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The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB’s goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.

In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.

The report summarizes the scientific content of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB) held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference in Long Beach, California on July 13, 2012.

We previously described the use of a differential hybridization screen of a genomic DNA library of Saccharomyces cerevisiae to identify sporulation-specific (SPS) genes (A. Percival-Smith and J. Segall, Mol. Cell. Biol. 4:142-150, 1984). This initial screen identified 14 SPS genes that are first expressed 6 to 8 h after transfer of cells to sporulation medium. Accumulation of transcripts corresponding to these genes becomes maximal at 8 to 12 h of sporulation, the time at which meiotic events are nearing completion, and by 15 h of sporulation, transcript levels are beginning to decrease. In the present study two additional SPS genes, first expressed at 12 h of sporulation, were isolated. The steady-state level of transcripts corresponding to these two genes, termed SPS100 and SPS101, remains unchanged from 15 to 35 h, a time coincident with spore wall maturation. The nature of the putative 34.2-kilodalton protein encoded by the SPS100 gene is consistent with its being a component of the glycoprotein matrix of the spore wall; the protein contains a potential signal sequence and cleavage site and numerous sites for potential glycosylation. A MATa sps100/MAT alpha sps100 strain was found to be indistinguishable from the wild-type strain when assessed for efficiency of ascus formation and spore viability. However, a more detailed analysis of the mutant strain revealed that the SPS100 gene product serves a protective role during the early stages of spore wall formation. The time at which resistance to ether could first be detected in developing spores was delayed by 5 h in the mutant strain relative to the wild-type strain. This phenotype is presumably a reflection of a defect in spore wall maturation. This study has confirmed that temporally distinct classes of sporulation-specific genes are sequentially activated during the process of meiosis and spore formation and has shown that the SPS100 gene, identified on the basis of its developmental-specific expression pattern, contributes to spore development.

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Background

Music-syntactic irregularities often co-occur with the processing of physical irregularities. In this study we constructed chord-sequences such that perceived differences in the cognitive processing between regular and irregular chords could not be due to the sensory processing of acoustic factors like pitch repetition or pitch commonality (the major component of ‘sensory dissonance’).

Methodology/Principal Findings

Two groups of subjects (musicians and nonmusicians) were investigated with electroencephalography (EEG). Irregular chords elicited an early right anterior negativity (ERAN) in the event-related brain potentials (ERPs). The ERAN had a latency of around 180 ms after the onset of the music-syntactically irregular chords, and had maximum amplitude values over right anterior electrode sites.

Conclusions/Significance

Because irregular chords were hardly detectable based on acoustical factors (such as pitch repetition and sensory dissonance), this ERAN effect reflects for the most part cognitive (not sensory) components of regularity-based, music-syntactic processing. Our study represents a methodological advance compared to previous ERP-studies investigating the neural processing of music-syntactically irregular chords.

The Batur Temple (Pura Ulun Danu Batur) in Kintamani is located at the geographic apex of a so-called ritual water hierarchy and has conventionally been described as a purely religious institution responsible for the coordination and distribution of the irrigation water. However, an analysis of historical palm leaf manuscripts reveals that the temple had a firm economic base with corresponding interests and that it was one of the most important land-owners in late pre-colonial Bali. The article therefore explores from a socio-political and economic perspective the implications of this form of temple landlordism and its combination with ritual water control, particularly for the peasants and the portion of their annual surplus that they were obliged to deliver to this temple.

The relationship of the frequency of temple headache to signs and symptoms of temporomandibular disorders (TMD) was investigated in a subset of a larger convenience sample of community TMD cases. The study sample included: 86 painful TMD, non-headache subjects; 309 painful TMD subjects with varied frequency of temple headaches; and 149 subjects without painful TMD or headache for descriptive comparison. Painful TMD included Research Diagnostic Criteria (RDC) diagnoses of myofascial pain, TMJ arthralgia and TMJ osteoarthritis. Mild to moderate intensity temple headaches were classified by frequency using criteria based on the ICHD-II classification of TTH. Outcomes included TMD signs and symptoms (pain duration, pain intensity, number of painful masticatory sites on palpation, mandibular range of motion), PPTs and temple headache resulting from masticatory provocation tests. Trend analyses across the painful TMD groups showed a substantial trend for aggravation of all of the TMD signs and symptoms associated with increased frequency of the temple headaches. In addition, increased headache frequency showed significant trends associated with reduced PPTs and reported temple headache with masticatory provocation tests. In conclusion, these findings suggest that these headaches may be TMD-related, as well as a possible role for peripheral and central sensitization in TMD patients.

This paper is a brief survey of the role of temples and holy places in nurturing the surrounding flora and its habitat. Eightysix kinds of plants in temple yards and gardens of orissa have been enlisted where they are cultivated and preserved for different temple rituals. These plants are seen rarely in wild but are saved from extinction by their association with temple rituals and ceremonies.

The purpose of this study was to review institutional statistics provided in dean's letters and determine the percentage of honors awarded by institution and clerkship specialty.

Institutional and clerkship aggregate data were compiled from a review of dean's letters from 80 United States medical schools. The percentage of honors awarded during 3rd year clerkships during 2005 were collected for analysis. Across clerkship specialties, there were no statistically significant differences between the mean percentage of honors given by the medical schools examined with Internal Medicine (27.6%) the low and Psychiatry (33.5%) the high. However, inter-institutional variability observed within each clerkship was high, with surgery clerkship percentage of honors ranging from 2% to 75% of the students. This suggests some schools may be more lenient and other more stringent in awarding honors to their students. This inter-institutional variability makes it difficult to compare honors received by students from different medical schools and weakens the receipt of honors as a primary tool for evaluating potential incoming residents.

Shame and honor are mechanisms that expose behavior that falls outside the social norm. With recent six-player public goods experiments, we demonstrated that the threat of shame or the promise of honor led to increased cooperation. Participants were told in advance that after ten rounds two participants would be asked to come forward and write their names on the board in front of the fellow group members. In the shame treatment, the least cooperative players were exposed and wrote their names under the sentence “I donated least” while the honored participants wrote their name under “I donated most.” In both the shame and honor treatments, participants contributed approximately 50% more to the public good, as compared with the control treatment in which all players retained their anonymity. Here, we also discuss how shame and honor differ from full transparency, and some of the challenges to understanding how anonymity and exposure modify behavior.

Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.

We describe the first reported transmission to a human of simian foamy virus (SFV) from a free-ranging population of nonhuman primates in Asia. The transmission of an exogenous retrovirus, SFV, from macaques (Macaca fascicularis) to a human at a monkey temple in Bali, Indonesia, was investigated with molecular and serologic techniques. Antibodies to SFV were detected by Western blotting of serum from 1 of 82 humans tested. SFV DNA was detected by nested polymerase chain reaction (PCR) from the blood of the same person. Cloning and sequencing of PCR products confirmed the virus's close phylogenetic relationship to SFV isolated from macaques at the same temple. This study raises concerns that persons who work at or live around monkey temples are at risk for infection with SFV.

Background

There is lack of neuroscientific studies investigating music processing with naturalistic stimuli, and brain responses to real music are, thus, largely unknown.

Methodology/Principal Findings

This study investigates event-related brain potentials (ERPs), skin conductance responses (SCRs) and heart rate (HR) elicited by unexpected chords of piano sonatas as they were originally arranged by composers, and as they were played by professional pianists. From the musical excerpts played by the pianists (with emotional expression), we also created versions without variations in tempo and loudness (without musical expression) to investigate effects of musical expression on ERPs and SCRs. Compared to expected chords, unexpected chords elicited an early right anterior negativity (ERAN, reflecting music-syntactic processing) and an N5 (reflecting processing of meaning information) in the ERPs, as well as clear changes in the SCRs (reflecting that unexpected chords also elicited emotional responses). The ERAN was not influenced by emotional expression, whereas N5 potentials elicited by chords in general (regardless of their chord function) differed between the expressive and the non-expressive condition.

Conclusions/Significance

These results show that the neural mechanisms of music-syntactic processing operate independently of the emotional qualities of a stimulus, justifying the use of stimuli without emotional expression to investigate the cognitive processing of musical structure. Moreover, the data indicate that musical expression affects the neural mechanisms underlying the processing of musical meaning. Our data are the first to reveal influences of musical performance on ERPs and SCRs, and to show physiological responses to unexpected chords in naturalistic music.

El objetivo del trabajo es conocer las disyuntivas entre los principios de beneficencia y autonomía, que se presentan en la relación médico-paciente, durante la terapéutica del intento de suicidio.

La investigación se realizó en dos hospitales psiquiátricos de la Ciudad de México. La muestra incluyó a tres sujetos con intento de suicidio, mayores de 18 años, que eran atendidos en consulta externa a causa de una lesión autoinfligida en el último año, y a tres psiquiatras que trataban a estos pacientes. La información se obtuvo previo consentimiento informado en entrevistas individuales. Se llevó a cabo un análisis de discurso argumentado para encontrar los significados que los participantes otorgaron a los principios bioéticos y las posibles disyuntivas entre éstos.

Las discordancias entre la beneficencia y la autonomía estuvieron relacionadas con el beneficio del tratamiento, el respeto por los valores y las creencias de los pacientes, entre otros. Este trabajo presenta consideraciones éticas relevantes en el escenario clínico, al ofrecer al psiquiatra un análisis bioético que le permita actuar de acuerdo con la beneficencia y respetando la autonomía del paciente frente a casos de intento de suicidio y, de esta forma procurar una mejor atención para ellos.

Background

Recent electrophysiological and neuroimaging studies have explored how and where musical syntax in Western music is processed in the human brain. An inappropriate chord progression elicits an event-related potential (ERP) component called an early right anterior negativity (ERAN) or simply an early anterior negativity (EAN) in an early stage of processing the musical syntax. Though the possible underlying mechanism of the EAN is assumed to be probabilistic learning, the effect of the probability of chord progressions on the EAN response has not been previously explored explicitly.

Methodology/Principal Findings

In the present study, the empirical conditional probabilities in a Western music corpus were employed as an approximation of the frequencies in previous exposure of participants. Three types of chord progression were presented to musicians and non-musicians in order to examine the correlation between the probability of chord progression and the neuromagnetic response using magnetoencephalography (MEG). Chord progressions were found to elicit early responses in a negatively correlating fashion with the conditional probability. Observed EANm (as a magnetic counterpart of the EAN component) responses were consistent with the previously reported EAN responses in terms of latency and location. The effect of conditional probability interacted with the effect of musical training. In addition, the neural response also correlated with the behavioral measures in the non-musicians.

Conclusions/Significance

Our study is the first to reveal the correlation between the probability of chord progression and the corresponding neuromagnetic response. The current results suggest that the physiological response is a reflection of the probabilistic representations of the musical syntax. Moreover, the results indicate that the probabilistic representation is related to the musical training as well as the sensitivity of an individual.

Resumen

Introducción

La encefalitis por anticuerpos contra el receptor de NMDA (NMDAR) suele desarrollarse como un síndrome característico de evolución multifásica y diagnóstico diferencial amplio.

Pacientes

Presentamos a 2 pacientes diagnosticadas de encefalitis por anticuerpos NMDAR con un cuadro clínico típico, pero que inicialmente señaló otras etiologías.

Discusión

La afectación frecuente de pacientes jóvenes con manifestaciones psiquiátricas prominentes indica frecuentemente otras consideraciones diagnósticas; las más frecuentes son las encefalitis virales, los procesos psiquiátricos y el síndrome neuroléptico maligno. Varios síndromes previamente definidos de manera parcial o descriptiva en adultos y pacientes pediátricos probablemente eran casos de encefalitis anti-NMDAR.

Conclusiones

La encefalitis anti-NMDAR debe considerarse en pacientes jóvenes con manifestaciones psiquiátricas subagudas, movimientos anormales y alteraciones autonómicas. La caracterización clínica e inmunológica de esta enfermedad ha llevado a la identificación de nuevos anticuerpos que afectan a procesos de memoria, aprendizaje, conducta y psicosis.

Rajaie Batniji and Eran Bendavid dispute recent suggestions that health aid to developing countries leads to a displacement of government spending and instead argue that current evidence about aid displacement cannot be used to guide policy.

Eran Bendavid and Rajaie Batniji provide a perspective on the ongoing debates about aid displacement - whether giving development aid to governments leads to reductions in their own domestic health financing.