Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

The reminiscence bump in the temporal distribution of the best football players of all time: Pelé, Cruijff or Maradona?

The reminiscence bump is the tendency to recall more autobiographical memories from adolescence and early adulthood than from adjacent lifetime periods. In this online study, the robustness of the reminiscence bump was examined by looking at participants' judgements about the quality of football players. Dutch participants (N = 619) were asked who they thought the five best players of all time were. The participants could select the names from a list or enter the names when their favourite players were not on the list. Johan Cruijff, Pelé, and Diego Maradona were the three most often mentioned players. Participants frequently named football players who reached the midpoint of their career when the participants were adolescents (mode = 17). The results indicate that the reminiscence bump can also be identified outside the autobiographical memory domain.

The temporal distribution of autobiographical memory: changes in reliving and vividness over the life span do not explain the reminiscence bump.

When autobiographical memories are elicited with word cues, personal events from middle childhood to early adulthood are overrepresented compared to events from other periods. It is, however, unclear whether these memories are also associated with greater recollection. In this online study, we examined whether autobiographical memories from adolescence and early adulthood are recollected more than memories from other lifetime periods. Participants rated personal events that were elicited with cue words on reliving or vividness. Consistent with previous studies, most memories came from the period in which the participants were between 6 and 20 years old. The memories from this period were not relived more or recalled more vividly than memories from other lifetime periods, suggesting that they do not involve more recollection. Recent events had higher levels of reliving and vividness than remote events, and older adults reported a stronger recollective experience than younger adults.

The short and long of it: neural correlates of temporal-order memory for autobiographical events.

Previous functional neuroimaging studies of temporal-order memory have investigated memory for laboratory stimuli that are causally unrelated and poor in sensory detail. In contrast, the present functional magnetic resonance imaging (fMRI) study investigated temporal-order memory for autobiographical events that were causally interconnected and rich in sensory detail. Participants took photographs at many campus locations over a period of several hours, and the following day they were scanned while making temporal-order judgments to pairs of photographs from different locations. By manipulating the temporal lag between the two locations in each trial, we compared the neural correlates associated with reconstruction processes, which we hypothesized depended on recollection and contribute mainly to short lags, and distance processes, which we hypothesized to depend on familiarity and contribute mainly to longer lags. Consistent with our hypotheses, parametric fMRI analyses linked shorter lags to activations in regions previously associated with recollection (left prefrontal, parahippocampal, precuneus, and visual cortices), and longer lags with regions previously associated with familiarity (right prefrontal cortex). The hemispheric asymmetry in prefrontal cortex activity fits very well with evidence and theories regarding the contributions of the left versus right prefrontal cortex to memory (recollection vs. familiarity processes) and cognition (systematic vs. heuristic processes). In sum, using a novel photo-paradigm, this study provided the first evidence regarding the neural correlates of temporal-order for autobiographical events.

Spatial and temporal scales of neuronal correlation in visual area V4.

The spiking activity of nearby cortical neurons is correlated on both short and long time scales. Understanding this shared variability in firing patterns is critical for appreciating the representation of sensory stimuli in ensembles of neurons, the coincident influences of neurons on common targets, and the functional implications of microcircuitry. Our knowledge about neuronal correlations, however, derives largely from experiments that used different recording methods, analysis techniques, and cortical regions. Here we studied the structure of neuronal correlation in area V4 of alert macaques using recording and analysis procedures designed to match those used previously in primary visual cortex (V1), the major input to V4. We found that the spatial and temporal properties of correlations in V4 were remarkably similar to those of V1, with two notable differences: correlated variability in V4 was approximately one-third the magnitude of that in V1 and synchrony in V4 was less temporally precise than in V1. In both areas, spontaneous activity (measured during fixation while viewing a blank screen) was approximately twice as correlated as visual-evoked activity. The results provide a foundation for understanding how the structure of neuronal correlation differs among brain regions and stages in cortical processing and suggest that it is likely governed by features of neuronal circuits that are shared across the visual cortex.

Temporal Stability of Molecular Diversity Measures in Natural Populations of Drosophila pseudoobscura and Drosophila persimilis

Many molecular ecological and evolutionary studies sample wild populations at a single point in time, failing to consider that data they collect represents genetic variation from a potentially unrepresentative snapshot in time. Variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. However, many studies of rapid contemporary microevolution examine phenotypic trait divergence as opposed to molecular evolutionary divergence. Here, we compare genetic diversity in wild caught populations of Drosophila persimilis and D. pseudoobscura collected 16 years apart at the same time of year and same site at four X-linked and two mitochondrial loci to assess genetic stability. We found no major changes in nucleotide diversity in either species, but we observed a drastic shift in Tajima’s D between D. pseudoobscura timepoints at one locus associated with the increased abundance of a set of related haplotypes. Our data also suggests that D. persimilis may have recently accelerated its demographic expansion. While the changes we observed were modest, this study reinforces the importance of considering potential temporal variation in genetic parameters within single populations over short evolutionary timescales.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak.

Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased virulence and drug resistance, but there have been only a few cases reported in Central America. Here we report the first whole genome sequencing of Central American Beijing-lineage strains of Mtb. We find that multiple Beijing-lineage strains, derived from independent founding events, are currently circulating in Guatemala, but overall still represent a relatively small proportion of disease burden. Finally, we identify a specific Beijing-lineage outbreak centered on a poor neighborhood in Guatemala City.

The temporal dynamics of metacognition: Dissociating task-related activity from later metacognitive processes

In recent years, neuroscience research spent much effort in revealing brain activity related to metacognition. Despite this endeavor, it remains unclear exactly when metacognitive experiences develop during task performance. To investigate this, the current study used EEG to temporally and spatially dissociate task-related activity from metacognitive activity. In a masked priming paradigm, metacognitive experiences of difficulty were induced by manipulating congruency between prime and target. As expected, participants more frequently rated incongruent trials as difficult and congruent trials as easy, while being completely unable to perceive the masked primes. Results showed that both the N2 and the P3 ERP components were modulated by congruency, but that only the P3 modulation interacted with metacognitive experiences. Single-trial analysis additionally showed that the magnitude of the P3 modulation by congruency accurately predicted the metacognitive response. Source localization indicated that the N2 task-related activity originated in the ACC, whereas the P3-interplay between task-related activation and metacognitive experiences originated from the precuneus. We conclude that task-related activity can be dissociated from later metacognitive processing.

Variación espacial y temporal de la producción primaria neta aérea y secundaria neta

Las actividades humanas impactan fuertemente sobre los procesos de los ecosistemas. En los sistemas ganaderos, las actividades humanas intentan maximizar el flujo de energía hacia la productividad secundaria. Las consecuencias sobre la transferencia de energía desde la productividad primaria neta aérea (PPNA) a la producción secundaria neta no están totalmente establecidas. Varios estudios describieron la relación entre la carga animal y la PPNA a lo largo de gradientes regionales de recursos, tanto en sistemas naturales como ganaderos. Pero persisten al menos tres vacíos de conocimiento sobre los sistemas ganaderos que fueron abordados en esta tesis. En primer lugar, no se conocía la relación entre la producción secundaria neta y la PPNA, a lo largo de un gradiente regional de recursos y se desconocía la medida en que la actividad humana afectaba diferencialmente a los procesos parciales entre la PPNA y la producción secundaria : la eficiencia de cosecha (consumo / PPNA) y la eficiencia de producción (producción secundaria / consumo). En segundo lugar, no se conocía la relación entre la variabilidad interanual del flujo de entrada de energía, la PPNA, y el de salida, la producción secundaria neta, entre sitios que difieren por la disponibilidad de recursos o por el impacto humano. Asociado a esto existían escasos antecedentes sobre la relación entre producción secundaria, o algún determinante de esta, y la disponibilidad de recursos a través del tiempo. En particular, no existían evidencias de si esta relación temporal cambiaba a lo largo de un gradiente espacial y regional de recursos. En tercer lugar, eran muy escasos los antecedentes sobre las variaciones estacionales del índice de cosecha, y la incidencia de la carga y la PPNA sobre tales variaciones. Para abordar los primeros dos vacíos de conocimiento se compiló información de precipitación, carga animal y producción secundaria, tanto de sistemas naturales como de sistemas ganaderos. La información de sistemas naturales se obtuvo de búsquedas bibliográficas y compilaciones a nivel mundial ya publicadas. La de los sistemas ganaderos se obtuvo de dos fuentes. La primera, contempló información de 113 establecimientos ubicados a lo largo de un amplio gradiente de precipitación regional el de Argentina, pertencecientes en su mayoría la movimiento CREA. La segunda, se realizó a partir de la información brindada por el plan nacional de vacunación de aftosa para departamentos ubicados al norte del río Colorado. Para este último análisis, se estimó la PPNA a partir de información satelital, usando la lógica del modelo propuesto por Monteith (...) Para abordar el tercer vacío de conocimiento, se llevó adelante un ensayo en el que se manipularon la PPNA y su calidad, a través de dos comunidades vegetales diferentes, y la carga animal, a través de tres niveles. Este ensayo se condujo a lo largo de un año para evaluar la dinámica estacional del índice de cosecha, y al mismo tiempo identificar los factores que la regulan. En relación al primer vacío, la relación entre la producción secundaria neta y la PPNA mostró un patrón unimodal. A su vez se observó que a igual PPNA la producción secundaria neta de los sistemas ganaderos fue mayor a la de los naturales. Este incremento de la producción secundaria se debió en mayor medida a un aumento del índice de cosecha y en menor medida a un aumento en la eficiencia de producción. En relación al segundo vacío, la variabilidad interanual de la lluvia, principal control abiótico del flujo de entrada, no se relacionó significativamente con la variabilidad de un componente del siguiente nivel trófico, la carga animal, tanto en sistemas naturales como ganaderos. Sin embargo, la variabilidad de la carga animal de los naturales fue mayor que la de los ganaderos. En estos últimos la variabilidad de la PPNA, fue el doble que la de la carga animal (...) En relación al tercer vacío, se mostró que el principal control de la variación estacional del índice de cosecha fue la PPNA. Esta tesis representa la primera evidencia del impacto de la introducción de herbívoros exóticos a lo largo de un gradiente regional sobre el flujo desde la PPNA a la producción secundaria neta y brinda una de las pocas evaluaciones sobre el impacto humano sobre la estabilidad de este flujo. Finalmente, se desarrolló un modelo que permitiría mejorar las estimaciones de carga animal al relacionar la dinámica del índice de cosecha con la biomasa acumulada estimada a partir de la PPNA acumulada por estación del año.

Variación espacial y temporal de la producción primaria neta aérea y secundaria neta

Las actividades humanas impactan fuertemente sobre los procesos de los ecosistemas. En los sistemas ganaderos, las actividades humanas intentan maximizar el flujo de energía hacia la productividad secundaria. Las consecuencias sobre la transferencia de energía desde la productividad primaria neta aérea (PPNA)a la producción secundaria neta no están totalmente establecidas. Varios estudios describieron la relación entre la carga animal y la PPNA a lo largo de gradientes regionales de recursos, tanto en sistemas naturales como ganaderos. Pero persisten al menos tres vacíos de conocimiento sobre los sistemas ganaderos que fueron abordados en esta tesis. En primer lugar, no se conocía la relación entre la producción secundaria neta y la PPNA, a lo largo de un gradiente regional de recursos y se desconocía la medida en que la actividad humana afectaba diferencialmente a los procesos parciales entre la PPNA y la producción secundaria : la eficiencia de cosecha (consumo / PPNA)y la eficiencia de producción (producción secundaria / consumo). En segundo lugar, no se conocía la relación entre la variabilidad interanual del flujo de entrada de energía, la PPNA, y el de salida, la producción secundaria neta, entre sitios que difieren por la disponibilidad de recursos o por el impacto humano. Asociado a esto existían escasos antecedentes sobre la relación entre producción secundaria, o algún determinante de esta, y la disponibilidad de recursos a través del tiempo. En particular, no existían evidencias de si esta relación temporal cambiaba a lo largo de un gradiente espacial y regional de recursos. En tercer lugar, eran muy escasos los antecedentes sobre las variaciones estacionales del índice de cosecha, y la incidencia de la carga y la PPNA sobre tales variaciones. Para abordar los primeros dos vacíos de conocimiento se compiló información de precipitación, carga animal y producción secundaria, tanto de sistemas naturales como de sistemas ganaderos. La información de sistemas naturales se obtuvo de búsquedas bibliográficas y compilaciones a nivel mundial ya publicadas. La de los sistemas ganaderos se obtuvo de dos fuentes. La primera, contempló información de 113 establecimientos ubicados a lo largo de un amplio gradiente de precipitación regional el de Argentina, pertencecientes en su mayoría la movimiento CREA. La segunda, se realizó a partir de la información brindada por el plan nacional de vacunación de aftosa para departamentos ubicados al norte del río Colorado. Para este último análisis, se estimó la PPNA a partir de información satelital, usando la lógica del modelo propuesto por Monteith (...)Para abordar el tercer vacío de conocimiento, se llevó adelante un ensayo en el que se manipularon la PPNA y su calidad, a través de dos comunidades vegetales diferentes, y la carga animal, a través de tres niveles. Este ensayo se condujo a lo largo de un año para evaluar la dinámica estacional del índice de cosecha, y al mismo tiempo identificar los factores que la regulan. En relación al primer vacío, la relación entre la producción secundaria neta y la PPNA mostró un patrón unimodal. A su vez se observó que a igual PPNA la producción secundaria neta de los sistemas ganaderos fue mayor a la de los naturales. Este incremento de la producción secundaria se debió en mayor medida a un aumento del índice de cosecha y en menor medida a un aumento en la eficiencia de producción. En relación al segundo vacío, la variabilidad interanual de la lluvia, principal control abiótico del flujo de entrada, no se relacionó significativamente con la variabilidad de un componente del siguiente nivel trófico, la carga animal, tanto en sistemas naturales como ganaderos. Sin embargo, la variabilidad de la carga animal de los naturales fue mayor que la de los ganaderos. En estos últimos la variabilidad de la PPNA, fue el doble que la de la carga animal (...)En relación al tercer vacío, se mostró que el principal control de la variación estacional del índice de cosecha fue la PPNA. Esta tesis representa la primera evidencia del impacto de la introducción de herbívoros exóticos a lo largo de un gradiente regional sobre el flujo desde la PPNA a la producción secundaria neta y brinda una de las pocas evaluaciones sobre el impacto humano sobre la estabilidad de este flujo. Finalmente, se desarrolló un modelo que permitiría mejorar las estimaciones de carga animal al relacionar la dinámica del índice de cosecha con la biomasa acumulada estimada a partir de la PPNA acumulada por estación del año.

A reified temporal logic

This paper presents a reified temporal logic for representing and reasoning about temporal and non-temporal relationships between non-temporal assertions. A clear syntax and semantics for the logic is formally provided. Three types of predicates, temporal predicates, non-temporal predicates and meta-predicates, are introduced. Terms of the proposed language are partitioned into three types, temporal terms, non-temporal terms and propositional terms. Reified propositions consist of formulae with each predicate being either a temporal predicate or a meta-predicate. Meta-predicates may take both temporal terms and propositional terms together as arguments or take propositional terms alone. A standard formula of the classical first-order language with each predicate being a non-temporal predicate taking only non-temporal terms as arguments is reified as just a propositional term. A general time ontology has been provided which can be specialized to a variety of existing temporal systems. The new logic allows one to predicate and quantify over propositional terms while according a special status of time; for example, assertions such as ‘effects cannot precede their causes’ is ensured in the logic, and some problematic temporal aspects including the delay time between events and their effects can be conveniently expressed. Applications of the logic are presented including the characterization of the negation of properties and their contextual sentences, and the expression of temporal relations between actions and effects.

Temporal management using relative time in knowledge-based process control

In this paper, a knowledge-based approach is proposed for the management of temporal information in process control. A common-sense theory of temporal constraints over processes/events, allowing relative temporal knowledge, is employed here as the temporal basis for the system. This theory supports duration reasoning and consistency checking, and accepts relative temporal knowledge which is in a form normally used by human operators. An architecture for process control is proposed which centres on an historical database consisting of events and processes, together with the qualitative temporal relationships between their occurrences. The dynamics of the system is expressed by means of three types of rule: database updating rules, process control rules, and data deletion rules. An example is provided in the form of a life scheduler, to illustrate the database and the rule sets. The example demonstrates the transitions of the database over time, and identifies the procedure in terms of a state transition model for the application. The dividing instant problem for logical inference is discussed with reference to this process control example, and it is shown how the temporal theory employed can be used to deal with the problem.