Spatially explicit estimates of stock size, structure and biomass of North Atlantic albacore tuna (Thunnus alalunga) in the North Atlantic for the period 1967-2008, compiled from statistics about ICCAT fishery region T10

The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.

Modelización del cálculo de Indicadores Ambientales, a partir de sensores ópticos de alta resolución temporal a bordo de satélite

La presente tesis doctoral tiene por objeto el estudio y análisis de técnicas y modelos de obtención de parámetros biofísicos e indicadores ambientales, de manera automatizada a partir de imágenes procedentes de satélite de alta resolución temporal. En primer lugar se revisan los diferentes programas espaciales de observación del territorio, con especial atención a los que proporcionan dicha resolución. También se han revisado las metodologías y procesos que permiten la obtención de diferentes parámetros cuantitativos y documentos cualitativos, relacionados con diversos aspectos de las cubiertas terrestres, atendiendo a su adaptabilidad a las particularidades de los datos. En segundo lugar se propone un modelo de obtención de parámetros ambientales, que integra información proveniente de sensores espaciales y de otras fuentes auxiliares utilizando, en cierta medida, las metodologías presentadas en apartados anteriores y optimizando algunas de las referidas o proponiendo otras nuevas, de manera que se permita dicha obtención de manera eficiente, a partir de los datos disponibles y de forma sistemática. Tras esta revisión de metodologías y propuesta del modelo, se ha procedido a la realización de experimentos, con la finalidad de comprobar su comportamiento en diferentes casos prácticos, depurar los flujos de datos y procesos, así como establecer las situaciones que pueden afectar a los resultados. De todo ello se deducirá la evaluación del referido modelo. Los sensores considerados en este trabajo han sido MODIS, de alta resolución temporal y Thematic Mapper (TM), de media resolución espacial, por tratarse de instrumentos de referencia en la realización de estudios ambientales. También por la duración de sus correspondientes misiones de registro de datos, lo que permite realizar estudios de evolución temporal de ciertos parámetros biofísicos, durante amplios periodos de tiempo. Así mismo. es de destacar que la continuidad de los correspondientes programas parece estar asegurada. Entre los experimentos realizados, se ha ensayado una metodología para la integración de datos procedentes de ambos sensores. También se ha analizado un método de interpolación temporal que permite obtener imágenes sintéticas con la resolución espacial de TM (30 m) y la temporal de MODIS (1 día), ampliando el rango de aplicación de este último sensor. Asimismo, se han analizado algunos de los factores que afectan a los datos registrados, tal como la geometría de la toma de los mismos y los episodios de precipitación, los cuales alteran los resultados obtenidos. Por otro lado, se ha comprobado la validez del modelo propuesto en el estudio de fenómenos ambientales dinámicos, en concreto la contaminación orgánica de aguas embalsadas. Finalmente, se ha demostrado un buen comportamiento del modelo en todos los casos ensayados, así como su flexibilidad, lo que le permite adaptarse a nuevos orígenes de datos, o nuevas metodologías de cálculo. Abstract This thesis aims to the study and analysis of techniques and models, in order to obtain biophysical parameters and environmental indicators in an automated way, using high temporal resolution satellite data. Firstly we have reviewed the main Earth Observation Programs, paying attention to those that provide high temporal resolution. Also have reviewed the methodologies and process flow diagrams in order to obtain quantitative parameters and qualitative documents, relating to various aspects of land cover, according to their adaptability to the peculiarities of the data. In the next stage, a model which allows obtaining environmental parameters, has been proposed. This structure integrates information from space sensors and ancillary data sources, using the methodologies presented in previous sections that permits the parameters calculation in an efficient and automated way. After this review of methodologies and the proposal of the model, we proceeded to carry out experiments, in order to check the behavior of the structure in real situations. From this, we derive the accuracy of the model. The sensors used in this work have been MODIS, which is a high temporal resolution sensor, and Thematic Mapper (TM), which is a medium spatial resolution instrument. This choice was motivated because they are reference sensors in environmental studies, as well as for the duration of their corresponding missions of data logging, and whose continuity seems assured. Among the experiments, we tested a methodology that allows the integration of data from cited sensors, we discussed a proposal for a temporal interpolation method for obtaining synthetic images with spatial resolution of TM (30 m) and temporal of MODIS (1 day), extending the application range of this one. Furthermore, we have analyzed some of the factors that affect the recorded data, such as the relative position of the satellite with the ground point, and the rainfall events, which alter the obtained results. On the other hand, we have proven the validity of the proposed model in the study of the organic contamination in inland water bodies. Finally, we have demonstrated a good performance of the proposed model in all cases tested, as well as its flexibility and adaptability.

Higher temporal variability of forest breeding bird communities in fragmented landscapes

Understanding the relationship between animal community dynamics and landscape structure has become a priority for biodiversity conservation. In particular, predicting the effects of habitat destruction that confine species to networks of small patches is an important prerequisite to conservation plan development. Theoretical models that predict the occurrence of species in fragmented landscapes, and relationships between stability and diversity do exist. However, reliable empirical investigations of the dynamics of biodiversity have been prevented by differences in species detection probabilities among landscapes. Using long-term data sampled at a large spatial scale in conjunction with a capture-recapture approach, we developed estimates of parameters of community changes over a 22-year period for forest breeding birds in selected areas of the eastern United States. We show that forest fragmentation was associated not only with a reduced number of forest bird species, but also with increased temporal variability in the number of species. This higher temporal variability was associated with higher local extinction and turnover rates. These results have major conservation implications. Moreover, the approach used provides a practical tool for the study of the dynamics of biodiversity.

Temporal distribution of the ganglion cell volleys in the normal rat optic nerve

We describe experiments on behaving rats with electrodes implanted on the cornea, in the optic chiasm, and on the visual cortex; in addition, two red light-emitting diodes (LED) are permanently attached to the skull over the left eye. Recordings timelocked to the LED flashes reveal both the local events at each electrode site and the orderly transfer of visual information from retina to cortex. The major finding is that every stimulus, regardless of its luminance, duration, or the state of retinal light adaptation, elicits an optic nerve volley with a latency of about 10 ms and a duration of about 300 ms. This phenomenon has not been reported previously, so far as we are aware. We conclude that the retina, which originates from the forebrain of the developing embryo, behaves like a typical brain structure: it translates, within a few hundred milliseconds, the chemical information in each pattern of bleached photoreceptors into a corresponding pattern of ganglion cell neuronal information that leaves via the optic nerve. The attributes of each rat ganglion cell appear to include whether the retinal neuropile calls on it to leave after a stimulus and, if so when, within a 300-ms poststimulus epoch. The resulting retinal analysis of the scene, on arrival at the cortical level, is presumed to participate importantly in the creation of visual perceptual experiences.

Structure and function of declarative and nondeclarative memory systems

This article reviews recent studies of memory systems in humans and nonhuman primates. Three major conclusions from recent work are that (i) the capacity for nondeclarative (nonconscious) learning can now be studied in a broad array of tasks that assess classification learning, perceptuomotor skill learning, artificial grammar learning, and prototype abstraction; (ii) cortical areas adjacent to the hippocampal formation, including entorhinal, perirhinal, and parahippocampal cortices, are an essential part of the medial temporal lobe memory system that supports declarative (conscious) memory; and (iii) in humans, bilateral damage limited to the hippocampal formation is nevertheless sufficient to produce severe anterograde amnesia and temporally graded retrograde amnesia covering as much as 25 years.

Temporal Sequence of Cell Wall Disassembly in Rapidly Ripening Melon Fruit1

The Charentais variety of melon (Cucumis melo cv Reticulatus F1 Alpha) was observed to undergo very rapid ripening, with the transition from the preripe to overripe stage occurring within 24 to 48 h. During this time, the flesh first softened and then exhibited substantial disintegration, suggesting that Charentais may represent a useful model system to examine the temporal sequence of changes in cell wall composition that typically take place in softening fruit. The total amount of pectin in the cell wall showed little reduction during ripening but its solubility changed substantially. Initial changes in pectin solubility coincided with a loss of galactose from tightly bound pectins, but preceded the expression of polygalacturonase (PG) mRNAs, suggesting early, PG-independent modification of pectin structure. Depolymerization of polyuronides occurred predominantly in the later ripening stages, and after the appearance of PG mRNAs, suggesting the existence of PG-dependent pectin degradation in later stages. Depolymerization of hemicelluloses was observed throughout ripening, and degradation of a tightly bound xyloglucan fraction was detected at the early onset of softening. Thus, metabolism of xyloglucan that may be closely associated with cellulose microfibrils may contribute to the initial stages of fruit softening. A model is presented of the temporal sequence of cell wall changes during cell wall disassembly in ripening Charentais melon.

Temporal fluctuations in coherence of brain waves.

As a measure of dynamical structure, short-term fluctuations of coherence between 0.3 and 100 Hz in the electroencephalogram (EEG) of humans were studied from recordings made by chronic subdural macroelectrodes 5-10 mm apart, on temporal, frontal, and parietal lobes, and from intracranial probes deep in the temporal lobe, including the hippocampus, during sleep, alert, and seizure states. The time series of coherence between adjacent sites calculated every second or less often varies widely in stability over time; sometimes it is stable for half a minute or more. Within 2-min samples, coherence commonly fluctuates by a factor up to 2-3, in all bands, within the time scale of seconds to tens of seconds. The power spectrum of the time series of these fluctuations is broad, extending to 0.02 Hz or slower, and is weighted toward the slower frequencies; little power is faster than 0.5 Hz. Some records show conspicuous swings with a preferred duration of 5-15s, either irregularly or quasirhythmically with a broad peak around 0.1 Hz. Periodicity is not statistically significant in most records. In our sampling, we have not found a consistent difference between lobes of the brain, subdural and depth electrodes, or sleeping and waking states. Seizures generally raise the mean coherence in all frequencies and may reduce the fluctuations by a ceiling effect. The coherence time series of different bands is positively correlated (0.45 overall); significant nonindependence extends for at least two octaves. Coherence fluctuations are quite local; the time series of adjacent electrodes is correlated with that of the nearest neighbor pairs (10 mm) to a coefficient averaging approximately 0.4, falling to approximately 0.2 for neighbors-but-one (20 mm) and to < 0.1 for neighbors-but-two (30 mm). The evidence indicates fine structure in time and space, a dynamic and local determination of this measure of cooperativity. Widely separated frequencies tending to fluctuate together exclude independent oscillators as the general or usual basis of the EEG, although a few rhythms are well known under special conditions. Broad-band events may be the more usual generators. Loci only a few millimeters apart can fluctuate widely in seconds, either in parallel or independently. Scalp EEG coherence cannot be predicted from subdural or deep recordings, or vice versa, and intracortical microelectrodes show still greater coherence fluctuation in space and time. Widely used computations of chaos and dimensionality made upon data from scalp or even subdural or depth electrodes, even when reproducible in successive samples, cannot be considered representative of the brain or the given structure or brain state but only of the scale or view (receptive field) of the electrodes used. Relevant to the evolution of more complex brains, which is an outstanding fact of animal evolution, we believe that measures of cooperativity are likely to be among the dynamic features by which major evolutionary grades of brains differ.

Primary structure of hepatocyte nuclear factor/forkhead homologue 4 and characterization of gene expression in the developing respiratory and reproductive epithelium.

Members of the winged helix/forkhead family of transcription factors are believed to play a role in cell-specific gene expression. A cDNA encoding a member of this family of proteins, termed hepatocyte nuclear factor/forkhead homologue 4 (HFH-4), has been isolated from rat lung and rat testis cDNA libraries. This cDNA contains an open reading frame of 421 amino acids with a conserved DNA binding domain and several potential transactivating regions. During murine lung development, a single species of HFH-4-specific transcript (2.4 kb long) is first detected precisely at the start of the late pseudoglandular stage (embryonic day 14.5) and, by in situ hybridization, is specifically localized to the proximal pulmonary epithelium. The unique temporal and spatial pattern of HFH-4 gene expression in the developing lung defines this protein as a marker for the initiation of bronchial epithelial cell differentiation and suggests that it may play an important role in cell fate determination during lung development. In addition to expression in the pulmonary epithelium, RNA blot analysis reveals 2.4-kb HFH-4 transcripts in the testis and oviduct. By using mice with genetic defects in spermatogenesis, HFH-4 expression in the testis is found to be associated with the appearance of haploid germ cells and in situ hybridization studies indicate that HFH-4 expression is confined to stages I-VII of spermatogenesis. This pattern of HFH-4 gene expression during the early stages of differentiation of haploid germ cells suggests that HFH-4 may play a role in regulating stage-specific gene expression and cell-fate determination during lung development and in spermatogenesis.

Heterogeneidade espacial e variabilidade temporal de dois reservatórios com diferentes graus de trofia, no Estado de São Paulo

O entendimento da comunidade fitoplanctônica em sistemas instáveis, como por exemplo reservatórios, necessita conhecimento de escalas de variabilidade. Com base nisso, um estudo sobre a heterogeneidade espacial e variabilidade temporal de dois reservatórios com diferentes graus de trofia, no Estado de São Paulo foi realizado em 20 estações no reservatório de Salto Grande e em 19 no reservatório do Lobo, em 3 dias consecutivos, em quatro períodos: outubro de 1999, janeiro, abril e junho e julho de 2000. Para tanto foram determinadas as concentrações de nutrientes totais e dissolvidos, material em suspensão, carbono inorgânico, clorofila a, biomassa, densidade, composição e produtividade primária da comunidade fitoplanctônica e os perfis de oxigênio dissolvido, temperatura, pH e condutividade. Os dois reservatórios tiveram estruturas espaciais semelhantes com a formação de três zonas distintas. A zona de rio, misturada, com menor penetração de luz e maior concentração de nutrientes, a zona de transição, e a zona lacustre, mais estratificada, com maior penetração de luz e menor concentração de nutrientes. Apesar dessa compartimentalização a heterogeneidade espacial no reservatório de Salto Grande foi maior que no reservatório do Lobo, sobretudo em função do gradiente longitudinal de nutrientes e luz. A variabilidade diária (3 dias) nos dois reservatórios não foi significativa na determinação da comunidade fitoplanctônica. A escala de variabilidade sazonal, nos dois reservatórios, foi determinada, principalmente pela variação nos padrões de estratificação e mistura sendo, assim, determinante na composição da comunidade fitoplanctônica. Essa influência foi mais evidente no reservatório do Lobo. A variação temporal e heterogeneidade espacial das mais abundantes espécies e grupos taxonômicos da comunidade fitoplanctônica, (Microcystis aeruginosa, Anabaena crassa e Anabaena circinalis em Salto Grande e Aphanocapsa delicatissima, Coelastrum reticulatum e Aulacoseira granulata no Lobo) nos dois reservatórios foram determinados pelos complexos processos de estratificação e mistura e da disponibilidade de luz. Os resultados obtidos são importantes para o entendimento da variabilidade ambiental de reservatórios tropicais e no planejamento de amostragens que visem o gerenciamento desses sistemas.

Evaluation of the potential of InSAR time series to study the spatio-temporal evolution of piezometric levels in the Madrid aquifer

The Tertiary detritic aquifer of Madrid (TDAM), with an average thickness of 1500 m and a heterogeneous, anisotropic structure, supplies water to Madrid, the most populated city of Spain (3.2 million inhabitants in the metropolitan area). Besides its complex structure, a previous work focused in the north-northwest of Madrid city showed that the aquifer behaves quasi elastically trough extraction/recovery cycles and ground uplifting during recovery periods compensates most of the ground subsidence measured during previous extraction periods (Ezquerro et al., 2014). Therefore, the relationship between ground deformation and groundwater level through time can be simulated using simple elastic models. In this work, we model the temporal evolution of the piezometric level in 19 wells of the TDAM in the period 1997–2010. Using InSAR and piezometric time series spanning the studied period, we first estimate the elastic storage coefficient (Ske) for every well. Both, the Ske of each well and the average Ske of all wells, are used to predict hydraulic heads at the different well locations during the study period and compared against the measured hydraulic heads, leading to very similar errors when using the Ske of each well and the average Ske of all wells: 14 and 16 % on average respectively. This result suggests that an average Ske can be used to estimate piezometric level variations in all the points where ground deformation has been measured by InSAR, thus allowing production of piezometric level maps for the different extraction/recovery cycles in the TDAM.

Temporal control of epigenetic centromere specification

All living organisms require accurate mechanisms to faithfully inherit their genetic material during cell division. The centromere is a unique locus on each chromosome that supports a multiprotein structure called the kinetochore. During mitosis, the kinetochore is responsible for connecting chromosomes to spindle microtubules, allowing faithful segregation of the duplicated genome. In most organisms, centromere position and function is not defined by the local DNA sequence context but rather by an epigenetic chromatin-based mechanism. Centromere protein A (CENP-A) is central to this process, as chromatin assembled from this histone H3 variant is essential for assembly of the centromere complex, as well as for its epigenetic maintenance. As a major determinant of centromere function, CENP-A assembly requires tight control, both in its specificity for the centromere and in timing of assembly. In the last few years, there have been several new insights into the molecular mechanism that allow this process to occur. We will review these here and discuss the general implications of the mechanism of cell cycle coupling of centromere inheritance.

Spatially explicit estimates of stock size, structure and biomass of North Atlantic albacore tuna (Thunnus alalunga) in the North Atlantic for the period 1987-2011, compiled from statistics about ICCAT fishery region L6

The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.

Spatially explicit estimates of stock size, structure and biomass of North Atlantic albacore tuna (Thunnus alalunga) in the North Atlantic for the period 1967-1986, compiled from statistics about ICCAT fishery region L5

The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.

Spatially explicit estimates of stock size, structure and biomass of North Atlantic albacore tuna (Thunnus alalunga) in the North Atlantic for the period 1974-1979, compiled from statistics about ICCAT fishery region L8

The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.

Spatially explicit estimates of stock size, structure and biomass of North Atlantic albacore tuna (Thunnus alalunga) in the North Atlantic for the period 1967-1986, compiled from statistics about ICCAT fishery region L4

The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.