ALBERT

Description: A simple but accurate interpolation procedure for obtaining the three-dimensional distribution of three-component velocity data, from moving acoustic doppler current profiler (ADCP) observation data, is proposed. For understanding actual flow structure within a river with complex bathymetry, the three-dimensional mean velocity field provides a basic picture of the flow. For obtaining the three-dimensional distribution of three-component velocity data, in this work, anisotropic gridding was introduced in order to remove the random component of measured velocity data caused by the turbulence of the flow and measurement error. A continuity correction based on the pressure equation was used to reduce both random and systematic errors. The accuracy of the developed method was evaluated using three-dimensional flow simulation data from a detached-eddy simulation (DES). By using the procedure developed, the complex flow structure surrounding the spur dikes section in the Uji River was successfully visualized and explored. The proposed method shows superiorities in both accuracy and consistency for the interpolated velocity field, as compared to the kriging and inverse-distance weighted (IDW) methods.

Description: Wolbachia is one of the most widespread bacteria on Earth. Previous research on Wolbachia-host interactions indicates that the bacterium is typically transferred vertically, from mothe...

Description: The in-plane effective thermal conductivity of free-standing Si thin films with periodic micropores was measured at -100 to 0 °C. The Si thin films with micropores were prepared from silicon-on-insulator (SOI) wafers by standard microfabrication processes. The dimensions of the free-standing Si thin films were 200μm×150μm×2 μm, with staggered 4 μm pores having an average pitch of 4 mm. The Si thin film serves both as a heater and thermometer. The average temperature rise of the thin film is a function of its in-plane thermal conductivity. The effective thermal conductivity was calculated using a simple one-dimensional heat conduction model. The measured thermal conductivity was much lower than that expected based on classical model evaluations. A significant phonon size effect was observed even in the microsized structures, and the mean free path for phonons is very long even at the room temperature.

Description: 〈p〉The distribution of defects and dislocations in graphene layers has become a very important concern with regard to the electrical and electronic transport properties of device applications. Although several experiments have shown the influence of defects on the electrical properties of graphene, these studies were limited to measuring microscopic areas because of their long measurement times. Here, we successfully imaged various local defects in a large area of chemical vapor deposition graphene within a reasonable amount of time by using lock-in thermography (LIT). The differences in electrical resistance caused by the micrometer-scale defects, such as cracks and wrinkles, and atomic-scale domain boundaries were apparent as nonuniform Joule heating on polycrystalline and epitaxially grown graphene. The present results indicate that LIT can serve as a fast and effective method of evaluating the quality and uniformity of large graphene films for device applications.〈/p〉

Description: Primary transcripts of certain microRNA (miRNA) genes are subject to RNA editing that converts adenosine to inosine. However, the importance of miRNA editing remains largely undetermined. Here we report that tissue-specific adenosine-to-inosine editing of miR-376 cluster transcripts leads to predominant expression of edited miR-376 isoform RNAs. One highly edited site is positioned in the middle of the 5'-proximal half "seed" region critical for the hybridization of miRNAs to targets. We provide evidence that the edited miR-376 RNA silences specifically a different set of genes. Repression of phosphoribosyl pyrophosphate synthetase 1, a target of the edited miR-376 RNA and an enzyme involved in the uric-acid synthesis pathway, contributes to tight and tissue-specific regulation of uric-acid levels, revealing a previously unknown role for RNA editing in miRNA-mediated gene silencing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953418/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953418/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawahara, Yukio -- Zinshteyn, Boris -- Sethupathy, Praveen -- Iizasa, Hisashi -- Hatzigeorgiou, Artemis G -- Nishikura, Kazuko -- P01 CA072765/CA/NCI NIH HHS/ -- P01 CA072765-050002/CA/NCI NIH HHS/ -- R01 GM040536/GM/NIGMS NIH HHS/ -- R01 GM040536-16/GM/NIGMS NIH HHS/ -- R01 HL070045/HL/NHLBI NIH HHS/ -- R01 HL070045-04/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 23;315(5815):1137-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA. ykawahara@wistar.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17322061" target="_blank"〉PubMed〈/a〉

Description: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Misof, Bernhard -- Liu, Shanlin -- Meusemann, Karen -- Peters, Ralph S -- Donath, Alexander -- Mayer, Christoph -- Frandsen, Paul B -- Ware, Jessica -- Flouri, Tomas -- Beutel, Rolf G -- Niehuis, Oliver -- Petersen, Malte -- Izquierdo-Carrasco, Fernando -- Wappler, Torsten -- Rust, Jes -- Aberer, Andre J -- Aspock, Ulrike -- Aspock, Horst -- Bartel, Daniela -- Blanke, Alexander -- Berger, Simon -- Bohm, Alexander -- Buckley, Thomas R -- Calcott, Brett -- Chen, Junqing -- Friedrich, Frank -- Fukui, Makiko -- Fujita, Mari -- Greve, Carola -- Grobe, Peter -- Gu, Shengchang -- Huang, Ying -- Jermiin, Lars S -- Kawahara, Akito Y -- Krogmann, Lars -- Kubiak, Martin -- Lanfear, Robert -- Letsch, Harald -- Li, Yiyuan -- Li, Zhenyu -- Li, Jiguang -- Lu, Haorong -- Machida, Ryuichiro -- Mashimo, Yuta -- Kapli, Pashalia -- McKenna, Duane D -- Meng, Guanliang -- Nakagaki, Yasutaka -- Navarrete-Heredia, Jose Luis -- Ott, Michael -- Ou, Yanxiang -- Pass, Gunther -- Podsiadlowski, Lars -- Pohl, Hans -- von Reumont, Bjorn M -- Schutte, Kai -- Sekiya, Kaoru -- Shimizu, Shota -- Slipinski, Adam -- Stamatakis, Alexandros -- Song, Wenhui -- Su, Xu -- Szucsich, Nikolaus U -- Tan, Meihua -- Tan, Xuemei -- Tang, Min -- Tang, Jingbo -- Timelthaler, Gerald -- Tomizuka, Shigekazu -- Trautwein, Michelle -- Tong, Xiaoli -- Uchifune, Toshiki -- Walzl, Manfred G -- Wiegmann, Brian M -- Wilbrandt, Jeanne -- Wipfler, Benjamin -- Wong, Thomas K F -- Wu, Qiong -- Wu, Gengxiong -- Xie, Yinlong -- Yang, Shenzhou -- Yang, Qing -- Yeates, David K -- Yoshizawa, Kazunori -- Zhang, Qing -- Zhang, Rui -- Zhang, Wenwei -- Zhang, Yunhui -- Zhao, Jing -- Zhou, Chengran -- Zhou, Lili -- Ziesmann, Tanja -- Zou, Shijie -- Li, Yingrui -- Xu, Xun -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Wang, Jun -- Kjer, Karl M -- Zhou, Xin -- New York, N.Y. -- Science. 2014 Nov 7;346(6210):763-7. doi: 10.1126/science.1257570. Epub 2014 Nov 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn. ; China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organization (Australia) (CSIRO), National Research Collections Australia, Canberra, ACT, Australia. ; Abteilung Arthropoda, Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. ; Department of Entomology, Rutgers University, New Brunswick, NJ 08854, USA. ; Department of Biological Sciences, Rutgers University, Newark, NJ 08854, USA. ; Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. ; Institut fur Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum Jena, FSU Jena, Germany. ; Steinmann-Institut, Bereich Palaontologie, Universitat Bonn, Germany. ; 2. Zoologische Abteilung (Insekten), Naturhistorisches Museum Wien, Vienna, Austria. Department of Integrative Zoology, Universitat Wien, Vienna, Austria. ; Institut fur Spezifische Prophylaxe und Tropenmedizin, Medizinische Parasitologie, Medizinische Universitat Wien (MUW), Vienna, Austria. ; Department of Integrative Zoology, Universitat Wien, Vienna, Austria. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fur Molekulare Biodiversitatsforschung (ZMB), Bonn, Germany. Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan. ; Manaaki Whenua Landcare Research, Auckland, New Zealand. ; Center for Advanced Modeling, Emergency Medicine Department, Johns Hopkins University, Baltimore, MD 21209, USA. ; BGI-Shenzhen, China. ; Biozentrum Grindel und Zoologisches Museum, Universitat Hamburg, Hamburg, Germany. ; Evolutionary Morphology Laboratory, Graduate School of Science and Engineering, Ehime University, Japan. ; Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan. ; Land and Water Flagship, CSIRO, Canberra, ACT, Australia. ; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. ; Entomology, Staatliches Museum fur Naturkunde Stuttgart (SMNS), Germany. ; Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia. National Evolutionary Synthesis Center, Durham, NC 27705, USA. Department of Biological Sciences, Macquarie University, Sydney, Australia. ; Department fur Botanik und Biodiversitatsforschung, Universitat Wien, Vienna, Austria. ; Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. Natural History Museum of Crete, University of Crete, Post Office Box 2208, Gr-71409, Iraklio, and Biology Department, University of Crete, Iraklio, Crete, Greece. ; Department of Biological Sciences and Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152, USA. ; Centro Universitario de Ciencias Biologicas y Agropecuarias, Centro de Estudios en Zoologia, Universidad de Guadalajara, Zapopan, Jalisco, Mexico. ; Leibniz Supercomputing Centre of the Bavarian Academy of Sciences and Humanities, Garching, Germany. ; Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Bonn, Germany. ; Department of Life Sciences, The Natural History Museum London, London, UK. ; Abteilung Entomologie, Biozentrum Grindel und Zoologisches Museum, Universitat Hamburg, Hamburg, Germany. ; Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organization (Australia) (CSIRO), National Research Collections Australia, Canberra, ACT, Australia. ; Scientific Computing, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. Fakultat fur Informatik, Karlsruher Institut fur Technologie, Karlsruhe, Germany. ; California Academy of Sciences, San Francisco, CA 94118, USA. ; Department of Entomology, College of Natural Resources and Environment, South China Agricultural University, China. ; Sugadaira Montane Research Center/Hexapod Comparative Embryology Laboratory, University of Tsukuba, Japan. Yokosuka City Museum, Yokosuka, Kanagawa, Japan. ; Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA. ; Systematic Entomology, Hokkaido University, Sapporo, Japan. ; BGI-Shenzhen, China. Department of Biology, University of Copenhagen, Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, China. Department of Medicine, University of Hong Kong, Hong Kong. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn. ; Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08854, USA. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn. ; China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China. xinzhou@genomics.cn b.misof.zfmk@uni-bonn.de kjer@aesop.rutgers.edu wangj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25378627" target="_blank"〉PubMed〈/a〉

Description: Tong et al. comment on the accuracy of the dating analysis presented in our work on the phylogeny of insects and provide a reanalysis of our data. They replace log-normal priors with uniform priors and add a "roachoid" fossil as a calibration point. Although the reanalysis provides an interesting alternative viewpoint, we maintain that our choices were appropriate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kjer, K M -- Ware, J L -- Rust, J -- Wappler, T -- Lanfear, R -- Jermiin, L S -- Zhou, X -- Aspock, H -- Aspock, U -- Beutel, R G -- Blanke, A -- Donath, A -- Flouri, T -- Frandsen, P B -- Kapli, P -- Kawahara, A Y -- Letsch, H -- Mayer, C -- McKenna, D D -- Meusemann, K -- Niehuis, O -- Peters, R S -- Wiegmann, B M -- Yeates, D K -- von Reumont, B M -- Stamatakis, A -- Misof, B -- New York, N.Y. -- Science. 2015 Jul 31;349(6247):487. doi: 10.1126/science.aaa7136.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Davis, CA, USA. ; Rutgers University, New Brunswick, NJ, USA. ; Universitat Bonn, Germany. ; Macquarie University, Sydney, Australia. ; Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia. ; China National GeneBank, BGI-Shenzhen, China. BGI-Shenzhen, China. ; Universitat Wien, Vienna, Austria. ; Universitat Wien, Vienna, Austria. Naturhistorisches Museum Wien, Vienna, Austria. ; Phyletischem Museum Jena, Friedrich-Schiller-Universitat Jena, Germany. ; University of Tsukuba, Japan. ; Universitat Bonn, Germany. Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany. ; Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. ; Rutgers University, New Brunswick, NJ, USA. Smithsonian Institution, Washington, DC, USA. ; University of Florida, Gainesville, FL, USA. ; University of Memphis, Memphis, TN, USA. ; Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia. Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany. Arizona State University, Tempe, AZ, USA. ; North Carolina State University, Raleigh, NC, USA. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany. Natural History Museum London, London, UK. ; Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany. bmisof@uni-bonn.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26228138" target="_blank"〉PubMed〈/a〉

Description: The recent decline in fertility is a serious problem in the dairy industry. To overcome this problem, we performed a genome-wide association study using 384 Holsteins and identified four loci associated with conception rates. Two of them contained gap junction-related genes: PKP2 and CTTNBP2NL. Further analysis confirmed that PKP2 increased...

Description: Anthropogenic noise is a widespread and growing form of sensory pollution associated with the expansion of human infrastructure. One specific source of constant and intense noise is that produced by compressors used for the extraction and transportation of natural gas. Terrestrial arthropods play a central role in many ecosystems, and given that numerous species rely upon airborne sounds and substrate-borne vibrations in their life histories, we predicted that increased background sound levels or the presence of compressor noise would influence their distributions. In the second largest natural gas field in the United States (San Juan Basin, New Mexico, USA), we assessed differences in the abundances of terrestrial arthropod families and community structure as a function of compressor noise and background sound level. Using pitfall traps, we simultaneously sampled five sites adjacent to well pads that possessed operating compressors, and five alternate, quieter well pad sites that lacked compressors, but were otherwise similar. We found a negative association between sites with compressor noise or higher levels of background sound and the abundance of five arthropod families and one genus, a positive relationship between loud sites and the abundance of one family, and no relationship between noise level or compressor presence and abundance for six families and two genera. Despite these changes, we found no evidence of community turnover as a function of background sound level or site type (compressor and noncompressor). Our results indicate that anthropogenic noise differentially affects the abundances of some arthropod families. These preliminary findings point to a need to determine the direct and indirect mechanisms driving these observed responses. Given the diverse and important ecological functions provided by arthropods, changes in abundances could have ecological implications. Therefore, we recommend the consideration of arthropods in the environmental assessment of noise-producing infrastructure. In the second largest natural gas basin in the US, we examined the effects of elevated background sound levels in general and compressor station noise specifically on terrestrial arthropod abundances. Findings indicate complex and varied responses of five arthropod families to these two patterns of noise exposure. These landscape scale changes may have ecological implications, due to the many important ecosystem functions provided by these organisms.