GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP

The release of vast quantities of DNA sequence data by large-scale genome and expressed sequence tag (EST) projects underlines the necessity for the development of efficient and inexpensive ways to link sequence databases with temporal and spatial expression profiles. Here we demonstrate the power of linking cDNA sequence data (including EST sequences) with transcript profiles revealed by cDNA-AFLP, a highly reproducible differential display method based on restriction enzyme digests and selective amplification under high stringency conditions. We have developed a computer program (GenEST) that predicts the sizes of virtual transcript-derived fragments (TDFs) of in silico-digested cDNA sequences retrieved from databases. The vast majority of the resulting virtual TDFs could be traced back among the thousands of TDFs displayed on cDNA-AFLP gels. Sequencing of the corresponding bands excised from cDNA-AFLP gels revealed no inconsistencies. As a consequence, cDNA sequence databases can be screened very efficiently to identify genes with relevant expression profiles. The other way round, it is possible to switch from cDNA-AFLP gels to sequences in the databases. Using the restriction enzyme recognition sites, the primer extensions and the estimated TDF size as identifiers, the DNA sequence(s) corresponding to a TDF with an interesting expression pattern can be identified. In this paper we show examples in both directions by analyzing the plant parasitic nematode Globodera rostochiensis. Various novel pathogenicity factors were identified by combining ESTs from the infective stage juveniles with expression profiles of ∼4000 genes in five developmental stages produced by cDNA-AFLP.

Effects of temporal association on recognition memory

The influence of temporal association on the representation and recognition of objects was investigated. Observers were shown sequences of novel faces in which the identity of the face changed as the head rotated. As a result, observers showed a tendency to treat the views as if they were of the same person. Additional experiments revealed that this was only true if the training sequences depicted head rotations rather than jumbled views; in other words, the sequence had to be spatially as well as temporally smooth. Results suggest that we are continuously associating views of objects to support later recognition, and that we do so not only on the basis of the physical similarity, but also the correlated appearance in time of the objects.

Perda auditiva unilateral: benefício da amplificação na ordenação e resolução temporal e localização sonora

A perda auditiva unilateral (PAUn) é caracterizada pela diminuição da audição em apenas uma orelha. Indivíduos com este tipo de perda auditiva podem apresentar comprometimento nas habilidades auditivas de localização sonora, processamento temporal, ordenação e resolução temporal. O objetivo deste estudo foi verificar as habilidades auditivas de ordenação temporal, resolução temporal e localização sonora, antes e após a adaptação do aparelho de amplificação sonora individual (AASI). Foram avaliados 22 indivíduos, com idades entre 18 e 60 anos, com diagnóstico de PAUn sensorioneural ou mista, de graus leve a severo. O estudo foi dividido em duas etapas: a pré e a pós-adaptação de AASI. Em ambas as etapas, os indivíduos foram submetidos a uma anamnese, aplicação do Questionário de Habilidade Auditiva da Localização da fonte sonora, avaliação simplificada do processamento auditivo (ASPA) e Random Gap Detection Test (RGDT). O presente estudo encontrou diferença estatisticamente significante na avaliação da ASPA, exceto no teste de memória para sons não verbais em sequência (TMSnV), no RGDT e no Questionário de Habilidade Auditiva da Localização Sonora. A conclusão do estudo foi que com o uso efetivo do AASI, indivíduos com PAUn apresentaram melhora nas habilidades auditivas de localização sonora, ordenação e resolução temporal.

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.

Spatio-temporal evaluation of neck muscle activation during postural perturbations in healthy subjects

The purpose of this study was to examine the spatio-temporal activation of the sternocleidomastoid (SCM) and cervical extensor (CE) muscles with respect to the deltoid muscle onset during rapid voluntary upper limb movement in healthy volunteers. The repeatability and reliability of the spatio-temporal aspects of the myoelectric signals were also examined. Ten subjects performed bilateral and unilateral rapid upper limb flexion, abduction and extension in response to a visual stimulus. EMG onsets and normalised root mean square (nRMS) values were calculated for the SCM and CE muscles. Subjects attended three testing sessions over non-consecutive days allowing the repeatability and reliability of these measures to be assessed. The SCM and CE muscles demonstrated feed-forward activation (activation within 50 ms of deltoid onset) during rapid arm movements in all directions. The sequence and magnitude of neck muscle activation displayed directional specificity, however, the neck flexor and extensor muscles displayed co-activation during all perturbations. EMG onsets demonstrated high repeatability in terms of repeated measure precision (nSEM in the range 1.9-5.7%). This was less evident for the repeatability of nRMS values. The results of this study provide a greater understanding of cervical neuromotor control strategies. During bilateral and unilateral upper limb perturbations, the SCM and CE muscles demonstrate feed-forward co-activation. It seems apparent that feed-forward activation of neck muscles is a mechanism necessary to achieve stability for the visual and vestibular systems, whilst ensuring stabilisation and protection of the cervical spine. (C) 2004 Elsevier Ltd. All rights reserved.

The role of Temporal Context in the Tritone Paradox

The Tritone Paradox refers to a sequence of two specially synthesised "Shepard" tones which may sound ascending to one listener, and descending to another. The present study examines a recent suggestion that people's responses on this task may be determined by neural processes which are sensitive to temporal variations in pitch - so-called spectral motion detectors. Twelve listeners with normal hearing were presented with pairs of Shepard tones in each of two conditions - first in the traditional sequential manner, and then simultaneously, with one tone presented to each ear. Results indicated that respondents were able to judge consistent relationships between the tones even when presented simultaneously, and a high degree of similarity was observed between responses in each condition. The implications of these results for current theories of the Tritone Paradox are discussed.

Finding negative event oriented patterns in long temporal sequences

Pattern discovery in a long temporal event sequence is of great importance in many application domains. Most of the previous work focuses on identifying positive associations among time stamped event types. In this paper, we introduce the problem of defining and discovering negative associations that, as positive rules, may also serve as a source of knowledge discovery. In general, an event-oriented pattern is a pattern that associates with a selected type of event, called a target event. As a counter-part of previous research, we identify patterns that have a negative relationship with the target events. A set of criteria is defined to evaluate the interestingness of patterns associated with such negative relationships. In the process of counting the frequency of a pattern, we propose a new approach, called unique minimal occurrence, which guarantees that the Apriori property holds for all patterns in a long sequence. Based on the interestingness measures, algorithms are proposed to discover potentially interesting patterns for this negative rule problem. Finally, the experiment is made for a real application.

Introducing uncertainty into pattern discovery in temporal event sequences

Pattern discovery in temporal event sequences is of great importance in many application domains, such as telecommunication network fault analysis. In reality, not every type of event has an accurate timestamp. Some of them, defined as inaccurate events may only have an interval as possible time of occurrence. The existence of inaccurate events may cause uncertainty in event ordering. The traditional support model cannot deal with this uncertainty, which would cause some interesting patterns to be missing. A new concept, precise support, is introduced to evaluate the probability of a pattern contained in a sequence. Based on this new metric, we define the uncertainty model and present an algorithm to discover interesting patterns in the sequence database that has one type of inaccurate event. In our model, the number of types of inaccurate events can be extended to k readily, however, at a cost of increasing computational complexity.

Dissociating the spatio-temporal characteristics of cortical neuronal activity associated with human volitional swallowing in the healthy adult brain

Human swallowing represents a complex highly coordinated sensorimotor function whose functional neuroanatomy remains incompletely understood. Specifically, previous studies have failed to delineate the temporo-spatial sequence of those cerebral loci active during the differing phases of swallowing. We therefore sought to define the temporal characteristics of cortical activity associated with human swallowing behaviour using a novel application of magnetoencephalography (MEG). In healthy volunteers (n = 8, aged 28-45), 151-channel whole cortex MEG was recorded during the conditions of oral water infusion, volitional wet swallowing (5 ml bolus), tongue thrust or rest. Each condition lasted for 5 s and was repeated 20 times. Synthetic aperture magnetometry (SAM) analysis was performed on each active epoch and compared to rest. Temporal sequencing of brain activations utilised time-frequency wavelet plots of regions selected using virtual electrodes. Following SAM analysis, water infusion preferentially activated the caudolateral sensorimotor cortex, whereas during volitional swallowing and tongue movement, the superior sensorimotor cortex was more strongly active. Time-frequency wavelet analysis indicated that sensory input from the tongue simultaneously activated caudolateral sensorimotor and primary gustatory cortex, which appeared to prime the superior sensory and motor cortical areas, involved in the volitional phase of swallowing. Our data support the existence of a temporal synchrony across the whole cortical swallowing network, with sensory input from the tongue being critical. Thus, the ability to non-invasively image this network, with intra-individual and high temporal resolution, provides new insights into the brain processing of human swallowing. © 2004 Elsevier Inc. All rights reserved.

Effects of the build-up and resetting of auditory stream segregation on temporal discrimination

The tendency to hear a tone sequence as 2 or more streams (segregated) builds up, but a sudden change in properties can reset the percept to 1 stream (integrated). This effect has not hitherto been explored using an objective measure of streaming. Stimuli comprised a 2.0-s fixed-frequency inducer followed by a 0.6-s test sequence of alternating pure tones (3 low [L]-high [H] cycles). Listeners compared intervals for which the test sequence was either isochronous or the H tones were slightly delayed. Resetting of segregation should make identifying the anisochronous interval easier. The HL frequency separation was varied (0-12 semitones), and properties of the inducer and test sequence were set to the same or different values. Inducer properties manipulated were frequency, number of onsets (several short bursts vs. one continuous tone), tone:silence ratio (short vs. extended bursts), level, and lateralization. All differences between the inducer and the L tones reduced temporal discrimination thresholds toward those for the no-inducer case, including properties shown previously not to affect segregation greatly. Overall, it is concluded that abrupt changes in a sequence cause resetting and improve subsequent temporal discrimination. (PsycINFO Database Record © 2009 APA, all rights reserved)

Auditory stream segregation in cochlear implant listeners:measures based on temporal discrimination and interleaved melody recognition

The evidence that cochlear implant listeners routinely experience stream segregation is limited and equivocal. Streaming in these listeners was explored using tone sequences matched to the center frequencies of the implant’s 22 electrodes. Experiment 1 measured temporal discrimination for short (ABA triplet) and longer (12 AB cycles) sequences (tone/silence durations = 60/40 ms). Tone A stimulated electrode 11; tone B stimulated one of 14 electrodes. On each trial, one sequence remained isochronous, and tone B was delayed in the other; listeners had to identify the anisochronous interval. The delay was introduced in the second half of the longer sequences. Prior build-up of streaming should cause thresholds to rise more steeply with increasing electrode separation, but no interaction with sequence length was found. Experiment 2 required listeners to identify which of two target sequences was present when interleaved with distractors (tone/silence durations = 120/80 ms). Accuracy was high for isolated targets, but most listeners performed near chance when loudness-matched distractors were added, even when remote from the target. Only a substantial reduction in distractor level improved performance, and this effect did not interact with target-distractor separation. These results indicate that implantees often do not achieve stream segregation, even in relatively unchallenging tasks.

Learning user and product distributed representations using a sequence model for sentiment analysis

In product reviews, it is observed that the distribution of polarity ratings over reviews written by different users or evaluated based on different products are often skewed in the real world. As such, incorporating user and product information would be helpful for the task of sentiment classification of reviews. However, existing approaches ignored the temporal nature of reviews posted by the same user or evaluated on the same product. We argue that the temporal relations of reviews might be potentially useful for learning user and product embedding and thus propose employing a sequence model to embed these temporal relations into user and product representations so as to improve the performance of document-level sentiment analysis. Specifically, we first learn a distributed representation of each review by a one-dimensional convolutional neural network. Then, taking these representations as pretrained vectors, we use a recurrent neural network with gated recurrent units to learn distributed representations of users and products. Finally, we feed the user, product and review representations into a machine learning classifier for sentiment classification. Our approach has been evaluated on three large-scale review datasets from the IMDB and Yelp. Experimental results show that: (1) sequence modeling for the purposes of distributed user and product representation learning can improve the performance of document-level sentiment classification; (2) the proposed approach achieves state-of-The-Art results on these benchmark datasets.

Characterizing Internet worm spatial-temporal infection structures

Since the Morris worm was released in 1988, Internet worms continue to be one of top security threats. For example, the Conficker worm infected 9 to 15 million machines in early 2009 and shut down the service of some critical government and medical networks. Moreover, it constructed a massive peer-to-peer (P2P) botnet. Botnets are zombie networks controlled by attackers setting out coordinated attacks. In recent years, botnets have become the number one threat to the Internet. The objective of this research is to characterize spatial-temporal infection structures of Internet worms, and apply the observations to study P2P-based botnets formed by worm infection. First, we infer temporal characteristics of the Internet worm infection structure, i.e., the host infection time and the worm infection sequence, and thus pinpoint patient zero or initially infected hosts. Specifically, we apply statistical estimation techniques on Darknet observations. We show analytically and empirically that our proposed estimators can significantly improve the inference accuracy. Second, we reveal two key spatial characteristics of the Internet worm infection structure, i.e., the number of children and the generation of the underlying tree topology formed by worm infection. Specifically, we apply probabilistic modeling methods and a sequential growth model. We show analytically and empirically that the number of children has asymptotically a geometric distribution with parameter 0.5, and the generation follows closely a Poisson distribution. Finally, we evaluate bot detection strategies and effects of user defenses in P2P-based botnets formed by worm infection. Specifically, we apply the observations of the number of children and demonstrate analytically and empirically that targeted detection that focuses on the nodes with the largest number of children is an efficient way to expose bots. However, we also point out that future botnets may self-stop scanning to weaken targeted detection, without greatly slowing down the speed of worm infection. We then extend the worm spatial infection structure and show empirically that user defenses, e.g. , patching or cleaning, can significantly mitigate the robustness and the effectiveness of P2P-based botnets. To counterattack, we evaluate a simple measure by future botnets that enhances topology robustness through worm re-infection.

Sequence and Structural Determinants of Specificity Differences between Paralogous Transcription Factors

Transcription factors (TFs) control the temporal and spatial expression of target genes by interacting with DNA in a sequence-specific manner. Recent advances in high throughput experiments that measure TF-DNA interactions in vitro and in vivo have facilitated the identification of DNA binding sites for thousands of TFs. However, it remains unclear how each individual TF achieves its specificity, especially in the case of paralogous TFs that recognize distinct target genomic sites despite sharing very similar DNA binding motifs. In my work, I used a combination of high throughput in vitro protein-DNA binding assays and machine-learning algorithms to characterize and model the binding specificity of 11 paralogous TFs from 4 distinct structural families. My work proves that even very closely related paralogous TFs, with indistinguishable DNA binding motifs, oftentimes exhibit differential binding specificity for their genomic target sites, especially for sites with moderate binding affinity. Importantly, the differences I identify in vitro and through computational modeling help explain, at least in part, the differential in vivo genomic targeting by paralogous TFs. Future work will focus on in vivo factors that might also be important for specificity differences between paralogous TFs, such as DNA methylation, interactions with protein cofactors, or the chromatin environment. In this larger context, my work emphasizes the importance of intrinsic DNA binding specificity in targeting of paralogous TFs to the genome.

Phylodynamic modelling of foot-and-mouth disease virus sequence data

The under-reporting of cases of infectious diseases is a substantial impediment to the control and management of infectious diseases in both epidemic and endemic contexts. Information about infectious disease dynamics can be recovered from sequence data using time-varying coalescent approaches, and phylodynamic models have been developed in order to reconstruct demographic changes of the numbers of infected hosts through time. In this study I have demonstrated the general concordance between empirically observed epidemiological incidence data and viral demography inferred through analysis of foot-and-mouth disease virus VP1 coding sequences belonging to the CATHAY topotype over large temporal and spatial scales. However a more precise and robust relationship between the effective population size (