and specificity preclude the use of serum markers such as the MUC-1 mucin glycoproteins ( CA 15.3, BR 27.29) and carcinoembryonic antigen in the diagnosis of early breast cancer. However, serial measurement of these markers can result in the early detection of recurrent disease as well as indicate the efficacy of therapy. Of the tissue-based markers, measurement of estrogen and progesterone receptors is mandatory in the selection of patients for treatment with hormone therapy, while HER-2 is essential in selecting patients with advanced breast cancer for treatment with Herceptin ( trastuzumab). Urokinase plasminogen activator and plasminogen activator inhibitor 1 are recently validated prognostic markers for lymph node-negative breast cancer patients and thus may be of value in selecting node-negative patients that do not require adjuvant chemotherapy. Copyright (C) 2005 S. Karger AG, Basel

Population Empirical Likelihood Estimation in Dual Frame Surveys

Dual frame surveys are a device to reduce the costs derived from data collection in surveys and improve coverage for the whole target population. Since their introduction, in the 1960’s, dual frame surveys have gained much attention and several estimators have been formulated based on a number of different approaches. In this work, we propose new dual frame estimators based on the population empirical likelihood method originally proposed by Chen and Kim (2014) and using both the dual and the single frame approach. The extension of the proposed methodology to more than two frame surveys is also sketched. The performance of the proposed estimators in terms of relative bias and relative mean squared error is tested through simulation experiments. These experiments indicate that the proposed estimators yield better results than other likelihood-based estimators proposed in the literature.Ministerio de Economía y Competitividad of Spai

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease

PMCID: PMC3710212This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Frequency distribution of TATA Box and extension sequences on human promoters

BACKGROUND: TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear. RESULTS: In this study, we conduct a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from the TATA Box motif, TATAWAWN, are classified into three distribution patterns: peak, bottom-peak, and bottom. Fourteen TATA extension sequences are predicted to be the new TATA Box elements due to their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mice, zebrafish and drosophila melanogaster verifies seven of these elements. It is also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human. CONCLUSION: The dedicated statistical analysis on TATA box and its extension sequences yields new TATA elements. The statistical significance of these elements has been verified on random data sets by calculating their p values

Litterfall, litter decomposition and associated nutrient fluxes in Pinus halepensis: influence of tree removal intensity in a Mediterranean forest

The online version of this article (doi:10.1007/s10342-015-0893-z) contains supplementary material, which is available to authorized users[EN] Our knowledge about the influence of silvicultural treatments on nutrient cycling processes in Mediterranean forests is still limited. Four levels of tree removal were compared in an Aleppo pine forest in eastern Spain to determine the effects on litterfall, litter decomposition and the associated nutrient fluxes after 12 years. Removal treatments included clearfelling, two shelterwood intensities (60 and 75 % of basal area removed) and untreated controls. Twelve years later, the basal area removed still explained 60 % of litterfall mass variance and 60 % of C, 52 % of N, 45 % of P, 17 % of K, 47 % of Ca and 60 % of Mg return variances. Litter decomposed somewhat more slowly in clearfellings compared to controls (p = 0.049), accumulated more Ca and released less K compared to the other three treatments. This was explained by contamination with mineral particles due to the poorly developed O horizon in clearfellings. We conclude that the management practices reduced the nutrient return via litterfall, but the nutrient release through decomposition seems poorly sensitive to canopy disturbance. In order to accurately quantify the harvesting impacts on nutrient cycling in this Mediterranean forest system, it is necessary to measure the litterfall of the understory layer.This work has been supported by a fellowship from the Generalitat Valenciana, Conselleria de Educacion, Formacion y Empleo awarded to L. Lado-Monserrat (BFPI/2008/041). Silvicultural treatments were carried out by the Mediterranean Centre for Environmental Studies (CEAM) through programme "I + D en relacion con la restauracion de la cubierta vegetal y otros aspectos de investigacion forestal". Dataloggers and probes were provided by the Generalitat Valenciana through Project "Efecto de diferentes sistemas de aclareo de masa forestal sobre la disponibilidad de agua, nutrientes y la regeneracion de la masa arborea y arbustiva en parcelas de pinar" (GV06/126). We acknowledge Joana Oliver, Ruth M. Tavera and Daniel Fortanet for their help in the laboratory and in the field. The authors wish to thank Francisco Galiana for his assistance, including help in fieldwork and providing information about the experimental design of the silvicultural treatments. Thanks also go to Rafael Herrera from the Centro de Ecologia, Instituto Venezolano de Investigaciones Cientificas, Caracas, Venezuela and two anonymous reviewers for critically reviewing the manuscript.Lado Monserrat, L.; Lidón, A.; Bautista, I. (2015). Litterfall, litter decomposition and associated nutrient fluxes in Pinus halepensis: influence of tree removal intensity in a Mediterranean forest. European Journal of Forest Research. 134(5):833-844. https://doi.org/10.1007/s10342-015-0893-zS8338441345Almagro M, Martínez-Mena M (2012) Exploring short-term leaf-litter decomposition dynamics in a Mediterranean ecosystem: dependence on litter type and site conditions. Plant Soil 358:323–335Alvarez A, Gracia M, Vayreda J, Retana J (2012) Patterns of fuel types and crown fire potential in Pinus halepensis forests in the Western Mediterranean Basin. For Ecol Manage 270:282–290Austin AT, Vivanco L (2006) Plant litter decomposition in a semi-arid ecosystem controlled by photodegradation. Nature 442:555–558Bates JD, Svejcar TS, Miller RF (2007) Litter decomposition in cut and uncut western juniper woodlands. J Arid Environ 70:222–236Binkley D (2008) Three key points in the design of forest experiments. For Ecol Manage 255:2022–2023Blair JM, Crossley DA Jr (1988) Litter decomposition, nitrogen dynamics and litter microarthropods in a southern Appalachian hardwood forest 8 years following clearcutting. J Appl Ecol 25:683–698Blanco JA, Zavala MA, Imbert JB, Castillo FJ (2005) Sustainability of forest management practices: evaluation through a simulation model of nutrient cycling. For Ecol Manage 213:209–228Blanco JA, Imbert JB, Castillo FJ (2006) Influence of site characteristics and thinning intensity on litterfall production in two Pinus sylvestris L. forests in the western Pyrenees. For Ecol Manage 237:342–352Blanco JA, Imbert JB, Castillo FJ (2008) Nutrient return via litterfall in two contrasting Pinus sylvestris forests in the Pyrenees under different thinning intensities. For Ecol Manage 256:1840–1852Blanco JA, Imbert JB, Castillo FJ (2011) Thinning affects Pinus sylvestris needle decomposition rates and chemistry differently depending on site conditions. Biogeochemistry 106:397–414Caldentey J, Ibarra M, Hernández J (2001) Litter fluxes and decomposition in Nothofagus pumilio stands in the region of Magallanes, Chile. For Ecol Manage 148:145–157Christensen JH, Krishna Kumar K, et al. (2013) Climate phenomena and their relevance for future regional climate change. In: Stocker TF, Qin D, Plattner G-K et al (Eds.) Climate change 2013: the physical science basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USACortina J, Vallejo VR (1994) Effects of clearfelling on forest floor accumulation and litter decomposition in a radiata pine plantation. For Ecol Manage 70:299–310Entry JA, Rose CL, Cromack K Jr (1991) Litter decomposition and nutrient release in ectomycorrhizal mat soils of a Douglas fir ecosystem. Soil Biol Biochem 23:285–290Fabbio G, Merlo M, Tosi V (2003) Silvicultural management in maintaining biodiversity and resistance of forests in Europe—the Mediterranean region. J Environ Manage 67:67–76Galiana F, Pérez-Badía R, Camarero E, Estruch V, Currás R (2001) Estimación de la Radiación solar incidente en pinares de Pinus halepensis sometidos a tratamientos selvícolas de cortas finales. In: Junta de Andalucía. Consejería de Medio Ambiente (Ed.) Actas del III Congreso Forestal Español. Junta de Andalucía. Granada (Original in Spanish)García-Plé C, Vanrell P, Morey M (1995) Litter fall and decomposition in a Pinus halepensis forest on Mallorca. J Veg Sci 6:17–22González Utrillas N, González Pérez E, Galiana F (2005) Variación del crecimiento diametral de la masa de pinar de carrasco en cortas finales experimentales, en los montes de Tuejar y Chelva (Valencia). IV Congreso Forestal Español. Zaragoza. Soc. Esp. Cien. For. (Original in Spanish)Guo LB, Sims REH (1999) Litter decomposition and nutrient release via litter decomposition in New Zealand eucalypt short rotation forests. Agric Ecosyst Environ 75:133–140GVA (1995) Mapa de Suelos de la Comunidad Valenciana. Chelva (666). Proyecto LUCDEME (Icona), Centro de Investigaciones sobre Desertificación y Conselleria d’Agricultura i Mig Ambient. Generalitat Valenciana. Valencia, Spain. (Original in Spanish)Hennessey TC, Dougherty PM, Cregg BM, Wittwer RF (1992) Annual variation in needle fall of a loblolly pine stand in relation to climate and stand density. For Ecol Manage 51:329–338Inagaki Y, Kuramoto S, Torii A, Shinomiya Y, Fukata H (2008) Effects of thinning on leaf-fall and leaf-litter nitrogen concentration in hinoki cypress (Chamaecyparis obtusa Endlicher) plantation stands in Japan. For Ecol Manage 255:1859–1867Jonard M, Misson L, Ponette Q (2006) Long-term thinning effects on the forest floor and the foliar nutrient status of Norway spruce stands in the Belgian Ardennes. Can J For Res 36:2684–2695Kim C, Sharik TL, Jurgensen MF (1996a) Canopy cover effects on mass loss, and nitrogen and phosphorus dynamics from decomposing litter in oak and pine stands in northern Lower Michigan. For Ecol Manage 80:13–20Kim C, Sharik TL, Jurgensen MF (1996b) Litterfall, nitrogen and phosphorus inputs at various levels of canopy removal in oak and pine stands in northern lower Michigan. Am Midl Nat 135:195–204Kim C, Son Y, Lee WK, Jeong J, Noh NJ, Kim SR, Yang AR, Ju NG (2012) Influence of forest tending (Soopkakkugi) works on litterfall and nutrient inputs in a Pinus densiflora stand. For Sci Technol 8:83–88Kimmins JP (2004) Forest ecology, a foundation for sustainable management and environmental ethics in forestry. Prentice-Hall, New JerseyKimmins JP, Mailly D, Seely B (1999) Modelling forest ecosystem net primary production: the hybrid simulation approach used in FORECAST. Ecol Modell 122:195–224Klemmedson JO, Meier CE, Campbell RE (1990) Litter fall transfers of dry matter and nutrients in ponderosa pine stands. Can J For Res 20:1105–1115Kunhamu TK, Kumar BM, Viswanath S (2009) Does thinning affect litterfall, litter decomposition, and associated nutrient release in Acacia mangium stands of Kerala in peninsular India? Can J For Res 39:792–801Lytle DE, Cronan CS (1998) Comparative soil CO2 evolution, litter decay, and root dynamics in clearcut and uncut spruce–fir forest. For Ecol Manage 103:121–128Molina AJ, Del Campo AD (2012) The effects of experimental thinning on throughfall and stemflow: a contribution towards hydrology-oriented silviculture in Aleppo pine plantations. For Ecol Manage 269:206–213Navarro FB, Romero-Freire A, Del Castillo T, Foronda A, Jiménez MN, Ripoll MA, Sánchez-Miranda A, Hutsinger L, Fernández-Ondoño E (2013) Effects of thinning on litterfall were found after years in a Pinus halepensis afforestation area at tree and stand levels. For Ecol Manage 289:354–362Olson JS (1963) Energy storage and the balance of producers and decomposers in ecological systems. Ecology 44:322–331Pérez Cueva AJ (1994) Atlas Climático de la Comunidad Valenciana. Colección Territori nº 4. Generalitat Valenciana. Conselleria d’Obres Publiques, Urbanisme i Transport, ValenciaPetritsch R, Hasenauer H, Pietsch SA (2007) Incorporating forest growth response to thinning within biome-BGC. For Ecol Manage 242:324–336Prescott CE (1997) Effects of clearcutting and alternative silvicultural systems on rates of decomposition and nitrogen mineralization in a coastal montane coniferous forest. For Ecol Manage 95:253–260Prescott CE (2002) The influence of the forest canopy on nutrient cycling. Tree Physiol 22:1193–1200Prescott CE, Blevins LL, Staley CL (2000) Effects of clear-cutting on decomposition rates of litter and forest floor in forests of British Columbia. Can J For Res 30:1751–1757Roig S, Del Río M, Cañellas I, Montero G (2005) Litter fall in Mediterranean Pinus pinaster Ait. stands under different thinning regimes. For Ecol Manage 206:179–190Sardans J, Peñuelas J, Rodà F (2005) Changes in nutrient use efficiency, status and retranslocation in young post-fire regeneration Pinus halepensis in response to sudden N and P input, irrigation and removal of competing vegetation. Trees 19:233–250Scarascia-Mugnozza G, Oswald H, Piussi P, Radoglou K (2000) Forests of the Mediterranean region: gaps in knowledge and research needs. For Ecol Manage 132:97–109Slovik S (1997) Tree physiology. In: Hüttl RF, Schaaf W (eds) Magnesium deficiency in forest ecosystems. Kluwer Academic Publishers, London, pp 101–214Taylor BR, Parkinson D (1988) Does repeated freezing and thawing accelerate decay of leaf litter? Soil Biol Biochem 20:657–665Torras O, Saura S (2008) Effects of silvicultural treatments on forest biodiversity indicators in the Mediterranean. For Ecol Manage 255:3322–3330Trofymow JA, Barclay HJ, McCullough KM (1991) Annual rates and elemental concentrations of litter fall in thinned and fertilized Douglas-fir. Can J For Res 21:1601–1615Wallace ES, Freedman B (1986) Forest floor dynamics in a chronosequence of hardwood stands in central Nova Scotia. Can J For Res 16:293–302Whitford WG, Meentemeyer V, Seastedt TR, Cromack Jr K, Crossley Jr DA, Santos P, Todd RL, Waide JB (1981) Exceptions to the AET model: deserts and clear-cut forest. Ecology 62:275–277Yin X, Perry JA, Dixon RK (1989) Influence of canopy removal on oak forest floor decomposition. Can J For Res 19:204–21

An Easy-To-Use Simulation Program Demonstrates Variations in Bacterial Cell Cycle Parameters Depending on Medium and Temperature

Many studies are performed on chromosome replication and segregation in Escherichia coli and other bacteria capable of complex replication with C phases spanning several generations. For such investigations an understanding of the replication patterns, including copy numbers of origins and replication forks, is crucial for correct interpretation of the results

Suppression of charged particle production at large transverse momentum in central Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}} = 2.76 TeV

Inclusive transverse momentum spectra of primary charged particles in Pb-Pb collisions at $\sqrt{s_{_{\rm NN}}}$ = 2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0-5% and 70-80% of the hadronic Pb-Pb cross section. The measured charged particle spectra in $|\eta|<0.8$ and $0.3 < p_T < 20$ GeV/$c$ are compared to the expectation in pp collisions at the same $\sqrt{s_{\rm NN}}$, scaled by the number of underlying nucleon-nucleon collisions. The comparison is expressed in terms of the nuclear modification factor $R_{\rm AA}$. The result indicates only weak medium effects ($R_{\rm AA} \approx$ 0.7) in peripheral collisions. In central collisions, $R_{\rm AA}$ reaches a minimum of about 0.14 at $p_{\rm T}=6$-7GeV/$c$ and increases significantly at larger $p_{\rm T}$. The measured suppression of high-$p_{\rm T}$ particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb-Pb collisions at the LHC.Comment: 15 pages, 5 captioned figures, 3 tables, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/98

Maximum in the Middle: Nonlinear Response of Microbial Plankton to Ultraviolet Radiation and Phosphorus

The responses of heterotrophic microbial food webs (HMFW) to the joint action of abiotic stressors related to global change have been studied in an oligotrophic high-mountain lake. A 2×5 factorial design field experiment performed with large mesocosms for >2 months was used to quantify the dynamics of the entire HMFW (bacteria, heterotrophic nanoflagellates, ciliates, and viruses) after an experimental P-enrichment gradient which approximated or surpassed current atmospheric P pulses in the presence vs. absence of ultraviolet radiation. HMFW underwent a mid-term (<20 days) acute development following a noticeable unimodal response to P enrichment, which peaked at intermediate P-enrichment levels and, unexpectedly, was more accentuated under ultraviolet radiation. However, after depletion of dissolved inorganic P, the HMFW collapsed and was outcompeted by a low-diversity autotrophic compartment, which constrained the development of HMFW and caused a significant loss of functional biodiversity. The dynamics and relationships among variables, and the response patterns found, suggest the importance of biotic interactions (predation/parasitism and competition) in restricting HMFW development, in contrast to the role of abiotic factors as main drivers of autotrophic compartment. The response of HMFW may contribute to ecosystem resilience by favoring the maintenance of the peculiar paths of energy and nutrient-mobilization in these pristine ecosystems, which are vulnerable to threats by the joint action of abiotic stressors related to global change.This research was supported by Junta de Andalucía (Excelencia P07-CVI-02598 to PC, and P09-RNM-5376 to JMMS), the Spanish Ministries of Medio Ambiente, Rural y Marino (PN2009/067 to PC) and Ciencia e Innovación (GLC2008-01127/BOS and CGL2011-23681 to PC), the ERC Advanced Grant project number 250254 “MINOS” (to GB), and two Spanish government grants (to JADM and FJB)