Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Subaru high-z exploration of low-luminosity quasars (SHELLQs). I. Discovery of 15 quasars and bright galaxies at 5.7 < z < 6.9

We report the discovery of 15 quasars and bright galaxies at 5.7 < z < 6.9. This is the initial result from the Subaru High-z Exploration of Low-Luminosity Quasars (SHELLQs) project, which exploits the exquisite multiband imaging data produced by the Subaru Hyper Suprime-Cam (HSC) Strategic Program survey. The candidate selection is performed by combining several photometric approaches including a Bayesian probabilistic algorithm to reject stars and dwarfs. The spectroscopic identification was carried out with the Gran Telescopio Canarias and the Subaru Telescope for the first 80 deg2 of the survey footprint. The success rate of our photometric selection is quite high, approaching 100 % at the brighter magnitudes (zAB < 23.5 mag). Our selection also recovered all the known high-z quasars on the HSC images. Among the 15 discovered objects, six are likely quasars, while the other six with interstellar absorption lines and in some cases narrow emission lines are likely bright Lyman-break galaxies. The remaining three objects have weak continua and very strong and narrow Ly alpha lines, which may be excited by ultraviolet light from both young stars and quasars. These results indicate that we are starting to see the steep rise of the luminosity function of z > 6 galaxies, compared with that of quasars, at magnitudes fainter than M1450 ~ -22 mag or zAB ~24 mag. Follow-up studies of the discovered objects as well as further survey observations are ongoing.Comment: Published in ApJ (828:26, 2016

Discovery of the First Low-Luminosity Quasar at z > 7

We report the discovery of a quasar at z = 7.07, which was selected from the deep multi-band imaging data collected by the Hyper Suprime-Cam (HSC) Subaru Strategic Program survey. This quasar, HSC J124353.93+010038.5, has an order of magnitude lower luminosity than do the other known quasars at z > 7. The rest-frame ultraviolet absolute magnitude is M1450 = -24.13 +/- 0.08 mag and the bolometric luminosity is Lbol = (1.4 +/- 0.1) x 10^{46} erg/s. Its spectrum in the optical to near-infrared shows strong emission lines, and shows evidence for a fast gas outflow, as the C IV line is blueshifted and there is indication of broad absorption lines. The Mg II-based black hole mass is Mbh = (3.3 +/- 2.0) x 10^8 Msun, thus indicating a moderate mass accretion rate with an Eddington ratio 0.34 +/- 0.20. It is the first z > 7 quasar with sub-Eddington accretion, besides being the third most distant quasar, known to date. The luminosity and black hole mass are comparable to, or even lower than, those measured for the majority of low-z quasars discovered by the Sloan Digital Sky Survey, and thus this quasar likely represents a z > 7 counterpart to quasars commonly observed in the low-z universe.Comment: Accepted for publication in ApJ Letter

Three lateral osteotomy designs for bilateral sagittal split osteotomy: biomechanical evaluation with three-dimensional finite element analysis

<p>Abstract</p> <p>Background</p> <p>The location of the lateral osteotomy cut during bilateral sagittal split osteotomy (BSSO) varies according to the surgeon's preference, and no consensus has been reached regarding the ideal location from the perspective of biomechanics. The purpose of this study was to evaluate the mechanical behavior of the mandible and screw-miniplate system among three lateral osteotomy designs for BSSO by using three-dimensional (3-D) finite element analysis (FEA).</p> <p>Methods</p> <p>The Trauner-Obwegeser (TO), Obwegeser (Ob), and Obwegeser-Dal Pont (OD) methods were used for BSSO. In all the FEA simulations, the distal segments were advanced by 5 mm. Each model was fixed by using miniplates. These were applied at four different locations, including along Champy's lines, to give 12 different FEA miniplate fixation methods. We examined these models under two different loads.</p> <p>Results</p> <p>The magnitudes of tooth displacement, the maximum bone stress in the vicinity of the screws, and the maximum stress on the screw-miniplate system were less in the OD method than in the Ob and TO methods at all the miniplate locations. In addition, Champy's lines models were less than those at the other miniplate locations.</p> <p>Conclusions</p> <p>The OD method allows greater mechanical stability of the mandible than the other two techniques. Further, miniplates placed along Champy's lines provide greater mechanical advantage than those placed at other locations.</p

A Tunable Lyot Filter at Prime Focus: a Method for Tracing Supercluster Scales at z ~ 1

Tunable narrow-band, emission-line surveys have begun to show the ease with which star forming galaxies can be identified in restricted redshift intervals to z ~ 5 with a 4m class telescope. These surveys have been carried out with imaging systems at the Cassegrain or Nasmyth focus and are therefore restricted to fields smaller than 10 arcmin. We now show that tunable narrowband imaging is possible over a 30 arcmin field with a high-performance Lyot filter placed directly in front of a CCD mosaic at the prime focus. Our design is intended for the f/3.3 prime focus of the AAT 3.9m, although similar devices can be envisaged for the Subaru 8m (f/2), Palomar 5m (f/3.4), VISTA 4m (f/6), Mayall 4m (f/2.6) or CFHT 3.6m (f/4). A modified Wynne doublet ensures sub-arcsecond performance over the field. In combination with the new Wide-Field Imaging 8K x 8K mosaic (WFI) at the AAT, the overall throughput (35%) of the system to unpolarised light is expected to be comparable to the TAURUS Tunable Filter (TTF). Unlike the TTF, the field is fully monochromatic and the instrumental profile has much better wing suppression. For targetted surveys of emission-line sources at z ~ 1, a low-resolution (R ~ 150 at 550nm) Lyot filter on a 4m telescope is expected to be comparable or superior to current instruments on 8-10m class telescopes. We demonstrate that the 30 arcmin field is well matched to superclusters at these redshifts such that large-scale structure should be directly observable.Comment: Astrophysical Journal, accepted. 53 pages, 16 figures, aaste

A Novel Quantum Dots–Based Point of Care Test for Syphilis

One-step lateral flow test is recommended as the first line screening of syphilis for primary healthcare settings in developing countries. However, it generally shows low sensitivity. We describe here the development of a novel fluorescent POC (Point Of Care) test method to be used for screening for syphilis. The method was designed to combine the rapidness of lateral flow test and sensitiveness of fluorescent method. 50 syphilis-positive specimens and 50 healthy specimens conformed by Treponema pallidum particle agglutination (TPPA) were tested with Quantum Dot-labeled and colloidal gold-labeled lateral flow test strips, respectively. The results showed that both sensitivity and specificity of the quantum dots–based method reached up to 100% (95% confidence interval [CI], 91–100%), while those of the colloidal gold-based method were 82% (95% CI, 68–91%) and 100% (95% CI, 91–100%), respectively. In addition, the naked-eye detection limit of quantum dot–based method could achieve 2 ng/ml of anti-TP47 polyclonal antibodies purified by affinity chromatography with TP47 antigen, which was tenfold higher than that of colloidal gold–based method. In conclusion, the quantum dots were found to be suitable for labels of lateral flow test strip. Its ease of use, sensitiveness and low cost make it well-suited for population-based on-the-site syphilis screening

Insulated gate and surface passivation structures for GaN-based power transistors

Recent years have witnessed GaN-based devices delivering their promise of unprecedented power and frequency levels and demonstrating their capability as an able replacement for Si-based devices. High-electron-mobility transistors (HEMTs), a key representative architecture of GaN-based devices, are well-suited for high-power and high frequency device applications, owing to highly desirable III-nitride physical properties. However, these devices are still hounded by issues not previously encountered in their more established Si- and GaAs-based devices counterparts. Metal–insulator–semiconductor (MIS) structures are usually employed with varying degrees of success in sidestepping the major problematic issues such as excessive leakage current and current instability. While different insulator materials have been applied to GaN-based transistors, the properties of insulator/III-N interfaces are still not fully understood. This is mainly due to the difficulty of characterizing insulator/AlGaN interfaces in a MIS HEMT because of the two resulting interfaces: insulator/AlGaN and AlGaN/GaN, making the potential modulation rather complicated. Although there have been many reports of low interface-trap densities in HEMT MIS capacitors, several papers have incorrectly evaluated their capacitance–voltage (C–V) characteristics. A HEMT MIS structure typically shows a 2-step C–V behavior. However, several groups reported C–V curves without the characteristic step at the forward bias regime, which is likely to the high-density states at the insulator/AlGaN interface impeding the potential control of the AlGaN surface by the gate bias. In this review paper, first we describe critical issues and problems including leakage current, current collapse and threshold voltage instability in AlGaN/GaN HEMTs. Then we present interface properties, focusing on interface states, of GaN MIS systems using oxides, nitrides and high-κ dielectrics. Next, the properties of a variety of AlGaN/GaN MIS structures as well as different characterization methods, including our own photo-assisted C–V technique, essential for understanding and developing successful surface passivation and interface control schemes, are given in the subsequent section. Finally we highlight the important progress in GaN MIS interfaces that have recently pushed the frontier of nitride-based device technology

The impact of diabetes mellitus on survival following resection and adjuvant chemotherapy for pancreatic cancer

BACKGROUND: Diabetes mellitus is frequently observed in pancreatic cancer patients and is both a risk factor and an early manifestation of the disease. METHODS: We analysed the prognostic impact of diabetes on the outcome of pancreatic cancer following resection and adjuvant chemotherapy using individual patient data from three European Study Group for Pancreatic Cancer randomised controlled trials. Analyses were carried out to assess the association between clinical characteristics and the presence of preoperative diabetes, as well as the effect of diabetic status on overall survival. RESULTS: In total, 1105 patients were included in the analysis, of whom 257 (23%) had confirmed diabetes and 848 (77%) did not. Median (95% confidence interval (CI)) unadjusted overall survival in non-diabetic patients was 22.3 (20.8–24.1) months compared with 18.8 (16.9–22.1) months for diabetic patients (P=0.24). Diabetic patients were older, had increased weight and more co-morbidities. Following adjustment, multivariable analysis demonstrated that diabetic patients had an increased risk of death (hazard ratio: 1.19 (95% CI 1.01, 1.40), P=0.034). Maximum tumour size of diabetic patients was larger at randomisation (33.6 vs 29.7 mm, P=0.026). CONCLUSIONS: Diabetes mellitus was associated with increased tumour size and reduced survival following pancreatic cancer resection and adjuvant chemotherapy

SynBlast: Assisting the analysis of conserved synteny information

<p>Abstract</p> <p>Motivation</p> <p>In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information.</p> <p>Results</p> <p>Here we present the <monospace>SynBlast</monospace> pipeline that is designed to construct and evaluate local synteny information. <monospace>SynBlast</monospace> uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how <monospace>SynBlast</monospace> is applied to retrieving orthologous and paralogous clusters using the vertebrate <it>Hox </it>and <it>ParaHox </it>clusters as examples.</p> <p>Software</p> <p>The <monospace>SynBlast</monospace> package written in <monospace>Perl</monospace> is available under the GNU General Public License at <url>http://www.bioinf.uni-leipzig.de/Software/SynBlast/</url>.</p