Mining condensed sets of frequent episodes with more accurate frequencies from complex sequences

Many previous approaches to frequent episode discovery only accept simple sequences. Although a recent approach has been able to nd frequent episodes from complex sequences, the discovered sets are neither condensed nor accurate. This paper investigates the discovery of condensed sets of frequent episodes from complex sequences. We adopt a novel anti-monotonic frequency measure based on non-redundant occurrences, and dene a condensed set, nDaCF (the set of non-derivable approximately closed frequent episodes) within a given maximal error bound of support. We then introduce a series of effective pruning strategies, and develop a method, nDaCF-Miner, for discovering nDaCF sets. Experimental results show that, when the error bound is somewhat high, the discovered nDaCF sets are two orders of magnitude smaller than complete sets, and nDaCF-miner is more efficient than previous mining approaches. In addition, the nDaCF sets are more accurate than the sets found by previous approaches.

Cultural influences on body dissatisfaction, body change behaviours and disordered eating of Japanese adolescents

We administered a paper-and-pencil questionnaire to 133 female and 99 male Japanese high school students 13–18 years old (M = 15.9, SD = 1.57) from the Kansai area to examine cultural influences on their body image and body change behaviours. Our aim was to ascertain the independent and combined influences from traditional Japanese, modern Japanese, and Western values. Cluster analyses identified four ‘acculturative’ groups: ‘anti-modern’, ‘traditional’, ‘pro-modern/anti-traditional’, and ‘pro-Western/anti-Japanese’. Pro-modern and pro-Western adolescents were most dissatisfied with their bodies, and pro-Western adolescents were also most likely to attempt weight loss. The results demonstrate the value of assessing cultural interactions in Japan along three dimensions.

Effects of alterations of primer-binding site sequences on human immunodeficiency virus type 1 replication

The human immunodeficiency virus type 1 genomic RNA primer-binding site (PBS) sequence comprises 18 nucleotides which are complementary to those at the 3' end of the replication initiation primer tRNA(3Lys). To investigate the role of the PBS in viral replication, we either deleted the original wild-type PBS (complementary to tRNA(3Lys) or replaced it with DNA sequences complementary to either tRNA(1,2Lys) or tRNA(Phe). Transfection of COS cells with such molecular constructs yielded similar levels of viral progeny that were indistinguishable with regard to viral proteins and tRNA content. Virus particles derived from PBS-deleted molecular clones were noninfectious for MT-4, Jurkat, and CEM-T4 cells. However, infectious viruses were derived from constructs in which the PBS had been altered to sequences complementary to either tRNA(1,2Lys) or tRNA(Phe), although mutated forms showed significant lags in replication efficiency in comparison with wild types. Molecular analysis of reverse-transcribed DNA in cells infected by the mutated viruses indicated that both tRNA(1,2Lys) and tRNA(Phe) could function as primers for reverse transcription during the early stages of infection. Sequencing of full-length proviral DNA, obtained 6 days after infection, revealed the mutated PBS, indicating that a complete cycle of reverse transcription had occurred. During subsequent rounds of infection, reversion of the mutated PBS to wild-type sequences was observed, accompanied by increased production of viral gene products. Reversion to wild-type PBS sequences was confirmed both by specific PCR analysis, using distinct primer pairs, and by direct sequencing of amplified segments. We also performed endogenous in vitro reverse transcription experiments in which synthesis of minus-strand strong-stop viral DNA was primed from a synthetic RNA template containing a PBS complementary to various tRNA isoacceptors. These results showed that tRNA(3Lys) was a much more efficient primer of such reactions than either tRNA(1,2Lys) or tRNA(Phe).

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

The bias of A-rich codons in HIV-1 pol is thought to be a record of hypermutations in viral genomes that lack biological functions. Bioinformatic analysis predicted that A-rich sequences are generally associated with minimal local RNA structures. Using codon modifications to reduce the amount of A-rich sequences within HIV-1 genomes, we have reduced the flexibility of RNA sequences in pol to analyze the functional significance of these A-rich ‘structurally poor’ RNA elements in HIV-1 pol. Our data showed that codon modification of HIV-1 sequences led to a suppression of virus infectivity by 5–100-fold, and this defect does not correlate with, viral entry, viral protein expression levels, viral protein profiles or virion packaging of genomic RNA. Codon modification of HIV-1 pol correlated with an enhanced dimer stability of the viral RNA genome, which was associated with a reduction of viral cDNA synthesis both during HIV-1 infection and in a cell free reverse transcription assay. Our data provided direct evidence that the HIV-1 A-rich pol sequence is not merely an evolutionary artifact of enzyme-induced hypermutations, and that HIV-1 has adapted to rely on A-rich RNA sequences to support the synthesis of viral cDNA during reverse transcription, highlighting the utility of using ‘structurally poor’ RNA domains in regulating biological process.

Disrupting disordered neurocircuitry : treating refractory psychiatric illness with neuromodulation

Despite the premature and somewhat infamous rise and fall of psychosurgery in the mid-20th century, the current era of functional neuromodulation proffers immense opportunity for surgical intervention in treatment-resistant psychiatric disorders. On the basis of recent successes with novel, focused, less invasive, and reversible treatment strategies for movement disorders, several therapeutic trials have been conducted to investigate the effectiveness of deep brain stimulation (DBS) in treatment-resistant depression, obsessive-compulsive disorder (OCD), and Tourette syndrome. The many anatomic targets for these psychiatric disorders are indicative of both the system-wide effects of DBS and the network-level dysfunction mediating the emotional and cognitive disturbances. To gain insight into the application of neuromodulation therapies and their further advancement, we must elucidate neuroanatomic networks involved in refractory psychiatric illness, the neurophysiological anomalies that contribute to disordered information processing therein, and the local and system-wide modulatory effects of DBS. This review discusses the history of psychosurgical procedures, recent DBS clinical data, current anatomic models of psychopathology, and possible therapeutic mechanisms of action of DBS neuromodulation. Our search criteria for PubMed included combinations of the following terms: neuromodulation, DBS, depression, OCD, Tourette syndrome, mechanism of action, and history. Dates were not restricted. As clinical and basic scientific investigations probe the neuromodulatory effects of DBS in the treatment of refractory neuropsychiatric illness, our knowledge of these disorders and our potential to treat them are rapidly expanding. Indeed, this modern era of neuromodulation may provide the key that unlocks many of the mysteries pertaining to the biological basis of disordered emotional neurocircuitry.

Does behavior reflect phylogeny in swiftlets (Aves: Apodidae)? A test using cytochrome b mitochondrial DNA sequences

Swiftlets are small insectivorous birds, many of which nest in caves and are known to echolocate. Due to a lack of distinguishing morphological characters, the taxonomy of swiftlets is primarily based on the presence or absence of echolocating ability, together with nest characters. To test the reliability of these behavioral characters, we constructed an independent phylogeny using cytochrome b mitochondrial DNA sequences from swiftlets and their relatives. This phylogeny is broadly consistent with the higher classification of swifts but does not support the monophyly of swiftlets. Echolocating swiftlets (Aerodramus) and the nonecholocating "giant swiftlet" (Hydrochous gigas) group together, but the remaining nonecholocating swiftlets belonging to Collocalia are not sister taxa to these swiftlets. While echolocation may be a synapomorphy of Aerodramus (perhaps secondarily lost in Hydrochous), no character of Aerodramus nests showed a statistically significant fit to the molecular phylogeny, indicating that nest characters are not phylogenetically reliable in this group.

A framework for identifying affinity classes of inorganic materials binding peptide sequences

With the rapid development of bionanotechnology, there has been a growing interest recently in identifying the affinity classes of the inorganic materials binding peptide sequences. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on our new amino acid transition matrix, and then the probability of test sequences belonging to a specific affinity class is calculated through solving an objective function. In addition, the objective function is solved through iterative propagation of probability estimates among sequences and sequence clusters. Experimental results on a real inorganic material binding sequence dataset show that the proposed framework is highly effective on identifying the affinity classes of inorganic material binding sequences.

Characteristics of Mentally Disordered Youth Referred to a Forensic Satellite Clinic for Violence Risk Assessment: A Case Control Study

There is a lack of appropriate services to manage youth with comorbid mental health problems and violence risks. To address this gap, we implemented a forensic satellite clinic in a youth mental health service. This paper characterises offending histories among 45 young patients referred to the clinic, and compares them with matched clinical controls (n = 45). Levels of prior risk taking and aggression were prominent among referred patients. Forensic cases and controls did not differ on demographic and clinical variables, with the exception of psychiatric inpatient admissions, which were higher among referred patients. Group differences were observed for prior offending variables (e.g., physical aggression), which were significantly higher among referred patients than controls. Findings suggest that referrals were made to the clinic based on challenging and aggressive behaviour rather than specific clinical characteristics. The role of specialist assessment, treatment and management of violence risks in youth mental health services are discussed.

Lithium storage in disordered graphitic materials: a semi-quantitative study of the relationship between structure disordering and capacity.

The application of the graphitic anode is restricted by its low theoretical specific capacity of 372 mA h g(-1). Higher capacity can be achieved in the graphitic anode by modifying its structure, but the detailed storage mechanism is still not clear. In this work, the mechanism of the lithium storage in a disordered graphitic structure has been systematically studied. It is found that the enhanced capacity of the distorted graphitic structure does not come from lithium-intercalation, but through a capacitive process, which depends on the disordering degree and the porous structure.

Identifying affinity classes of inorganic materials binding sequences via a graph-based model

Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins (SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.