Real-time object tracking based on scale-invariant features employing bio-inspired hardware

We developed a vision sensor system that performs a scale-invariant feature transform (SIFT) in real time. To apply the SIFT algorithm efficiently, we focus on a two-fold process performed by the visual system: whole-image parallel filtering and frequency-band parallel processing. The vision sensor system comprises an active pixel sensor, a metal-oxide semiconductor (MOS)-based resistive network, a field-programmable gate array (FPGA), and a digital computer. We employed the MOS-based resistive network for instantaneous spatial filtering and a configurable filter size. The FPGA is used to pipeline process the frequency-band signals. The proposed system was evaluated by tracking the feature points detected on an object in a video.

Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes

Background

For plant species with unsequenced genomes, cDNA contigs created by de novo assembly of RNA-Seq reads are used as reference sequences for comparative analysis of RNA-Seq datasets and the detection of differentially expressed genes (DEGs). Redundancies in such contigs are evident in previous RNA-Seq studies, and such redundancies can lead to difficulties in subsequent analysis. Nevertheless, the effects of removing redundancy from contig assemblies on comparative RNA-Seq analysis have not been evaluated.

Results

Here we describe a method for removing redundancy from raw contigs that were primarily created by de novo assembly of Arabidopsis thaliana RNA-Seq reads. Specifically, the contigs with the highest bit scores were selected from raw contigs by a homology search against the gene dataset in the TAIR10 database. The two existing methods for removal of redundancy based on contig length or clustering analysis used to eliminate redundancies from raw contigs. Contig number was reduced most effectively with the method based on homology search. In a comparative analysis of RNA-Seq datasets, DEGs detected in contigs that underwent redundancy removal via the homology search method showed the highest identity to the DEGs detected when the TAIR10 gene dataset was used as an exact reference. Redundancy in raw contigs could also be removed by a homology search against integrated protein datasets from several plant species other than A. thaliana. DEGs detected using contigs that underwent such redundancy-removed also showed high homology to DEGs detected using the TAIR10 gene dataset.

Conclusion

Here we describe a method for removing redundant contigs within raw contigs; this method involves a homology search against a gene or protein database. In principal, this method can be used with unsequenced plant genomes that lack a well-developed gene database. Redundant contigs were not removed adequately via either of two existing methods, but our method allowed for removal of all redundant contigs. To our knowledge, this is the first reported improvement in accurate detection of DEGs via comparative RNA-Seq analysis that involved preparation of a non-redundant reference sequence. This method could be used to rapidly and cost-effectively detect useful genes in unsequenced plants.

Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea

The basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues) with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC). To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.

An Artificial Potential Field Based Mobile Robot Navigation Method To Prevent From Deadlock

Artificial Potential Filed (APF) is the most well-known method that is used in mobile robot path planning, however, the shortcoming is that the local minima. To overcome this issue, we present a deadlock free APF based path planning algorithm for mobile robot navigation. The Proposed-APF (P-APF) algorithm searches the goal point in unknown 2D environments. This method is capable of escaping from deadlock and non-reachability problems of mobile robot navigation. In this method, the effective front-face obstacle information associated with the velocity direction is used to modify the Traditional APF (T-APF) algorithm. This modification solves the deadlock problem that the T-APF algorithm often converges to local minima. The proposed algorithm is explained in details and to show the effectiveness of the proposed approach, the simulation experiments were carried out in the MATLAB environment. Furthermore, the numerical analysis of the proposed approach is given to prove a deadlock free motion of the mobile robot.

Biological tests for major depressive disorder that involve leukocyte gene expression assays

BACKGROUND

Development of easy-to-use biological diagnostic tests for major depressive disorder (MDD) may facilitate MDD diagnosis and delivery of optimal treatment. Here, we examined leukocyte gene expression to develop a biological diagnostic test for MDD.

METHODS

25 drug-naive MDD patients (MDDs) and 25 age- and sex-matched healthy subjects (Controls) participated in a pilot study. A subsequent replication study involved 20 MDDs and 18 Controls. We used custom-made PCR array plates to examine mRNA levels of 40 candidate genes in leukocyte samples to assess whether any combination of these genes could be used to differentiate MDDs from Controls based on expression profiles.

RESULTS

Among 40 candidate genes, we identified a set of seven genes (PDGFC, SLC6A4, PDLIM5, ARHGAP24, PRNP, HDAC5, and IL1R2), each of which had expression levels that differed significantly between MDD and Control samples in the pilot study. To identify genes whose expression best differentiated between MDDs and Controls, a linear discriminant function was developed to discriminate between MDDs and Controls based on the standardized values of gene expression after Z-score transformation. Ultimately, five genes (PDGFC, SLC6A4, ARHGAP24, PRNP, and HDAC5) were selected for a multi-assay diagnostic test. In the pilot study, this diagnostic test demonstrated sensitivity and specificity of 80% and 92%, respectively. The replication study yielded nearly identical results, sensitivity of 85% and specificity of 89%.

CONCLUSIONS

Using leukocyte gene expression profiles, we could differentiate MDDs from Controls with adequate sensitivity and specificity. Additional markers not yet identified might further improve the performance of this test.

Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost

Biofiltration technology based on microbial degradation and assimilation is used for the removal of malodorous compounds, such as ammonia. Microbes that degrade malodorous and/or organic substances are involved in composting and are retained after composting; therefore, mature composts can serve as an ideal candidate for a biofilter medium. In this study, we focused on different types of raw compost materials, as these are important factors determining the bacterial community profile and the chemical component of the compost. Therefore, bacterial community profiles, the abundance of the bacterial ammonia monooxygenase gene (amoA), and the quantities of chemical components were analyzed in composts produced from either food waste or cattle manure. The community profiles with the lowest beta diversity were obtained from single type of cattle manure compost. However, cattle manure composts showed greater alpha diversity, contained higher amounts of various rRNA gene fragments than those of food waste composts and contained the amoA gene by relative quantification, and Proteobacteria were abundantly found and nitrifying bacteria were detected in it. Nitrifying bacteria are responsible for ammonia oxidation and mainly belong to the Proteobacteria or Nitrospira phyla. The quantities of chemical components, such as salt, phosphorus, and nitrogen, differed between the cattle manure and food waste composts, indicating that the raw materials provided different fermentation environments that were crucial for the formation of different community profiles. The results also suggest that cattle manure might be a more suitable raw material for the production of composts to be used in the biofiltration of ammonia.

Direct heating of a laser-imploded core by ultraintense laser-driven ions

A novel direct core heating fusion process is introduced, in which a preimploded core is predominantly heated by energetic ions driven by LFEX, an extremely energetic ultrashort pulse laser. Consequently, we have observed the D(d,n)^{3}He-reacted neutrons (DD beam-fusion neutrons) with the yield of 5×10^{8} n/4π sr. Examination of the beam-fusion neutrons verified that the ions directly collide with the core plasma. While the hot electrons heat the whole core volume, the energetic ions deposit their energies locally in the core, forming hot spots for fuel ignition. As evidenced in the spectrum, the process simultaneously excited thermal neutrons with the yield of 6×10^{7} n/4π sr, raising the local core temperature from 0.8 to 1.8 keV. A one-dimensional hydrocode STAR 1D explains the shell implosion dynamics including the beam fusion and thermal fusion initiated by fast deuterons and carbon ions. A two-dimensional collisional particle-in-cell code predicts the core heating due to resistive processes driven by hot electrons, and also the generation of fast ions, which could be an additional heating source when they reach the core. Since the core density is limited to 2 g/cm^{3} in the current experiment, neither hot electrons nor fast ions can efficiently deposit their energy and the neutron yield remains low. In future work, we will achieve the higher core density (>10 g/cm^{3}); then hot electrons could contribute more to the core heating via drag heating. Together with hot electrons, the ion contribution to fast ignition is indispensable for realizing high-gain fusion. By virtue of its core heating and ignition, the proposed scheme can potentially achieve high gain fusion.

Kondo interactions from band reconstruction in YbInCu(4)

We combine resonant inelastic x-ray scattering and model calculations in the Kondo lattice compound YbInCu_{4}, a system characterized by a dramatic increase in Kondo temperature and associated valence fluctuations below a first-order valence transition at T≃42  K. The bulk-sensitive, element-specific, and valence-projected charge excitation spectra reveal an unusual quasigap in the Yb-derived state density which drives an instability of the electronic structure and renormalizes the low-energy effective Hamiltonian at the transition. Our results provide long-sought experimental evidence for a link between temperature-driven changes in the low-energy Kondo scale and the higher-energy electronic structure of this system.

Highly accurate scattering spectra of strongly absorbing samples obtained using an integrating sphere system by considering the angular distribution of diffusely reflected light

An integrating sphere system has been used to investigate the estimation error in the scattering coefficient for biological tissues. Since the angular distribution of diffusely reflected light from a sample may depend on the sample absorbance, leakage at the entrance port may affect estimates of the scattering coefficient based on measurement of diffuse reflectance. In the present study, the dependence of the angular distribution of the diffusely reflected light on the hemoglobin (Hb) concentration in a sample was investigated. Subsequently, the effect of the entrance port diameter on the error in the scattering coefficient estimated based on diffuse reflectance measurements was evaluated. For a biological tissue phantom, the angular reflectance distribution at a wavelength of 405 nm, at which strong absorption occurred, showed an increasing bias toward specular reflection as the Hb concentration was increased. No such concentration dependence was found at a wavelength of 664 nm, where the absorbance was low. In addition, it was found that the estimation error in the scattering coefficient was reduced for smaller entrance port diameters. Therefore, when attempting to determine the scattering coefficient for strongly absorbing samples, it is necessary to consider both the angular distribution of the diffusely reflected light and the optimal entrance port diameter.

Blood diagnostic biomarkers for major depressive disorder using multiplex DNA methylation profiles: discovery and validation

Aberrant DNA methylation in the blood of patients with major depressive disorder (MDD) has been reported in several previous studies. However, no comprehensive studies using medication-free subjects with MDD have been conducted. Furthermore, the majority of these previous studies has been limited to the analysis of the CpG sites in CpG islands (CGIs) in the gene promoter regions. The main aim of the present study is to identify DNA methylation markers that distinguish patients with MDD from non-psychiatric controls. Genome-wide DNA methylation profiling of peripheral leukocytes was conducted in two set of samples, a discovery set (20 medication-free patients with MDD and 19 controls) and a replication set (12 medication-free patients with MDD and 12 controls), using Infinium HumanMethylation450 BeadChips. Significant diagnostic differences in DNA methylation were observed at 363 CpG sites in the discovery set. All of these loci demonstrated lower DNA methylation in patients with MDD than in the controls, and most of them (85.7%) were located in the CGIs in the gene promoter regions. We were able to distinguish patients with MDD from the control subjects with high accuracy in the discriminant analysis using the top DNA methylation markers. We also validated these selected DNA methylation markers in the replication set. Our results indicate that multiplex DNA methylation markers may be useful for distinguishing patients with MDD from non-psychiatric controls.

Evaluation of two-stage system for neutron measurement aiming at increase in count rate at Japan Atomic Energy Agency-Fusion Neutronics Source

In order to increase the count rate capability of a neutron detection system as a whole, we propose a multi-stage neutron detection system. Experiments to test the effectiveness of this concept were carried out on Fusion Neutronics Source. Comparing four configurations of alignment, it was found that the influence of an anterior stage on a posterior stage was negligible for the pulse height distribution. The two-stage system using 25 mm thickness scintillator was about 1.65 times the count rate capability of a single detector system for d-D neutrons and was about 1.8 times the count rate capability for d-T neutrons. The results suggested that the concept of a multi-stage detection system will work in practice.

The bifunctional plant receptor, OsCERK1, regulates both chitin-triggered immunity and arbuscular mycorrhizal symbiosis in rice

Plants are constantly exposed to threats from pathogenic microbes and thus developed an innate immune system to protect themselves. On the other hand, many plants also have the ability to establish endosymbiosis with beneficial microbes such as arbuscular mycorrhizal (AM) fungi or rhizobial bacteria, which improves the growth of host plants. How plants evolved these systems managing such opposite plant-microbe interactions is unclear. We show here that knockout (KO) mutants of OsCERK1, a rice receptor kinase essential for chitin signaling, were impaired not only for chitin-triggered defense responses but also for AM symbiosis, indicating the bifunctionality of OsCERK1 in defense and symbiosis. On the other hand, a KO mutant of OsCEBiP, which forms a receptor complex with OsCERK1 and is essential for chitin-triggered immunity, established mycorrhizal symbiosis normally. Therefore, OsCERK1 but not chitin-triggered immunity is required for AM symbiosis. Furthermore, experiments with chimeric receptors showed that the kinase domains of OsCERK1 and homologs from non-leguminous, mycorrhizal plants could trigger nodulation signaling in legume-rhizobium interactions as the kinase domain of Nod factor receptor1 (NFR1), which is essential for triggering the nodulation program in leguminous plants, did. Because leguminous plants are believed to have developed the rhizobial symbiosis on the basis of AM symbiosis, our results suggest that the symbiotic function of ancestral CERK1 in AM symbiosis enabled the molecular evolution to leguminous NFR1 and resulted in the establishment of legume-rhizobia symbiosis. These results also suggest that OsCERK1 and homologs serve as a molecular switch that activates defense or symbiotic responses depending on the infecting microbes.

Clinical characteristics of monochorionic twins with large hemoglobin level discordance at birth

OBJECTIVES

To evaluate neonatal outcomes and clinical characteristics of monochorionic diamniotic (MCDA) twins with a large intertwin hemoglobin (Hb) difference at birth.

METHODS

This was a retrospective cohort study of MCDA twin gestations delivered at Osaka Medical Center and Research Institute for Maternal and Child Health between 2003 and 2012. Cases of pregnancy termination, acardiac twins or intrauterine death were excluded. A large intertwin Hb difference at birth was defined as > 8.0 g/dL according to the postnatal criteria for twin anemia-polycythemia sequence (TAPS). The intertwin reticulocyte count ratio (RCR) was calculated by dividing the reticulocyte count of the anemic twin by that of the polycythemic twin. Cases with Hb differences were divided into two groups according to the RCR, TAPS when the RCR was > 1.7 and acute fetofetal hemorrhage (AFFH) when the RCR was ≤ 1.7. Neonatal outcomes were compared between the TAPS and AFFH groups.

RESULTS

During the study period, 432 MCDA twin pregnancies of a total of 532 born at our hospital were analyzed. There were 12 (2.8%) cases of a large intertwin Hb difference. The median gestational age at birth of these cases was 34 (range, 23-38) weeks, and all were delivered by Cesarean section. There were seven (1.6%) cases of TAPS and five (1.2%) of AFFH. The neonatal survival rate was 91.7%; in one pair of twins with TAPS neonatal death occurred. All (100%) cases with TAPS and two (40%) with AFFH required blood transfusion or partial-exchange transfusion for at least one infant.

CONCLUSIONS

Although the incidence of TAPS and AFFH may be low in MCDA twins, many affected neonates required treatment for hematological abnormalities. Delivery of MCDA twins via Cesarean section does not appear to prevent AFFH, despite the absence of labor.