Decomposing the Gender Wage Gap: The effect of firms, occupations and Job Stratification

This paper presents new evidence on the role of segregation into firms, occupations within a firm and stratification into professional categories within firm-occupations in explaining the gender wage gap. I use a generalized earnings model that allows observed and unobserved group characteristics to have different impact on wages of men and women within the same group. The database is a large sample of individual wage data from the 1995 Spanish Wage Structure Survey. Results indicate that firm segregation in our sample accounts for around one-fifth of the raw gender wage gap. Occupational segregation within firms accounts for about one-third of the raw wage gap, and stratification into different professional categories within firms and occupations explains another one-third of it. The remaining one-fifth of the overall gap arises from better outcomes of men relative to women within professional categories. It is also found that rewards to both observable and unobservable skills, particularly those related to education, are higher for males than for females within the same group. Finally, mean wages in occupations or job categories with a higher fraction of female co-workers are lower, but the negative impact of femaleness in higher for women.

Régimen jurídico de las lenguas y reconocimiento de la diversidad lingüística en el Tratado por el que se establece una Constitución para Europa

The territory of the European Union is made up of a rich and wide-ranging universe of languages, which is not circumscribed to the «State languages». The existence of multilingualism is one of Europe’s defining characteristics and it should remain so in the constantly evolving model of Europe’s political structure. Nonetheless, until now, the official use of languages has been limited to the «State languages» and has been based on a concept of state monolingualism that has led to a first level of hierarchization among the languages of Europe. This has affected the very concept of European language diversity. The draft of the treaty establishing a European Constitution contains various language-related references that can be grouped in two major categories: on the one hand, those references having to do the constitutional status of languages, and on the other, those regarding the recognition of European language diversity. Both issues are dealt with in this article. In analyzing the legal regime governing languages set forth in the draft of the constitutional treaty, we note that the draft is not based on the concept of the official status of languages. The language regulation contained in the draft of the constitutional treaty is limited in character. The constitutional language regime is based on the concept of Constitutional languages but the official status of languages is not governed by this rule. The European Constitution merely enunciates rights governing language use for European citizens vis-à-vis the languages of the Constitution and refers the regulation of the official status of languages to the Council, which is empowered to set and modify that status by unanimous decision. Because of its broad scope, this constitutes a regulatory reservation. In the final phase of the negotiation process a second level of constitutional recognition of languages would be introduced, linked to those that are official languages in the member states (Catalan, Basque, Galician, etc.). These languages, however, would be excluded from the right to petition; they would constitute a tertium genus, an intermediate category between the lan guages benefiting from the language rights recognized under the Constitution and those other languages for which no status is recognized in the European institutional context. The legal functionality of this second, intermediate category will depend on the development of standards, i.e., it will depend on the entrée provided such languages in future reforms of the institutional language regime. In a later section, the article reflects on European Union language policy with regard to regional or minority languages, concluding that the Union has not acted in accordance with defined language policy guidelines when it has been confronted, in the exercise of its powers, with regional or minority languages (or domestic legislation having to do with language demands). The Court of Justice has endeavoured to resolve on a case by case basis the conflicts raised between community freedoms and the normative measures that protect languages. Thus, using case law, the Court has set certain language boundaries for community freedoms. The article concludes by reflecting on the legal scope of the recognition of European language diversity referred to in Article II-82 of the European Constitution and the possible measures to implement the precept that might constitute the definition of a true European language policy on regional or minority languages. Such a policy has yet to be defined.

Las deficiencias formativas en la Educación Superior: El caso de las Ingenierías

[ES] El entorno en el que desarrollan sus actividades las instituciones universitarias está poniendo de manifiesto algunas debilidades en la formación impartida a sus egresados. Entre ellas destaca la falta de adecuación entre las competencias potenciadas por las universidades en sus alumnos y las demandadas por las organizaciones. Ante esta situación, este artículo pretende analizar el estado de la cuestión, concretamente centrándonos en el caso de los ingenieros y para el contexto de la Comunidad Autónoma de Aragón. Para ello, se analizan las opiniones manifestadas, a través de un cuestionario, a un grupo de empleadores.

Marcas de distribuidor: análisis del espacio en el lineal por categorías y enseñas

[ES] El objetivo principal de este trabajo es confirmar si la ocupación de espacio por parte de las marcas de distribuidor en los lineales es excesivo, tal y como parecen afirmar los productores de marcas de fabricante. Para ello, se presentan los resultados de una observación del espacio ocupado por estas marcas en una muestra representativa de 40 categorías en 55 establecimientos. Con los datos obtenidos, se muestran las diferencias existentes entre categorías y entre enseñas. Además se observa si los establecimientos han llegado a un punto de lineal máximo y si el espacio ocupado por sus marcas propias es desproporcionado en relación a su cuota de mercado.

Evolución y tendencias de la marca de distribuidor en los mercados de gran consumo: el caso de España

[ES] La marca de distribuidor está experimentando un proceso de crecimiento notable en nuestro país, especialmente en los mercados de productos de gran consumo. Sobre este particular, este trabajo tiene por objeto analizar la situación actual así como las tendencias futuras en la comercialización de marcas de distribuidor en la industria de productos de gran consumo. Para ello, se tendrá en cuenta la penetración de las marcas de distribuidor en distintas categorías de productos de gran consumo, exponiéndose una serie de argumentos con objeto de explicar las tendencias observadas.

La elección de la marca del distribuidor en productos duraderos: factores de influencia

[ES] La apuesta de la distribución por la extensión de su marca a las categorías de productos duraderos, como electrodomésticos y productos electrónicos para el hogar, ha demostrado ser acertada, a pesar de las críticas en contra de esta estrategia. Posiblemente, la mayor familiaridad del consumidor con las marcas del distribuidor, el cambio de actitud favorable hacia éstas, la disponibilidad de la tecnología, y por qué no, la crisis económica internacional que afecta a las economías domésticas, pueden ser factores explicativos de este éxito.

An Analysis of English, Spanish and Basque Demonstratives in Narrative: a Matter of Viewpoint

[EN]This paper undertakes the study of the occurrence of non-corresponding demonstrative forms in Spanish, Basque and English in exactly the same linguistic context. It is proposed that the differenccs in the choice of the demonstratives result from the differences in the kind of iniormation that must be coded in each of the languages. Thus, I will argue that in Spanish and Basque the obligatory coding of the aspectual categories of the imperfect and the preterit has the function of imposing specific viewing arrangements onto the situations they designate. By contrast, in English, where the aspectual distinction is not overtly coded, the demonstrativcs are proposed to fulfil this function.

Introducción de peces exóticos en la República Argentina

A review and analysis of the exotic fish distribution and introduction is made using bibliographic information. Both lentic and lotic environments were considered. In order to classify the state of the populations, different categories were defined as follow: permanent, probably permanent, reported and unknown. Results show that 15 species were attempted to be introduced from 1904. Only 8 of them arose an successfull aclimatization: raimbow trout, brown trout, lake trout, landlocked salmon, carp, goldfish, and mosquitofish. For the salmonids, ecological features were analized, in order to explain the disappearence or the permanence in some regions. (Document contains 90 pages)

Territorial Integrity and Self-Determination : The Approach of the International Court of Justice in the Advisory Opinion on Kosovo

[EN] On 17 February 2008 Kosovo approved its declaration of independence from Serbia. The declaration was raised as a unilateral secession, a category which to date is widely debated by the international community, but supported in that case by a respectable number of the United Nation member states. A great many legal issues have been raised by the International Court of Justice's Advisory Opinion on Kosovo. This opinion was eagerly awaited by legal scholars due to both its possible effects and the scope of its principles outside the context of decolonization in what it could constitute of new approach to the international scenario for the twenty-first century. The ICJ stated that the declaration of independence was in accordance with international law if it was not prohibited. The answer turned on whether or not international law prohibited the declaration of independence, without ever examining whether an entity seeking secession is entitled with a positive right to secede and if so, under which circumstances. The basic issue can be summarised as whether or not we are facing a new course in the interpretation of certain classical categories of international law: the principle of territorial integrity, statehood, sovereignty, recognition, the right to external self-determination, etc. In this study we shall analyse some of the aspects arising from the Advisory Opinion of the International Court of Justice on the Accordance with international law of the unilateral declaration of independence in respect of Kosovo focusing on the territorial issue. Firstly we shall analyse the scope of the principle of territorial integrity of States and how it operates ; secondly, we shall focus on the scope of that principle in relation to the interior of the State, and ask ourselves how international law operates in relation to declarations of independence. Lastly, we shall deal with the principle of respect for territorial integrity in the specific case of Serbia with respect to Kosovo, and then end with a series of general conclusions. This study aims, definitely, to contribute to the theoretical debate on the challenges to the traditional certainties of international law in this area.

Deportividad y violencia en el fútbol base: un programa de evaluación y de prevención de partidos de riesgo

Este trabajo ha recibido el “Primer Premio Delegación del Gobierno en Aragón a las buenas prácticas contra la delincuencia juvenil” (Convocatoria 2007).

Elaboración del registro de evaluación del continuo deportividad-violencia en la competición del fútbol base (REPF)

[ES] En este estudio se describe el proceso seguido para la elaboración del auto-registro, diseñado específicamente para la medición de los estructos "deportividad”, “agresividad" y “violencia”. Este instrumento permite la recogida de información sobre actitudes y conductas relacionadas con la deportividad, la agresividad y la violencia de los diferentes agentes sociales que rodean a los jóvenes deportistas en categorías deportivas de formación (padres/espectadores, entrenadores y árbitros). Por otro lado, se detalla la estructura de este instrumento y las características psicométricas del mismo -validez y fiabilidad-.

The Annual Economic Survey of Federal Gulf Shrimp Permit Holders: Report on the Design, Implementation, and Descriptive Results for 2006

This technical memorandum documents the design, implementation, data preparation, and descriptive results for the 2006 Annual Economic Survey of Federal Gulf Shrimp Permit Holders. The data collection was designed by the NOAA Fisheries Southeast Fisheries Science Center Social Science Research Group to track the financial and economic status and performance by vessels holding a federal moratorium permit for harvesting shrimp in the Gulf of Mexico. A two page, self-administered mail survey collected total annual costs broken out into seven categories and auxiliary economic data. In May 2007, 580 vessels were randomly selected, stratified by state, from a preliminary population of 1,709 vessels with federal permits to shrimp in offshore waters of the Gulf of Mexico. The survey was implemented during the rest of 2007. After many reminder and verification phone calls, 509 surveys were deemed complete, for an ineligibility-adjusted response rate of 90.7%. The linking of each individual vessel’s cost data to its revenue data from a different data collection was imperfect, and hence the final number of observations used in the analyses is 484. Based on various measures and tests of validity throughout the technical memorandum, the quality of the data is high. The results are presented in a standardized table format, linking vessel characteristics and operations to simple balance sheet, cash flow, and income statements. In the text, results are discussed for the total fleet, the Gulf shrimp fleet, the active Gulf shrimp fleet, and the inactive Gulf shrimp fleet. Additional results for shrimp vessels grouped by state, by vessel characteristics, by landings volume, and by ownership structure are available in the appendices. The general conclusion of this report is that the financial and economic situation is bleak for the average vessels in most of the categories that were evaluated. With few exceptions, cash flow for the average vessel is positive while the net revenue from operations and the “profit” are negative. With negative net revenue from operations, the economic return for average shrimp vessels is less than zero. Only with the help of government payments does the average owner just about break even. In the short-term, this will discourage any new investments in the industry. The financial situation in 2006, especially if it endures over multiple years, also is economically unsustainable for the average established business. Vessels in the active and inactive Gulf shrimp fleet are, on average, 69 feet long, weigh 105 gross tons, are powered by 505 hp motor(s), and are 23 years old. Three-quarters of the vessels have steel hulls and 59% use a freezer for refrigeration. The average market value of these vessels was $175,149 in 2006, about a hundred-thousand dollars less than the average original purchase price. The outstanding loans averaged $91,955, leading to an average owner equity of $83,194. Based on the sample, 85% of the federally permitted Gulf shrimp fleet was actively shrimping in 2006. Of these 386 active Gulf shrimp vessels, just under half (46%) were owner-operated. On average, these vessels burned 52,931 gallons of fuel, landed 101,268 pounds of shrimp, and received $2.47 per pound of shrimp. Non-shrimp landings added less than 1% to cash flow, indicating that the federal Gulf shrimp fishery is very specialized. The average total cash outflow was $243,415 of which $108,775 was due to fuel expenses alone. The expenses for hired crew and captains were on average $54,866 which indicates the importance of the industry as a source of wage income. The resulting average net cash flow is $16,225 but has a large standard deviation. For the population of active Gulf shrimp vessels we can state with 95% certainty that the average net cash flow was between $9,500 and $23,000 in 2006. The median net cash flow was $11,843. Based on the income statement for active Gulf shrimp vessels, the average fixed costs accounted for just under a quarter of operating expenses (23.1%), labor costs for just over a quarter (25.3%), and the non-labor variable costs for just over half (51.6%). The fuel costs alone accounted for 42.9% of total operating expenses in 2006. It should be noted that the labor cost category in the income statement includes both the actual cash payments to hired labor and an estimate of the opportunity cost of owner-operators’ time spent as captain. The average labor contribution (as captain) of an owner-operator is estimated at about $19,800. The average net revenue from operations is negative $7,429, and is statistically different and less than zero in spite of a large standard deviation. The economic return to Gulf shrimping is negative 4%. Including non-operating activities, foremost an average government payment of $13,662, leads to an average loss before taxes of $907 for the vessel owners. The confidence interval of this value straddles zero, so we cannot reject, with 95% certainty, that the population average is zero. The average inactive Gulf shrimp vessel is generally of a smaller scale than the average active vessel. Inactive vessels are physically smaller, are valued much lower, and are less dependent on loans. Fixed costs account for nearly three quarters of the total operating expenses of $11,926, and only 6% of these vessels have hull insurance. With an average net cash flow of negative $7,537, the inactive Gulf shrimp fleet has a major liquidity problem. On average, net revenue from operations is negative $11,396, which amounts to a negative 15% economic return, and owners lose $9,381 on their vessels before taxes. To sustain such losses and especially to survive the negative cash flow, many of the owners must be subsidizing their shrimp vessels with the help of other income or wealth sources or are drawing down their equity. Active Gulf shrimp vessels in all states but Texas exhibited negative returns. The Alabama and Mississippi fleets have the highest assets (vessel values), on average, yet they generate zero cash flow and negative $32,224 net revenue from operations. Due to their high (loan) leverage ratio the negative 11% economic return is amplified into a negative 21% return on equity. In contrast, for Texas vessels, which actually have the highest leverage ratio among the states, a 1% economic return is amplified into a 13% return on equity. From a financial perspective, the average Florida and Louisiana vessels conform roughly to the overall average of the active Gulf shrimp fleet. It should be noted that these results are averages and hence hide the variation that clearly exists within all fleets and all categories. Although the financial situation for the average vessel is bleak, some vessels are profitable. (PDF contains 101 pages)

Support for Integrated Ecosystem Assessments of NOAA’s National Estuarine Research Reserves System (NERRS), Volume II: Assessment of Ecological Condition and Stressor Impacts in Subtidal Waters of the North Carolina NERRS

A study was conducted to assess the status of ecological condition and potential human-health risks in subtidal estuarine waters throughout the North Carolina National Estuarine Research Reserve System (NERRS) (Currituck Sound, Rachel Carson, Masonboro Island, and Zeke’s Island). Field work was conducted in September 2006 and incorporated multiple indicators of ecosystem condition including measures of water quality (dissolved oxygen, salinity, temperature, pH, nutrients and chlorophyll, suspended solids), sediment quality (granulometry, organic matter content, chemical contaminant concentrations), biological condition (diversity and abundances of benthic fauna, fish contaminant levels and pathologies), and human dimensions (fish-tissue contaminant levels relative to human-health consumption limits, various aesthetic properties). A probabilistic sampling design permitted statistical estimation of the spatial extent of degraded versus non-degraded condition across these estuaries relative to specified threshold levels of the various indicators (where possible). With some exceptions, the status of these reserves appeared to be in relatively good to fair ecological condition overall, with the majority of the area (about 54%) having various water quality, sediment quality, and biological (benthic) condition indicators rated in the healthy to intermediate range of corresponding guideline thresholds. Only three stations, representing 10.5% of the area, had one or more of these indicators rated as poor/degraded in all three categories. While such a conclusion is encouraging from a coastal management perspective, it should be viewed with some caution. For example, although co-occurrences of adverse biological and abiotic environmental conditions were limited, at least one indicator of ecological condition rated in the poor/degraded range was observed over a broader area (35.5%) represented by 11 of the 30 stations sampled. In addition, the fish-tissue contaminant data were not included in these overall spatial estimates; however, the majority of samples (77% of fish that were analyzed, from 79%, of stations where fish were caught) contained inorganic arsenic above the consumption limits for human cancer risks, though most likely derived from natural sources. Similarly, aesthetic indicators are not reflected in these spatial estimates of ecological condition, though there was evidence of noxious odors in sediments at many of the stations. Such symptoms reflect a growing realization that North Carolina estuaries are under multiple pressures from a variety of natural and human influences. These data also suggest that, while the current status of overall ecological condition appears to be good to fair, long-term monitoring is warranted to track potential changes in the future. This study establishes an important baseline of overall ecological condition within NC NERRS that can be used to evaluate any such future changes and to trigger appropriate management actions in this rapidly evolving coastal environment. (PDF contains 76 pages)

Characterization of the benthos, marine debris and bottom fish at Gray’s Reef National Marine Sanctuary

Executive Summary: Baseline characterization of resources is an essential part of marine protected area (MPA) management and is critical to inform adaptive management. Gray’s Reef National Marine Sanctuary (GRNMS) currently lacks adequate characterization of several key resources as identified in the 2006 Final Management Plan. The objectives of this characterization were to fulfill this need by characterizing the bottom fish, benthic features, marine debris, and the relationships among them for the different bottom types within the sanctuary: ledges, sparse live bottom, rippled sand, and flat sand. Particular attention was given to characterizing the different ledge types, their fish communities, and the marine debris associated with them given the importance of this bottom type to the sanctuary. The characterization has been divided into four sections. Section 1 provides a brief overview of the project, its relevance to sanctuary needs, methods of site selection, and general field procedures. Section 2 provides the survey methods, results, discussion, and recommendations for monitoring specific to the benthic characterization. Section 3 describes the characterization of marine debris. Section 4 is specific to the characterization of bottom fish. Field surveys were conducted during August 2004, May 2005, and August 2005. A total of 179 surveys were completed over ledge bottom (n=92), sparse live bottom (n=51), flat sand (n=20), and rippled sand (n=16). There were three components to each field survey: fish counting, benthic assessment, and quantification of marine debris. All components occurred within a 25 x 4 m belt transect. Two divers performed the transect at each survey site. One diver was responsible for identification of fish species, size, and abundance using a visual survey. The second diver was responsible for characterization of benthic features using five randomly placed 1 m2 quadrats, measuring ledge height and other benthic structures, and quantifying marine debris within the entire transect. GRNMS is composed of four main bottom types: flat sand, rippled sand, sparsely colonized live bottom, and densely colonized live bottom (ledges). Independent evaluation of the thematic accuracy of the GRNMS benthic map produced by Kendall et al. (2005) revealed high overall accuracy (93%). Most discrepancies between map and diver classification occurred during August 2004 and likely can be attributed to several factors, including actual map or diver errors, and changes in the bottom type due to physical forces. The four bottom types have distinct physical and biological characteristics. Flat and rippled sand bottom types were composed primarily of sand substrate and secondarily shell rubble. Flat sand and rippled sand bottom types were characterized by low percent cover (0-2%) of benthic organisms at all sites. Although the sand bottom types were largely devoid of epifauna, numerous burrows indicate the presence of infaunal organisms. Sparse live bottom and ledges were colonized by macroalgae and numerous invertebrates, including coral, gorgonians, sponges, and “other” benthic species (such as tunicates, anemones, and bryozoans). Ledges and sparse live bottom were similar in terms of diversity (H’) given the level of classification used here. However, percent cover of benthic species, with the exception of gorgonians, was significantly greater on ledge than on sparse live bottom. Percent biotic cover at sparse live bottom ranged from 0.7-26.3%, but was greater than 10% at only 7 out of 51 sites. Colonization on sparse live bottom is likely inhibited by shifting sands, as most sites were covered in a layer of sediment up to several centimeters thick. On ledge bottom type, percent cover ranged from 0.42-100%, with the highest percent cover at ledges in the central and south-central region of GRNMS. Biotic cover on ledges is influenced by local ledge characteristics. Cluster analysis of ledge dimensions (total height, undercut height, undercut width) resulted in three main categories of ledges, which were classified as short, medium, and tall. Median total percent cover was 97.6%, 75.1%, and 17.7% on tall, medium, and short ledges, respectively. Total percent cover and cover of macroalgae, sponges, and other organisms was significantly lower on short ledges compared to medium and tall ledges, but did not vary significantly between medium and tall ledges. Like sparse live bottom, short ledges may be susceptible to burial by sand, however the results indicate that ledge height may only be important to a certain threshold. There are likely other factors not considered here that also influence spatial distribution and community structure (e.g., small scale complexity, ocean currents, differential settlement patterns, and biological interactions). GRNMS is a popular site for recreational fishing and boating, and there has been increased concern about the accumulation of debris in the sanctuary and potential effects on sanctuary resources. Understanding the types, abundance, and distribution of debris is essential to improving debris removal and education efforts. Approximately two-thirds of all observed debris items found during the field surveys were fishing gear, and about half of the fishing related debris was monofilament fishing line. Other fishing related debris included leaders and spear gun parts, and non-gear debris included cans, bottles, and rope. The spatial distribution of debris was concentrated in the center of the sanctuary and was most frequently associated with ledges rather than at other bottom types. Several factors may contribute to this observation. Ledges are often targeted by fishermen due to the association of recreationally important fish species with this bottom type. In addition, ledges are structurally complex and are often densely colonized by biota, providing numerous places for debris to become stuck or entangled. Analysis of observed boat locations indicated that higher boat activity, which is an indication of fishing, occurs in the center of the sanctuary. On ledges, the presence and abundance of debris was significantly related to observed boat density and physiographic features including ledge height, ledge area, and percent cover. While it is likely that most fishing related debris originates from boats inside the sanctuary, preliminary investigation of ocean current data indicate that currents may influence the distribution and local retention of more mobile items. Fish communities at GRNMS are closely linked to benthic habitats. A list of species encountered, probability of occurrence, abundance, and biomass by habitat is provided. Species richness, diversity, composition, abundance, and biomass of fish all showed striking differences depending on bottom type with ledges showing the highest values of nearly all metrics. Species membership was distinctly separated by bottom type as well, although very short, sparsely colonized ledges often had a similar community composition to that of sparse live bottom. Analysis of fish communities at ledges alone indicated that species richness and total abundance of fish were positively related to total percent cover of sessile invertebrates and ledge height. Either ledge attribute was sufficient to result in high abundance or species richness of fish. Fish diversity (H`) was negatively correlated with undercut height due to schools of fish species that utilize ledge undercuts such as Pareques species. Concurrent analysis of ledge types and fish communities indicated that there are five distinct combinations of ledge type and species assemblage. These include, 1) short ledges with little or no undercut that lacked many of the undercut associated species except Urophycis earlii ; 2) tall, heavily colonized, deeply undercut ledges typically with Archosargus probatocephalus, Mycteroperca sp., and Pareques sp.; 3) tall, heavily colonized but less undercut with high occurrence of Lagodon rhomboides and Balistes capriscus; 4) short, heavily colonized ledges typically with Centropristis ocyurus, Halichoeres caudalis, and Stenotomus sp.; and 5) tall, heavily colonized, less undercut typically with Archosargus probatocephalus, Caranx crysos and Seriola sp.. Higher levels of boating activity and presumably fishing pressure did not appear to influence species composition or abundance at the community level although individual species appeared affected. These results indicate that merely knowing the basic characteristics of a ledge such as total height, undercut width, and percent cover of sessile invertebrates would allow good prediction of not only species richness and abundance of fish but also which particular fish species assemblages are likely to occur there. Comparisons with prior studies indicate some major changes in the fish community at GRNMS over the last two decades although the causes of the changes are unknown. Species of interest to recreational fishermen including Centropristis striata, Mycteroperca microlepis, and Mycteroperca phenax were examined in relation to bottom features, areas of assumed high versus low fishing pressure, and spatial dispersion. Both Mycteroperca species were found more frequently when undercut height of ledges was taller. They often were found together in small mixed species groups at ledges in the north central and southwest central regions of the sanctuary. Both had lower mode size and proportion of fish above the fishery size limit in heavily fished areas of the sanctuary (i.e. high boat density) despite the presence of better habitat in that region. Black sea bass, C. striata, occurred at 98% of the ledges surveyed and appeared to be evenly distributed throughout the sanctuary. Abundance was best explained by a positive relationship with percent cover of sessile biota but was also negatively related to presence of either Mycteroperca species. This may be due to predation by the Mycteroperca species or avoidance of sites where they are present by C. striata. Suggestions for monitoring bottom features, marine debris, and bottom fish at GRNMS are provided at the end of each chapter. The present assessment has established quantitative baseline characteristics of many of the key resources and use issues at GRNMS. The methods can be used as a model for future assessments to track the trajectory of GRNMS resources. Belt transects are ideally suited to providing efficient and quantitative assessment of bottom features, debris, and fish at GRNMS. The limited visibility, sensitivity of sessile biota, and linear nature of ledge habitats greatly diminish the utility of other sampling techniques. Ledges should receive the bulk of future characterization effort due to their importance to the sanctuary and high variability in physical structure, benthic composition, and fish assemblages. (PDF contains 107 pages.)

PAnalyzer: A software tool for protein inference in shotgun proteomics

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.