1,943 research outputs found
Temporal-offset dual-comb vibrometer with picometer axial precision
We demonstrate a dual-comb vibrometer where the pulses of one frequency-comb
are split into pulse pairs. We introduce a delay between the two pulses of each
pulse pair in front of the sample, and after the corresponding two consecutive
reflections at the vibrating sample surface, the initially introduced delay is
cancelled by a modified Sagnac geometry. The remaining phase difference between
the two pulses corresponds to the change in the axial position of the surface
during the two consecutive reflections. The Sagnac geometry reduces the effect
of phase jitter since both pulses propagate through nearly the same optical
path (in opposite directions), and spurious signals are eliminated by time
gating. We determine the amplitude of a surface vibration on a
surface-acoustic-wave device with an axial precision of 4 pm. This technique
enables highly accurate determination of extremely small displacements.Comment: 22 pages, 5 figure
Activity of Japanese Society of Grassland Science
The Japanese Society of Grassland Science (JSGS) was founded in 1954 for the purposes of progressing grassland and forage crop sciences and fostering grassland agriculture and better management of grassland for animal production in Japan. From the first, the members of JSGS have included interdisciplinary scientists from forage crop science, forestry, animal science, agribusiness and many related fields. In the 50 years since its foundation, JSGS has made large contributions to the progress of both science and industry in Japan. The number of JSGS members is now declining slightly, but there are still about 950 including 800 individual members and 150 organisations or private companies. The profile of the current members is mainly scientists working in university or governmental and private research institutes
DDBJ dealing with mass data produced by the second generation sequencer
DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period include genome scale data of Bombyx mori, Oryzas latipes, Drosophila and Lotus japonicus. In addition, from this year we collected and released trace archive data in collaboration with National Center for Biotechnology Information (NCBI). The first release contains those of O. latipes and bacterial meta genomes in human gut. To cope with the current progress of sequencing technology, we also accepted and released more than 100 million of short reads of parasitic protozoa and their hosts that were produced by using a Solexa sequencer
Collective dynamics of two-mode stochastic oscillators
We study a system of two-mode stochastic oscillators coupled through their
collective output. As a function of a relevant parameter four qualitatively
distinct regimes of collective behavior are observed. In an extended region of
the parameter space the periodicity of the collective output is enhanced by the
considered coupling. This system can be used as a new model to describe
synchronization-like phenomena in systems of units with two or more oscillation
modes. The model can also explain how periodic dynamics can be generated by
coupling largely stochastic units. Similar systems could be responsible for the
emergence of rhythmic behavior in complex biological or sociological systems.Comment: 4 pages, RevTex, 5 figure
Siglec-F is a novel intestinal M cell marker
Intestinal microfold (M) cells are epithelial cells primarily present on Peyer's patches (PPs) in the small intestine. The ability of M cells to shuttle antigens into the PP for appropriate immune responses makes M cells a target for next-generation oral vaccine delivery. In this regard, discovery of M cell specific receptors are of great interest, which could act as molecular tags for targeted delivery of cargo to M cells. Here, using a monoclonal antibody we generated to the Sialic acid-binding immunoglobulin-like lectin F (Siglec-F), we show that Siglec-F is expressed on mouse M cells in the small intestine. Immunohistochemical analysis of the PP tissue sections shows that Siglec-F is expressed on the surface of the M cell membrane exposed to the intestinal lumen. Anti-Siglec-F antibody injected into the mouse small intestine bound to M-cells, demonstrating the potential to target M cells via Siglec-F
Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks
Prediction of one-dimensional protein structures such as secondary structures
and contact numbers is useful for the three-dimensional structure prediction
and important for the understanding of sequence-structure relationship. Here we
present a new machine-learning method, critical random networks (CRNs), for
predicting one-dimensional structures, and apply it, with position-specific
scoring matrices, to the prediction of secondary structures (SS), contact
numbers (CN), and residue-wise contact orders (RWCO). The present method
achieves, on average, accuracy of 77.8% for SS, correlation coefficients
of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS
prediction is comparable to other state-of-the-art methods, and that of the CN
prediction is a significant improvement over previous methods. We give a
detailed formulation of critical random networks-based prediction scheme, and
examine the context-dependence of prediction accuracies. In order to study the
nonlinear and multi-body effects, we compare the CRNs-based method with a
purely linear method based on position-specific scoring matrices. Although not
superior to the CRNs-based method, the surprisingly good accuracy achieved by
the linear method highlights the difficulty in extracting structural features
of higher order from amino acid sequence beyond that provided by the
position-specific scoring matrices.Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for
publication in BIOPHYSIC
Admission to hospital following head injury in England: Incidence and socio-economic associations
BACKGROUND:
Head injury in England is common. Evidence suggests that socio-economic factors may cause variation in incidence, and this variation may affect planning for services to meet the needs of those who have sustained a head injury.
METHODS:
Socio-economic data were obtained from the UK Office for National Statistics and merged with Hospital Episodes Statistics obtained from the Department of Health. All patients admitted for head injury with ICD-10 codes S00.0–S09.9 during 2001–2 and 2002–3 were included and collated at the level of the extant Health Authorities (HA) for 2002, and Primary Care Trust (PCT) for 2003. Incidence was determined, and cluster analysis and multiple regression analysis were used to look at patterns and associations.
Results: 112,718 patients were admitted during 2001–2 giving a hospitalised incidence rate for England of 229 per 100,000. This rate varied across the English HA's ranging from 91–419 per 100,000. The rate remained unchanged for 2002–3 with a similar magnitude of variation across PCT's. Three clusters of HA's were identified from the 2001–2 data; those typical of London, those of the Shire counties, and those of Other Urban authorities. Socio-economic factors were found to account for a high proportion of the variance in incidence for 2001–2. The same pattern emerged for 2002–3 at the PCT level. The use of public transport for travel to work is associated with a
decreased incidence and lifestyle indicators, such as the numbers of young unemployed, increase the incidence.
CONCLUSION:
Head injury incidence in England varies by a factor of 4.6 across HA's and PCT's.
Planning head injury related services at the local level thus needs to be based on local incidence
figures rather than regional or national estimates. Socio-economic factors are shown to be
associated with admission, including travel to work patterns and lifestyle indicators, which suggests
that incidence is amenable to policy initiatives at the macro level as well as preventive programmes
targeted at key groups
Apolipoprotein E4 Frequencies in a Japanese Population with Alzheimer's Disease and Dementia with Lewy Bodies
BACKGROUND: The apolipoprotein E (APOE) ε4 allele has been reported to be a risk factor for Alzheimer's disease (AD) and dementia with Lewy bodies (DLB). Previous neuropathological studies have demonstrated similar frequencies of the APOE ε4 allele in AD and DLB. However, the few ante-mortem studies on APOE allele frequencies in DLB have shown lower frequencies than post-mortem studies. One reason for this may be inaccuracy of diagnosis. We examined APOE genotypes in subjects with AD, DLB, and a control group using the latest diagnostic criteria and MRI, SPECT, and MIBG myocardial scintigraphy. METHODS: The subjects of this study consisted of 145 patients with probable AD, 50 subjects with probable DLB, and a control group. AD subjects were divided into two groups based on age of onset: early onset AD (EOAD) and late onset AD (LOAD). All subjects had characteristic features on MRI, SPECT, and/or myocardial scintigraphy. RESULTS: The rate of APOE4 carrier status was 18.3% and the frequency of the ε4 allele was 9.7% in controls. The rate of APOE4 carrier status and the frequency of the ε4 allele were 47% and 27% for LOAD, 50% and 31% for EOAD, and 42% and 31% for DLB, respectively. CONCLUSION: The APOE4 genotypes in this study are consistent with previous neuropathological studies suggesting accurate diagnosis of AD and DLB. APOE4 genotypes were similar in AD and DLB, giving further evidence that the ε4 allele is a risk factor for both disorders
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions
The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and functions obtained by application of various computational tools to the amino acid sequences of entirely sequenced genomes. GTOP contains annotations of 3D structures, protein families, functions, and other useful data of a protein of interest in user-friendly ways to give a deep insight into the protein structure. From the initial 1999 version, GTOP has been continually updated to reap the fruits of genome projects and augmented to supply novel information, in particular intrinsically disordered regions. As intrinsically disordered regions constitute a considerable fraction of proteins and often play crucial roles especially in eukaryotes, their assignments give important additional clues to the functionality of proteins. Additionally, we have incorporated the following features into GTOP: a platform independent structural viewer, results of HMM searches against SCOP and Pfam, secondary structure predictions, color display of exon boundaries in eukaryotic proteins, assignments of gene ontology terms, search tools, and master files
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