Exact Inference on Gaussian Graphical Models of Arbitrary Topology using Path-Sums

We present the path-sum formulation for exact statistical inference of marginals on Gaussian graphical models of arbitrary topology. The path-sum formulation gives the covariance between each pair of variables as a branched continued fraction of finite depth and breadth. Our method originates from the closed-form resummation of infinite families of terms of the walk-sum representation of the covariance matrix. We prove that the path-sum formulation always exists for models whose covariance matrix is positive definite: i.e.~it is valid for both walk-summable and non-walk-summable graphical models of arbitrary topology. We show that for graphical models on trees the path-sum formulation is equivalent to Gaussian belief propagation. We also recover, as a corollary, an existing result that uses determinants to calculate the covariance matrix. We show that the path-sum formulation formulation is valid for arbitrary partitions of the inverse covariance matrix. We give detailed examples demonstrating our results

Raman spectroscopy of human teeth using integrated optical spectrometers

We have designed an arrayed-waveguide grating in silicon oxynitride technology for the detection of Raman signals from tooth enamel in the spectral region between 890 nm and 912 nm. The detected signals for both parallel and cross polarizations are used to distinguish between healthy and carious regions on the tooth surface of extracted human teeth. Our experimental results are in very good agreement with those achieved using conventional Raman spectrometers. Our results represent a step toward the realization of compact, hand-held, integrated spectrometers

Thermophysical and elastic properties of Cu50Zr50 and (Cu50Zr50)95Al5 bulk-metallic-glass-forming alloys

By employing a containerless high-temperature high-vacuum electrostatic levitation technique, the thermophysical properties, including the ratio between the specific heat capacity and the hemispherical total emissivity, the specific volume, and the viscosity, of Cu50Zr50 and (Cu50Zr50)95Al5 bulk-metallic-glass (BMG)-forming liquids have been measured. Compared with Cu50Zr50, the improved glass-forming ability of (Cu50Zr50)95Al5 can be attributed to its dense liquid structure and its high value of viscosity. Additionally, the relationship between the viscosity of various BMG forming liquids at the melting temperature and the elastic properties of the corresponding glasses at room temperature will be compared

Psychological Safety and Norm Clarity in Software Engineering Teams

In the software engineering industry today, companies primarily conduct their work in teams. To increase organizational productivity, it is thus crucial to know the factors that affect team effectiveness. Two team-related concepts that have gained prominence lately are psychological safety and team norms. Still, few studies exist that explore these in a software engineering context. Therefore, with the aim of extending the knowledge of these concepts, we examined if psychological safety and team norm clarity associate positively with software developers' self-assessed team performance and job satisfaction, two important elements of effectiveness. We collected industry survey data from practitioners (N = 217) in 38 development teams working for five different organizations. The result of multiple linear regression analyses indicates that both psychological safety and team norm clarity predict team members' self-assessed performance and job satisfaction. The findings also suggest that clarity of norms is a stronger (30\% and 71\% stronger, respectively) predictor than psychological safety. This research highlights the need to examine, in more detail, the relationship between social norms and software development. The findings of this study could serve as an empirical baseline for such, future work.Comment: Submitted to CHASE'201

Dynamics of axial separation in long rotating drums

We propose a continuum description for the axial separation of granular materials in a long rotating drum. The model, operating with two local variables, concentration difference and the dynamic angle of repose, describes both initial transient traveling wave dynamics and long-term segregation of the binary mixture. Segregation proceeds through ultra-slow logarithmic coarsening.Comment: 4 pages, 3 Postscript figures; submitted to PR

A low‐cost, sensitive and specific PCR ‐based tool for rapid clinical detection of HLA‐B*35 alleles associated with delayed drug hypersensitivity reactions

HLA (HLA) alleles are risk factors for CD8+ T-cell-mediated drug hypersensitivity reactions. However, as most HLA associations are incompletely predictive and/or involve risk alleles at low frequency, costly sequence-based typing can elude an economically productive cost: benefit ratio for clinical validation studies and diagnostic and/or preventative screening. Hence rapid and low-cost detection assays are now required, both for single alleles but also across risk loci associated with broader multi-disease risk; exemplified by associations with diverse alleles in HLA-B*35, including HLA-B*35:01 and green tea- or co-trimoxazole-induced liver injury. Here, we developed a cost-effective (<$10USD) qPCR assay for rapid (<2.5 h) clinical detection of HLA-B*35 alleles. The assay was validated using 430 DNA samples with previous American society for histocompatibility and immunogenetics-accredited sequence-based high-resolution HLA typing, positively detecting all HLA-B*35 allelic variants in our cohort, and as expected by primer design, the six samples that expressed low-frequency B*78:01. The assay did not result in positive detection for any negative control allele. With expected detection of B*35 and B*78, our assay sensitivity (95% CI, 95.07%–100.00%) and specificity (95% CI, 98.97%–100.00%) of 100% using as low as 10 ng of DNA provides a reliable HLA-B*35 screening tool for clinical validation and HLA–risk-based prevention and diagnostics

Primitive Shape Imagery Classification from Electroencephalography

Introduction: Brain-computer interfaces (BCIs) augment traditional interfaces for human-computer interaction and provide alternative communication devices to enable the physically impaired to work. Imagined object/shape classification from electroencephalography (EEG) may lead, for example, to enhanced tools for fields such as engineering, design, and the visual arts. Evidence to support such a proposition from non-invasive neuroimaging techniques to date has mainly involved functional magnetic resonance tomography (fMRI) [1] indicating that visual perception and mental imagery show similar brain activity patterns [2] and, although the primary visual cortex has an important role in mental imagery and perception, the occipitotemporal cortex also encodes sensory, semantic and emotional properties during shape imagery [3]. Here we investigate if five imagined primitive shapes (sphere, cone, pyramid, cylinder, cube) can be classified from EEG using filter bank common spatial patterns (FBCSP) [4]. Material, Methods, and Results: Ten healthy volunteers (8 males and 2 females, aged 26-44) participated in a single session study (three runs, four blocks/run, 30 trials/block (i.e., six repetitions of five primitive shapes in random order)). Trials lasted 7s as shown in Fig. 1 and ended with an auditory tone. Thirty EEG channels were recorded with a g.BSamp EEG system using active electrodes (g.tec, Austria). EEG channels with high-level noise were removed. Signals were band-pass filtered in six non-overlapped, 4Hz width bands covering the 4-40Hz frequency range. Filter bank common spatial pattern (FBCSP) based feature extraction and mutual information (MI) based feature selection methods provided input features for 2-class classification using linear discriminant analysis (LDA) for target shape versus the rest, separately. The final 5-class classification was decided by assessing the signed distance in the 2-class discriminant hyperplane for each of the five binary classifiers as shown in Fig. 1. Classifiers were trained on two runs and tested on the one unseen run (i.e., 3 fold cross-validation). A Wilcoxon non-parametric test was used to validate the difference of DA at end of the resting period (-1s) and at the maximal peak accuracy occurring during the shape imagery task (0-3s) is significant (p<0.001). Fig. 1 shows the between-subject average time-varying classification accuracies with standard deviation (shaded area). Discussion: The results indicate that there is separability provided by the shape imagery and there is significantly higher accuracy compared to the ~20% chance level prior the display period with maximum accuracy reaching 34%. In [5] classification of five imagined primitive and complex shapes with 44% accuracy is reported using a 14 channel Emotiv headset. Differences in performance reported may be influenced by EEG recording (EEG in [5] appears to have different dynamics (significant mean shifts)), the study had more sessions/trials, applied ICA for noise removal and the participants had designer experience whilst our study did not. Improvement of our methods is required to achieve higher accuracy rate. It is unclear if an online feedback to shape imagery training and learning will an impact performance – a multisession online study with feedback is the next step in this research. Significance: To best of our knowledge this is only the second study of shape imagery classification from EEG

Genetic characterization of Porcine Circovirus 2 found in Malaysia

Background: Porcine circovirus type 2 is the primary etiological agent associated with a group of complex multi-factorial diseases classified as Porcine Circovirus Associated Diseases (PCVAD). Sporadic cases reported in Malaysia in 2007 caused major economic losses to the 2.2 billion Malaysian ringgit (MYR) (approximately 0.7 billion US dollar) swine industry. The objective of the present study was to determine the association between the presence of PCV2 and occurrences of PCVAD. Results: This study showed that 37 out of 42 farms sampled were positive for PCV2 using PCR screening. Thirteen whole genome of PCV2 isolates from pigs with typical PCVAD symptoms were successfully sequenced. These isolates shared 98.3-99.2% similarities with sequences of isolates from the Netherlands. All thirteen isolates fell into the same clade as PCV2b isolates from other countries. Amino acid sequence analysis of the putative capsid protein (ORF2) of the PCV2 revealed that there are three clusters found in Malaysia, namely cluster 1C and 1A/1B. Of interest, three of the isolates (isolates Mal 005, Mal 006 and Mal 010) had a proline substitution for arginine or isoleucine encoded at nt. position 88-89. Eight of the isolates had mutations at the C terminus of the putative capsid protein suggestive of higher pathogenicity which may account for the high reports of PCVAD clinical symptoms in 2007. Conclusion: Phylogenetic study suggests that there may be a link between movements of animals by import of breeders into the country being the route of entry of the virus. While it is not possible to eradicate the virus from commercial pigs, the swine industry in Malaysia can be safeguarded by control measures implemented throughout the country. These measures should include improved biosecurity, disease surveillance; vaccination as well as enforcement of regulations formulated to control and prevent the spread of this disease on a national scale