Database construction and Peptide identification strategies for proteogenomic studies on sequenced genomes.

Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene product( s). Mass-spectrometry based proteomics provides the necessary high throughput technology to show evidences of protein presence and, from the identified sequences, confirmation or invalidation of predicted annotations. We review here different strategies used to perform a MS-based proteogenomics experiment with a bottom-up approach. We start from the strengths and weaknesses of the different database construction strategies, based on different genomic information (whole genome, ORF, cDNA, EST or RNA-Seq data), which are then used for matching mass spectra to peptides and proteins. We also review the important points to be considered for a correct statistical assessment of the peptide identifications. Finally, we provide references for tools used to map and visualize the peptide identifications back to the original genomic information.

Bank versus venture capital

Why do some start-up firms raise funds from banks andothers from venture capitalists? To answer this question,I develop a model of start-up financing when intellectualproperty rights are not well protected. The upside of VCfinancing is that the VC understands the business betterthan a bank. The downside, however, is that the VC maysteal the idea and use it himself. The results of themodel are consistent with empirical regularities onstart-up financing. The model implies that thecharacteristics of the firms financing from venturecapitalists are low-collateral, high-growth and high-profitability. The model also suggests that thetighter protection of intellectual property rightscontributes to the recent dramatic growth of the USventure capital industry.

Lobbying, innovation and protectionist cycles

This paper explains why trade liberalizations occur in developing countries,and why they are often reversed. It does so by focusing on the use oflobbying for protection by import competing firms as a means to postponecostly product quality upgrades to keep up with foreign competitors. Giventhe availability of a political market for import tariffs, domestic firmswill lobby for a sequence of tariffs that insulate domestic profits from awidening quality gap, thereby allowing adjustment to be postponed. But asthe contributions required by the government grow with the size of thequality gap, it will be optimal to adjust quality and to decrease thelobbying effort at some time, leading to liberalization and technologicalcatch-up. But then the equilibrium tariff will again be small and "cheap",and it will pay to start lobbying anew, until the next quality adjustment.Therefore, cycles in protection will occur as a result of the use oflobbying as a substitute for innovation. The model thus sheds new light onthe impact of the costs of protection on the effectiveness of the lobbyingeffort over time, and on their implications for the timing and the timehorizon of trade reforms in developing countries.

Building adaptive capacity and resilience to climate change in the water sector in Cape Verde

Purpose of the evaluation This is a scheduled standard mid-term evaluation (MTR) of a UNDP implemented GEF LDCF co-financed project. It is conducted by a team of an international and a national independent evaluator. The objective of the MTR, as set out in the Terms of Reference (TORs; Annex 1), is to provide an independent analysis of the progress of the project so far. The MTR aims to:  identify potential project design problems,  assess progress towards the achievement of the project objective and outcomes,  identify and document lessons learned (including lessons that might improve design and implementation of other projects, including UNDP-GEF supported projects), and  make recommendations regarding specific actions that should be taken to improve the project. The MTR is intended to assess signs of project success or failure and identify the necessary changes to be made. The project commenced its implementation in the first half of 2010 with the recruitment of project staff. According to the updated project plan, it is due to close in July 201410 with operations scaling down in December 2013 due to funding limits. Because of a slow implementation start, the mid-term evaluation was delayed to July 201311 The intended target audience of the evaluation are:  The project team and decision makers in the INGRH  The GEF and UNFCCC Operational Focal Points  The project partners and beneficiaries  UNDP in Cape Verde as well as the regional and headquarter (HQ) office levels  The GEF Secretariat.

Seasonality in insect abundance in the "Cerrado" of Goiás State, Brazil

Seasonality in insect abundance in the "Cerrado" of Goiás State, Brazil. Many studies have provided evidence that tropical insects undergo seasonal changes in abundance and that this is partly due to alternation between the dry and rainy seasons. In the Brazilian "Cerrado" (savannah), this season alternation is particularly evident. The purpose of this work was to study the seasonal abundance of insects in a "Cerrado" area in the municipality of Pirenópolis, Goiás State, Brazil. The insects were captured fortnightly using a light trap between September 2005 and August 2006. The insects collected were separated at the order level and counted. Faunistic analysis was performed to select the predominant insect orders, a multiple linear regression to examine the relation between climatic variables (temperature and precipitation) with the abundance of insects and a circular distribution analysis to evaluate the existence of seasonality in the abundance of insect orders. A total of 34,741 insect specimens were captured, belonging to 19 orders. The orders with the greatest number of specimens were Hymenoptera (8,022), Coleoptera (6,680), Diptera (6,394), Lepidoptera (6,223), Isoptera (2,272), Hemiptera (2,240) and Trichoptera (1,967), which represent 97.3% of all the specimens collected. All the orders, except for Diptera, Isoptera and Trichoptera, showed a relationship with the climate variables (temperature), and all the orders, except for Diptera, presented a grouped distribution, with greater abundance in the transition from the end of the dry season (September) to the start of the rainy one (October/November). A discussion about seasonality on the abundance of the insects is presented.

Basic indicators for better governance in international sport (BIBGIS) : an assessment tool for international sport governing bodies

This working paper presents the Basic Indicators for Better Governance in International Sport (BIBGIS) as a tool to assess and measure the state of governance of international sport governing bodies. The working paper is organised as follows. We start by presenting different definitions of governance and some examples of principles of good governance in sport and critique them. We then introduce our approach which is based on a limited number of indicators divided among seven dimensions and apply it to the International Olympic Committee (IOC) and other international sport governing bodies. Although our approach can also be used to benchmark the governance of different sport organisations, we demonstrate that it faces limitations. We conclude with suggested next steps for future BIBGIS developments.

Informal care and labour force participation among middle-aged women in Spain

Informal care is today the form of support most commonly used by those who need other peoplein order to carry out certain activities that are considered basic (eating, dressing, taking a shower,etc.), in Spain and in most other countries in the region. The possible labour opportunity costsincurred by these informal carers, the vast majority of whom are middle-aged women, have not asyet been properly quantified in Spain. It is, however, crucially important to know these quantities ata time when public authorities appear to be determined to extend the coverage offered up to nowas regards long-term care.In this context, we use the Spanish subsample of the European Community Household Panel (1994-2001) to estimate a dynamic ordered probit and so attempt to examine the effects of various typesof informal care on labour behaviour. The results obtained indicate the existence of labouropportunity costs for those women who live with the dependent person they care for, but not forthose who care for someone outside the household. Furthermore, whereas caregiving for morethan a year has negative effects on labour force participation, the same cannot be said of those who start caregiving and stop caregiving .

When "hope springs eternal": The role of chance in risk taking

In most naturally occurring situations, success depends on both skill and chance. We contrastexperimental market entry decisions where payoffs depend on skill as opposed tocombinations of skill and chance. Our data show differential attitudes toward chance by thosewhose self-assessed skills are low and high. Making chance more important induces greateroptimism for the former who start taking more risk, while the latter maintain a belief that highlevels of skill are sufficient to overcome the vagaries of chance. Finally, although weobserved excess entry (i.e., too many participants entered markets), this could not beattributed to overconfidence.

Sweet diversity: Colonial goods and the rise of European living standards after 1492

When did overseas trade start to matter for living standards? Traditional real-wage indices suggest that living standards in Europe stagnated before 1800. In this paper, we argue thatwelfare rose substantially, but surreptitiously, because of an influx of new goods as a result ofoverseas trade. Colonial luxuries such as tea, coffee, and sugar transformed European diets afterthe discovery of America and the rounding of the Cape of Good Hope. These goods became household items in many countries by the end of the 18th century. We use three different methodsto calculate welfare gains based on price data and the rate of adoption of these new colonialgoods. Our results suggest that by 1800, the average Englishman would have been willing to forego 10% or more of his income in order to maintain access to sugar and tea alone. These findings are robust to a wide range of alternative assumptions, data series, and valuation methods.

Sex-ratio regulation: the economics of fratricide in ants

In many insect societies, workers can manipulate the reproductive output of their colony by killing kin of lesser value to them. For instance, workers of the mound-building For mica exsecta eliminate male brood in colonies headed by a single-mated queen. By combining an inclusive fitness model and empirical data, we investigated the selective causes underlying these fratricides. Our model examines until which threshold stage in male brood development do the workers benefit from eliminating males to rear extra females instead. We then determined the minimal developmental stage reached by male larvae before elimination in F. exsecta field colonies. Surprisingly, many male larvae were kept until they were close to pupation, and only then eliminated. According to our model, part of the eliminated males were so large that workers would not benefit from replacing them with new females. Moreover, males were eliminated late in the season, so that new females could no longer be initiated, because matings take place synchronously during a short period. Together, these results indicate that workers did not replace male brood with new females, but rather reduced total brood size during late larval development. Male destruction was probably triggered by resource limitation, and the timing of brood elimination suggests that males may have been fed to females when these start to grow exponentially during the final larval stage. Hence, the evolution of fratricides in ants is best explained by a combination of ecological, demographic and genetic parameters.

Tidibi

Tidibi es una nueva comunidad digital que permite a sus miembros hacer pujas por ofertas de ocio exclusivas al precio que ellos decidan. En este momento estas ofertas de ocio se centran en hoteles de cuatro y cinco estrellas, pero está previsto lanzar pronto packs de esquí, cruceros y, más adelante, espectáculos. El usuario ganador de la oferta es aquel queha ofrecido un precio más alto (apéndices 1, 2 y 3) cuando el cronómetro que cuenta atrás llega a cero, y puede decidir cuántas noches quiere pasar en ese hotel (hasta un máximo de tres) a ese precio.La sociedad gestora de Tidibi, “Dragon Deal”, se constituyó jurídicamente como una S.L. el 6 de julio de 2012, pero el lanzamiento oficial de la página web www.tidibi.com no ocurrió hasta el 4 de octubre de este año. Sus creadores son un grupo de cuatro emprendedores (apéndice 4) que se conocieron en el curso de sus estudios MBA en la escuela de negocios IESE de Barcelona.Tidibi es un concepto innovador, basado en los nuevos usos de las tecnologías y en la línea de las nuevas tendencias del mercado, en el que existe una relación participativa por partede los clientes, en vez del tradicional rol del agente pasivo que espera que le hagan llegar la información. Dado que el precio es la principal barrera para que los compradores cibernéticos hagan sus compras on-line (iPerceptions “Hospitality and Tourism Industryreport” para Q4 2011), parece que Tidibi puede ofrecer una solución a esta problemática y hacer "business" con ello.Por lo que respecta a la inversión requerida, los emprendedores estiman una cantidad total de 450.000€, que se desglosa de la siguiente manera: 60.000€ fondos iniciales de la start-up, 140.000€ necesidades de capital circulante y 250.000€ de marketing y esfuerzo de ventas.Sin embargo, también reconocen que podrían funcionar con una inversión inferior, dadoque podrían adaptar y reducir la última de las partidas arriba mencionadas. A pesar de ello, creemos que una reducción significativa de esfuerzos en marketing podría comprometer eléxito de la empresa. Por ahora han conseguido cerca de la mitad del presupuesto en una ronda de financiación interna y un préstamo participativo de un fondo de capital riesgo. No podemos proveer más datos por razones de confidencialidad.

Fish ecology in Lake Banyoles (NE Spain): a tribute to Ramon Margalef

Lake Banyoles is the second largest lake in the Iberian Peninsula and due to this relative uniqueness, its peculiar geological origin, and its considerable age attracted the early attention of the late Professor Ramon Margalef. One of the first papers by Margalef was on the biota of Lake Banyoles and two of the first four Ph.D. theses that he supervised were about the limnology of this lake. Unfortunately, the uniqueness of this lake also implied that it was the first place of introduction into the Iberian Peninsula of several exotic fish species, early in the XXth Century and nowadays the lake fish assemblage is dominated by invasive species, and some native ones have been extirpated. Although the limnological studies in Lake Banyoles were pioneering within the Iberian Peninsula, studies on fish ecology of the lake did not start until 1989. Thereafter, four Ph.D. theses have been completed on different aspects of the fish assemblages of Lake Banyoles. The aim of this paper is to provide a short overview of this research, largely brought about by the considerable limnological information previously available for this lake, thanks to the insightful, pioneering work of Professor Margalef

RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family.

In the Gac/Rsm signal transduction pathway of Pseudomonas fluorescens CHA0, the dimeric RNA-binding proteins RsmA and RsmE, which belong to the vast bacterial RsmA/CsrA family, effectively repress translation of target mRNAs containing a typical recognition sequence near the translation start site. Three small RNAs (RsmX, RsmY, RsmZ) with clustered recognition sequences can sequester RsmA and RsmE and thereby relieve translational repression. According to a previously established structural model, the RsmE protein makes optimal contacts with an RNA sequence 5'- (A)/(U)CANGGANG(U)/(A)-3', in which the central ribonucleotides form a hexaloop. Here, we questioned the relevance of the hexaloop structure in target RNAs. We found that two predicted pentaloop structures, AGGGA (in pltA mRNA encoding a pyoluteorin biosynthetic enzyme) and AAGGA (in mutated pltA mRNA), allowed effective interaction with the RsmE protein in vivo. By contrast, ACGGA and AUGGA were poor targets. Isothermal titration calorimetry measurements confirmed the strong binding of RsmE to the AGGGA pentaloop structure in an RNA oligomer. Modeling studies highlighted the crucial role of the second ribonucleotide in the loop structure. In conclusion, a refined structural model of RsmE-RNA interaction accommodates certain pentaloop RNAs among the preferred hexaloop RNAs.

Nilotinib compassionate use in advanced GIST : a retrospective analysis

Introduction: Tyrosine kinase inhibitors (TKI) have considerably improved outcome of patients with advanced GIST and extended overall survival to more than 5 years. Yet, the median progression-free survival is approximately 2 years with first-line imatinib and 24 weeks with second-line sunitinib, which calls for treatment alternatives. Nilotinib is a second-generation TKI with at least similar inhibitory activity as imatinib. A Phase I study has shown that nilotinib monotherapy has clinical activity in GIST. Methods: After failure of all available therapeutic options patients had access to nilotinib on a compassionate use (CU) programm. Nilotinib was started at a dose of 400 mg bid, with dose reduction to 400mg qd allowed in the case of toxicity. 94 pts were approved for nilotinib CU in 10 European countries. We herein present retrospective data of 42 pts from 5 European countries treated in 11 centers. Results: Median age at nilotinib treatment start was 59 years (median; range 24-79 y). 30 of 42 patients were male. Most pts had metastatic disease of gastric origin at initial diagnosis. KIT exon 11 mutations were most frequent. The median number of surgical resections was 1 (range 0-8). All pts had failed both imatinib and sunitinib before nilotinib, and few had also received additional investigational treatments. Nilotinib was well tolerated, and discontinued due to toxicity in 15% only. Median follow-up is 176 days (range 15-876 d). Nilotinib treatment duration is 75 days (median; range 3-727 d). Partial remission with nilotinib treatment was seen in 11% of pts. Median OS was 263 days (Kaplan-Meier). Conclusion: This is the largest series reported assessing efficacy of nilotinib for imatinib- and sunitinib-refractory GIST reported yet. Nilotinib displays significant clinical activity in this heavily pretreated group of pts. These results warrant further investigation of nilotinib in GIST, including its use in first or second-line treatment. Patient and data collection is ongoing, updated results will be presented.