Transposon-mediated BAC transgenesis in zebrafish and mice

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Sumiyama Kenta

2009-10-01

Full Text Available Abstract Background Bacterial artificial chromosomes (BACs are among the most widely used tools for studies of gene regulation and function in model vertebrates, yet methods for predictable delivery of BAC transgenes to the genome are currently limited. This is because BAC transgenes are usually microinjected as naked DNA into fertilized eggs and are known to integrate as multi-copy concatamers in the genome. Although conventional methods for BAC transgenesis have been very fruitful, complementary methods for generating single copy BAC integrations would be desirable for many applications. Results We took advantage of the precise cut-and-paste behavior of a natural transposon, Tol2, to develop a new method for BAC transgenesis. In this new method, the minimal sequences of the Tol2 transposon were used to deliver precisely single copies of a ~70 kb BAC transgene to the zebrafish and mouse genomes. We mapped the BAC insertion sites in the genome by standard PCR methods and confirmed transposase-mediated integrations. Conclusion The Tol2 transposon has a surprisingly large cargo capacity that can be harnessed for BAC transgenesis. The precise delivery of single-copy BAC transgenes by Tol2 represents a useful complement to conventional BAC transgenesis, and could aid greatly in the production of transgenic fish and mice for genomics projects, especially those in which single-copy integrations are desired.

A set of BAC clones spanning the human genome.

NARCIS (Netherlands)

Krzywinski, M.; Bosdet, I.; Smailus, D.; Chiu, R.; Mathewson, C.; Wye, N.; Barber, S.; Brown-John, M.; Chan, S.; Chand, S.; Cloutier, A.; Girn, N.; Lee, D.; Masson, A.; Mayo, M.; Olson, T.; Pandoh, P.; Prabhu, A.L.; Schoenmakers, E.F.P.M.; Tsai, M.Y.; Albertson, D.; Lam, W.W.; Choy, C.O.; Osoegawa, K.; Zhao, S.; Jong, P.J. de; Schein, J.; Jones, S.; Marra, M.A.

2004-01-01

Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC clones spanning the human genome. The clone set provides coverage for at least 98% of the human

Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization.

Science.gov (United States)

Jiang, Likun; You, Weiwei; Zhang, Xiaojun; Xu, Jian; Jiang, Yanliang; Wang, Kai; Zhao, Zixia; Chen, Baohua; Zhao, Yunfeng; Mahboob, Shahid; Al-Ghanim, Khalid A; Ke, Caihuan; Xu, Peng

2016-02-01

The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.

The first insight into the salvia (lamiaceae) genome via bac library construction and high-throughput sequencing of target bac clones

International Nuclear Information System (INIS)

Hao, D.C.; Vautrin, S.; Berges, H.; Chen, S.L.

2015-01-01

Salvia is a representative genus of Lamiaceae, a eudicot family with significant species diversity and population adaptibility. One of the key goals of Salvia genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of medicinal plants to increase their health and productivity. Large-insert genomic libraries are a fundamental tool for achieving this purpose. We report herein the construction, characterization and screening of a gridded BAC library for Salvia officinalis (sage). The S. officinalis BAC library consists of 17,764 clones and the average insert size is 107 Kb, corresponding to 3 haploid genome equivalents. Seventeen positive clones (average insert size 115 Kb) containing five terpene synthase (TPS) genes were screened out by PCR and 12 of them were subject to Illumina HiSeq 2000 sequencing, which yielded 28,097,480 90-bp raw reads (2.53 Gb). Scaffolds containing sabinene synthase (Sab), a Sab homolog, TPS3 (kaurene synthase-like 2), copalyl diphosphate synthase 2 and one cytochrome P450 gene were retrieved via de novo assembly and annotation, which also have flanking noncoding sequences, including predicted promoters and repeat sequences. Among 2,638 repeat sequences, there are 330 amplifiable microsatellites. This BAC library provides a new resource for Lamiaceae genomic studies, including microsatellite marker development, physical mapping, comparative genomics and genome sequencing. Characterization of positive clones provided insights into the structure of the Salvia genome. These sequences will be used in the assembly of a future genome sequence for S. officinalis. (author)

The Functionality of Minimal PiggyBac Transposons in Mammalian Cells

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Boris Troyanovsky

2016-01-01

Full Text Available Minimal piggyBac vectors are a modified single-plasmid version of the classical piggyBac delivery system that can be used for stable transgene integration. These vectors have a truncated terminal domain in the delivery cassette and thus, integrate significantly less flanking transposon DNA into host cell chromatin than classical piggyBac vectors. Herein, we test various characteristics of this modified transposon. The integration efficiency of minimal piggyBac vectors was inversely related to the size of both the transposon and the entire plasmid, but inserts as large as 15 kb were efficiently integrated. Open and super-coiled vectors demonstrated the same integration efficiency while DNA methylation decreased the integration efficiency and silenced the expression of previously integrated sequences in some cell types. Importantly, the incidence of plasmid backbone integration was not increased above that seen in nontransposon control vectors. In BALB/c mice, we demonstrated prolonged expression of two transgenes (intracellular mCherry and secretable Gaussia luciferase when delivered by the minimal piggyBac that resulted in a more sustained antibody production against the immunogenic luciferase than when delivered by a transient (nontransposon vector plasmid. We conclude that minimal piggyBac vectors are an effective alternative to other integrative systems for stable DNA delivery in vitro and in vivo.

Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome.

Science.gov (United States)

Santos, Anselmo Azevedo; Penha, Helen Alves; Bellec, Arnaud; Munhoz, Carla de Freitas; Pedrosa-Harand, Andrea; Bergès, Hélène; Vieira, Maria Lucia Carneiro

2014-09-26

The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n=9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome

MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes.

Science.gov (United States)

Gradia, Scott D; Ishida, Justin P; Tsai, Miaw-Sheue; Jeans, Chris; Tainer, John A; Fuss, Jill O

2017-01-01

Recombinant expression of large, multiprotein complexes is essential and often rate limiting for determining structural, biophysical, and biochemical properties of DNA repair, replication, transcription, and other key cellular processes. Baculovirus-infected insect cell expression systems are especially well suited for producing large, human proteins recombinantly, and multigene baculovirus systems have facilitated studies of multiprotein complexes. In this chapter, we describe a multigene baculovirus system called MacroBac that uses a Biobricks-type assembly method based on restriction and ligation (Series 11) or ligation-independent cloning (Series 438). MacroBac cloning and assembly is efficient and equally well suited for either single subcloning reactions or high-throughput cloning using 96-well plates and liquid handling robotics. MacroBac vectors are polypromoter with each gene flanked by a strong polyhedrin promoter and an SV40 poly(A) termination signal that minimize gene order expression level effects seen in many polycistronic assemblies. Large assemblies are robustly achievable, and we have successfully assembled as many as 10 genes into a single MacroBac vector. Importantly, we have observed significant increases in expression levels and quality of large, multiprotein complexes using a single, multigene, polypromoter virus rather than coinfection with multiple, single-gene viruses. Given the importance of characterizing functional complexes, we believe that MacroBac provides a critical enabling technology that may change the way that structural, biophysical, and biochemical research is done. © 2017 Elsevier Inc. All rights reserved.

Estimating P-coverage of biosynthetic pathways in DNA libraries and screening by genetic selection: biotin biosynthesis in the marine microorganism Chromohalobacter.

Science.gov (United States)

Kim, Eun Jin; Angell, Scott; Janes, Jeff; Watanabe, Coran M H

2008-06-01

Traditional approaches to natural product discovery involve cell-based screening of natural product extracts followed by compound isolation and characterization. Their importance notwithstanding, continued mining leads to depletion of natural resources and the reisolation of previously identified metabolites. Metagenomic strategies aimed at localizing the biosynthetic cluster genes and expressing them in surrogate hosts offers one possible alternative. A fundamental question that naturally arises when pursuing such a strategy is, how large must the genomic library be to effectively represent the genome of an organism(s) and the biosynthetic gene clusters they harbor? Such an issue is certainly augmented in the absence of expensive robotics to expedite colony picking and/or screening of clones. We have developed an algorism, named BPC (biosynthetic pathway coverage), supported by molecular simulations to deduce the number of BAC clones required to achieve proper coverage of the genome and their respective biosynthetic pathways. The strategy has been applied to the construction of a large-insert BAC library from a marine microorganism, Hon6 (isolated from Honokohau, Maui) thought to represent a new species. The genomic library is constructed with a BAC yeast shuttle vector pClasper lacZ paving the way for the culturing of libraries in both prokaryotic and eukaryotic hosts. Flow cytometric methods are utilized to estimate the genome size of the organism and BPC implemented to assess P-coverage or percent coverage. A genetic selection strategy is illustrated, applications of which could expedite screening efforts in the identification and localization of biosynthetic pathways from marine microbial consortia, offering a powerful complement to genome sequencing and degenerate probe strategies. Implementing this approach, we report on the biotin biosynthetic pathway from the marine microorganism Hon6.

A Blumeria graminis f.sp. hordei BAC library - contig building and microsynteny studies

DEFF Research Database (Denmark)

Pedersen, C.; Wu, B.; Giese, H.

2002-01-01

A bacterial artificial chromosome (BAC) library of Blumeria graminis f.sp. hordei, containing 12,000 clones with an average insert size of 41 kb, was constructed. The library represents about three genome equivalents and BAC-end sequencing showed a high content of repetitive sequences, making...... contigs, at or close to avirulence loci, were constructed. Single nucleotide polymorphism (SNP) markers were developed from BAC-end sequences to link the contigs to the genetic maps. Two other BAC contigs were used to study microsynteny between B. graminis and two other ascomycetes, Neurospora crassa...

A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurata L.

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Heiner Kuhl

2011-01-01

Full Text Available This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata, a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp. Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome.

Giant panda BAC library construction and assembly of a 650-kb contig spanning major histocompatibility complex class II region

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Pan Hui-Juan

2007-09-01

Full Text Available Abstract Background Giant panda is rare and endangered species endemic to China. The low rates of reproductive success and infectious disease resistance have severely hampered the development of captive and wild populations of the giant panda. The major histocompatibility complex (MHC plays important roles in immune response and reproductive system such as mate choice and mother-fetus bio-compatibility. It is thus essential to understand genetic details of the giant panda MHC. Construction of a bacterial artificial chromosome (BAC library will provide a new tool for panda genome physical mapping and thus facilitate understanding of panda MHC genes. Results A giant panda BAC library consisting of 205,800 clones has been constructed. The average insert size was calculated to be 97 kb based on the examination of 174 randomly selected clones, indicating that the giant panda library contained 6.8-fold genome equivalents. Screening of the library with 16 giant panda PCR primer pairs revealed 6.4 positive clones per locus, in good agreement with an expected 6.8-fold genomic coverage of the library. Based on this BAC library, we constructed a contig map of the giant panda MHC class II region from BTNL2 to DAXX spanning about 650 kb by a three-step method: (1 PCR-based screening of the BAC library with primers from homologous MHC class II gene loci, end sequences and BAC clone shotgun sequences, (2 DNA sequencing validation of positive clones, and (3 restriction digest fingerprinting verification of inter-clone overlapping. Conclusion The identifications of genes and genomic regions of interest are greatly favored by the availability of this giant panda BAC library. The giant panda BAC library thus provides a useful platform for physical mapping, genome sequencing or complex analysis of targeted genomic regions. The 650 kb sequence-ready BAC contig map of the giant panda MHC class II region from BTNL2 to DAXX, verified by the three-step method, offers a

Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

A bacterial artificial chromosome (BAC) library containing a large genomic DNA insert is an important tool for genome physical mapping, map-based cloning, and genome sequencing. To isolate genes via a map-based cloning strategy and to perform physical mapping of the cotton genome, a high-quality BAC library containing large cotton DNA inserts is needed. We have developed a BAC library of the restoring line 0-613-2R for isolating the fertility restorer (Rf1) gene and genomic research in cotton (Gossypium hirsutum L.). The BAC library contains 97 825 clones stored in 255 pieces of a 384-well microtiter plate. Random samples of BACs digested with the Notl enzyme indicated that the average insert size is approximately 130 kb, with a range of 80-275 kb,and 95.7% of the BAC clones in the library have an average insert size larger than 100 kb. Based on a cotton genome size of 2 250 Mb, library coverage is 5.7 x haploid genome equivalents. Four clones were selected randomly from the library to determine the stability of the BAC clones. There were no different fingerprints for 0 and 100 generations of each clone digested with Notl and Hindlll enzymes. Thus, the stability of a single BAC clone can be sustained at least for 100 generations. Eight simple sequence repeat (SSR) markers flanking the Rf1 gene were chosen to screen the BAC library by pool using PCR method and 25 positive clones were identified with 3.1 positive clones per SSR marker.

Toward a molecular cytogenetic map for cultivated sunflower (Helianthus annuus L.) by landed BAC/BIBAC clones.

Science.gov (United States)

Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

2013-01-01

Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (~100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC-fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)-derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources.

Isolation of Specific Clones from Nonarrayed BAC Libraries through Homologous Recombination

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Mikhail Nefedov

2011-01-01

Full Text Available We have developed a new approach to screen bacterial artificial chromosome (BAC libraries by recombination selection. To test this method, we constructed an orangutan BAC library using an E. coli strain (DY380 with temperature inducible homologous recombination (HR capability. We amplified one library segment, induced HR at 42∘C to make it recombination proficient, and prepared electrocompetent cells for transformation with a kanamycin cassette to target sequences in the orangutan genome through terminal recombineering homologies. Kanamycin-resistant colonies were tested for the presence of BACs containing the targeted genes by the use of a PCR-assay to confirm the presence of the kanamycin insertion. The results indicate that this is an effective approach for screening clones. The advantage of recombination screening is that it avoids the high costs associated with the preparation, screening, and archival storage of arrayed BAC libraries. In addition, the screening can be conceivably combined with genetic engineering to create knockout and reporter constructs for functional studies.

A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC libraries using High Resolution Melt analysis

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Caligari Peter DS

2010-05-01

Full Text Available Abstract Background The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries is a widely used alternative to high density filter hybridisation of bacterial colonies. To date, concerns over reliability have led most if not all groups engaged in high throughput physical mapping projects to favour BAC DNA isolation prior to amplification by conventional PCR. Results Here, we report the first combined use of Multiplex Tandem PCR (MT-PCR and High Resolution Melt (HRM analysis on bacterial stocks of BAC library superpools as a means of rapidly anchoring markers to BAC colonies and thereby to integrate genetic and physical maps. We exemplify the approach using a BAC library of the model plant Arabidopsis thaliana. Super pools of twenty five 384-well plates and two-dimension matrix pools of the BAC library were prepared for marker screening. The entire procedure only requires around 3 h to anchor one marker. Conclusions A pre-amplification step during MT-PCR allows high multiplexing and increases the sensitivity and reliability of subsequent HRM discrimination. This simple gel-free protocol is more reliable, faster and far less costly than conventional PCR screening. The option to screen in parallel 3 genetic markers in one MT-PCR-HRM reaction using templates from directly pooled bacterial stocks of BAC-containing bacteria further reduces time for anchoring markers in physical maps of species with large genomes.

Peripherally inserted central catheters and upper extremity deep vein thrombosis

International Nuclear Information System (INIS)

Ong, B.; Gibbs, H.; Catchpole, I.; Hetherington, R.; Harper, J.

2006-01-01

The purpose of the study was to determine the incidence and risk factors for venous thrombosis in patients with a peripherally inserted central catheter (PICC). A retrospective study of all upper extremity venous duplex scans was carried out in the Vascular Medicine department from year 2000 to 2002 inclusive. A chart review of positive scans was undertaken to identify possible thrombotic risk factors. Of 317 upper extremity venous duplex scans carried out, 115, or 32%, were positive for upper extremity deep vein thrombosis. Three main risk factors were identified - presence of a central line, malignancy and administration of chemotherapy. PICC were the most common central line present. Symptomatic thrombosis occurred in 7% of PICC inserted for chemotherapy compared with 1% of PICC inserted for other reasons. Ten per cent of the patients receiving chemotherapy through a PICC developed a thrombosis. The post-thrombotic syndrome was infrequent following upper extremity deep vein thrombosis. Patients receiving chemotherapy through a PICC are at increased risk of thrombosis. There may be a role for prophylactic low-dose anticoagulation in these high-risk patients

Transposon-mediated BAC transgenesis in human ES cells

Science.gov (United States)

Rostovskaya, Maria; Fu, Jun; Obst, Mandy; Baer, Isabell; Weidlich, Stefanie; Wang, Hailong; Smith, Andrew J. H.; Anastassiadis, Konstantinos; Stewart, A. Francis

2012-01-01

Transgenesis is a cornerstone of molecular biology. The ability to integrate a specifically engineered piece of DNA into the genome of a living system is fundamental to our efforts to understand life and exploit its implications for medicine, nanotechnology and bioprospecting. However, transgenesis has been hampered by position effects and multi-copy integration problems, which are mainly due to the use of small, plasmid-based transgenes. Large transgenes based on native genomic regions cloned into bacterial artificial chromosomes (BACs) circumvent these problems but are prone to fragmentation. Herein, we report that contrary to widely held notions, large BAC-sized constructs do not prohibit transposition. We also report the first reliable method for BAC transgenesis in human embryonic stem cells (hESCs). The PiggyBac or Sleeping Beauty transposon inverted repeats were integrated into BAC vectors by recombineering, followed by co-lipofection with the corresponding transposase in hESCs to generate robust fluorescent protein reporter lines for OCT4, NANOG, GATA4 and PAX6. BAC transposition delivers several advantages, including increased frequencies of single-copy, full-length integration, which will be useful in all transgenic systems but especially in difficult venues like hESCs. PMID:22753106

Self-Paced Prioritized Curriculum Learning With Coverage Penalty in Deep Reinforcement Learning.

Science.gov (United States)

Ren, Zhipeng; Dong, Daoyi; Li, Huaxiong; Chen, Chunlin; Zhipeng Ren; Daoyi Dong; Huaxiong Li; Chunlin Chen; Dong, Daoyi; Li, Huaxiong; Chen, Chunlin; Ren, Zhipeng

2018-06-01

In this paper, a new training paradigm is proposed for deep reinforcement learning using self-paced prioritized curriculum learning with coverage penalty. The proposed deep curriculum reinforcement learning (DCRL) takes the most advantage of experience replay by adaptively selecting appropriate transitions from replay memory based on the complexity of each transition. The criteria of complexity in DCRL consist of self-paced priority as well as coverage penalty. The self-paced priority reflects the relationship between the temporal-difference error and the difficulty of the current curriculum for sample efficiency. The coverage penalty is taken into account for sample diversity. With comparison to deep Q network (DQN) and prioritized experience replay (PER) methods, the DCRL algorithm is evaluated on Atari 2600 games, and the experimental results show that DCRL outperforms DQN and PER on most of these games. More results further show that the proposed curriculum training paradigm of DCRL is also applicable and effective for other memory-based deep reinforcement learning approaches, such as double DQN and dueling network. All the experimental results demonstrate that DCRL can achieve improved training efficiency and robustness for deep reinforcement learning.

Deep round window insertion versus standard approach in cochlear implant surgery.

Science.gov (United States)

Nordfalk, Karl Fredrik; Rasmussen, Kjell; Bunne, Marie; Jablonski, Greg Eigner

2016-01-01

The aim of this study was to compare the outcomes of vestibular tests and the residual hearing of patients who have undergone full insertion cochlear implant surgery using the round window approach with a hearing preservation protocol (RW-HP) or the standard cochleostomy approach (SCA) without hearing preservation. A prospective study of 34 adults who underwent unilateral cochlear implantation was carried out. One group was operated using the RW-HP (n = 17) approach with Med-El +Flex(SOFT) electrode array with full insertion, while the control group underwent a more conventional SCA surgery (n = 17) with shorter perimodiolar electrodes. Assessments of residual hearing, cervical vestibular-evoked myogenic potentials (cVEMP), videonystagmography, subjective visual vertical/horizontal (SVH/SVV) were performed before and after surgery. There was a significantly (p < 0.05) greater number of subjects who exhibited complete or partial hearing preservation in the deep insertion RW-HP group (9/17) compared to the SCA group (2/15). A higher degree of vestibular loss but a lower degree of vertigo symptoms could be seen in the RW-HP group, but the differences were not statistically significant. It is possible to preserve residual hearing to a certain extent also with deep insertion. Full insertion with hearing preservation was less harmful to residual hearing particularly at 125 Hz (p < 0.05), than was the standard cochleostomy approach.

End Sequencing and Finger Printing of Human & Mouse BAC Libraries

Energy Technology Data Exchange (ETDEWEB)

Fraser, C

2005-09-27

This project provided for continued end sequencing of existing and new BAC libraries constructed to support human sequencing as well as to initiate BAC end sequencing from the mouse BAC libraries constructed to support mouse sequencing. The clones, the sequences, and the fingerprints are now an available resource for the community at large. Research and development of new metaodologies for BAC end sequencing have reduced costs and increase throughput.

BAC-HAPPY mapping (BAP mapping: a new and efficient protocol for physical mapping.

Directory of Open Access Journals (Sweden)

Giang T H Vu

2010-02-01

Full Text Available Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping, that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS markers spanning approximately 10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual "BAC-HAPPY-mapping" to convert BAC landing data into BAC linkage contigs is possible.

BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

Science.gov (United States)

Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

2012-05-01

Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti.

Science.gov (United States)

Adelman, Zach N; Jasinskiene, Nijole; Vally, K J M; Peek, Corrie; Travanty, Emily A; Olson, Ken E; Brown, Susan E; Stephens, Janice L; Knudson, Dennis L; Coates, Craig J; James, Anthony A

2004-10-01

The Class II transposable element, piggyBac, was used to transform the yellow fever mosquito, Aedes aegypti. In two transformed lines only 15-30% of progeny inherited the transgene, with these individuals displaying mosaic expression of the EGFP marker gene. Southern analyses, gene amplification of genomic DNA, and plasmid rescue experiments provided evidence that these lines contained a high copy number of piggyBac transformation constructs and that much of this DNA consisted of both donor and helper plasmids. A detailed analysis of one line showed that the majority of piggyBac sequences were unit-length donor or helper plasmids arranged in a large tandem array that could be lost en masse in a single generation. Despite the presence of a transposase source and many intact donor elements, no conservative (cut and paste) transposition of piggyBac was observed in these lines. These results reveal one possible outcome of uncontrolled and/or unexpected recombination in this mosquito, and support the conclusion that further investigation is necessary before transposable elements such as piggyBac can be used as genetic drive mechanisms to move pathogen-resistance genes into mosquito populations.

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.

Science.gov (United States)

Gillet-Markowska, Alexandre; Richard, Hugues; Fischer, Gilles; Lafontaine, Ingrid

2015-03-15

The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis; FINAL

International Nuclear Information System (INIS)

Simon, M. I.; Kim, U.-J.

2002-01-01

We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year

Recombineering strategies for developing next generation BAC transgenic tools for optogenetics and beyond.

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Ting, Jonathan T; Feng, Guoping

2014-01-01

The development and application of diverse BAC transgenic rodent lines has enabled rapid progress for precise molecular targeting of genetically-defined cell types in the mammalian central nervous system. These transgenic tools have played a central role in the optogenetic revolution in neuroscience. Indeed, an overwhelming proportion of studies in this field have made use of BAC transgenic Cre driver lines to achieve targeted expression of optogenetic probes in the brain. In addition, several BAC transgenic mouse lines have been established for direct cell-type specific expression of Channelrhodopsin-2 (ChR2). While the benefits of these new tools largely outweigh any accompanying challenges, many available BAC transgenic lines may suffer from confounds due in part to increased gene dosage of one or more "extra" genes contained within the large BAC DNA sequences. Here we discuss this under-appreciated issue and propose strategies for developing the next generation of BAC transgenic lines that are devoid of extra genes. Furthermore, we provide evidence that these strategies are simple, reproducible, and do not disrupt the intended cell-type specific transgene expression patterns for several distinct BAC clones. These strategies may be widely implemented for improved BAC transgenesis across diverse disciplines.

Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri

Institute of Scientific and Technical Information of China (English)

ZHANG Yang; ZHANG Xiaojun; Chantel F.SCHEURING; ZHANG Hongbin; LI Fuhua; XIANG Jianhai

2008-01-01

Two Large-insert genomic bacterial artificial chromosome (BAC) libraries of Zhikong scallop Chlamys farreri were constructed to promote our genetic and genomic research.High-quality megabase-sized DNA was isolated from the adductor muscle of the scallop and partially digested by BamH I and Mbo I,respectively.The BamH I library consisted of 53760 clones while the Mbo I library consisted of 7680 clones.Approximately 96% of the clones in BamH I library contained nuclear DNA inserts in average size of 100 kb,providing a coverage of 5.3 haploid genome equivalents.Similarly,the Mbo I library with an average insert of 145 kb and no insert-empty clones,thus providing a genome coverage of 1.1 haploid genome equivalents.

Transposon Invasion of the Paramecium Germline Genome Countered by a Domesticated PiggyBac Transposase and the NHEJ Pathway

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Dubois, Emeline; Bischerour, Julien; Marmignon, Antoine; Mathy, Nathalie; Régnier, Vinciane; Bétermier, Mireille

2012-01-01

Sequences related to transposons constitute a large fraction of extant genomes, but insertions within coding sequences have generally not been tolerated during evolution. Thanks to their unique nuclear dimorphism and to their original mechanism of programmed DNA elimination from their somatic nucleus (macronucleus), ciliates are emerging model organisms for the study of the impact of transposable elements on genomes. The germline genome of the ciliate Paramecium, located in its micronucleus, contains thousands of short intervening sequences, the IESs, which interrupt 47% of genes. Recent data provided support to the hypothesis that an evolutionary link exists between Paramecium IESs and Tc1/mariner transposons. During development of the macronucleus, IESs are excised precisely thanks to the coordinated action of PiggyMac, a domesticated piggyBac transposase, and of the NHEJ double-strand break repair pathway. A PiggyMac homolog is also required for developmentally programmed DNA elimination in another ciliate, Tetrahymena. Here, we present an overview of the life cycle of these unicellular eukaryotes and of the developmentally programmed genome rearrangements that take place at each sexual cycle. We discuss how ancient domestication of a piggyBac transposase might have allowed Tc1/mariner elements to spread throughout the germline genome of Paramecium, without strong counterselection against insertion within genes. PMID:22888464

Insect transformation with piggyBac: getting the number of injections just right

Science.gov (United States)

Morrison, N. I.; Shimeld, S. M.

2016-01-01

Abstract The insertion of exogenous genetic cargo into insects using transposable elements is a powerful research tool with potential applications in meeting food security and public health challenges facing humanity. piggyBac is the transposable element most commonly utilized for insect germline transformation. The described efficiency of this process is variable in the published literature, and a comprehensive review of transformation efficiency in insects is lacking. This study compared and contrasted all available published data with a comprehensive data set provided by a biotechnology group specializing in insect transformation. Based on analysis of these data, with particular focus on the more complete observational data from the biotechnology group, we designed a decision tool to aid researchers' decision‐making when using piggyBac to transform insects by microinjection. A combination of statistical techniques was used to define appropriate summary statistics of piggyBac transformation efficiency by species and insect order. Publication bias was assessed by comparing the data sets. The bias was assessed using strategies co‐opted from the medical literature. The work culminated in building the Goldilocks decision tool, a Markov‐Chain Monte‐Carlo simulation operated via a graphical interface and providing guidance on best practice for those seeking to transform insects using piggyBac. PMID:27027400

PLE-wu, a new member of piggyBac transposon family from insect, is active in mammalian cells.

Science.gov (United States)

Wu, Chunxiao; Wang, Shu

2014-10-01

piggyBac, a highly active transposon in insect and mammalian cells, is a very useful tool in genome manipulation. A new piggyBac-like element (PLE), named PLE-wu, was identified from a mutant baculovirus cultured in sf9 insect cells. This new transposon is 2931 bp in length and encodes two active forms of transposase, a 708-amino acid-long transposase and a short 576-residue-long transposase translated from a downstream in-frame initiation codon. PLE-wu has asymmetric terminal structures, containing 6-bp inverted terminal repeats, 32-bp imperfect inverted and direct sub-terminal repeats. Similar to piggyBac, PLE-wu exhibits traceless excision activity in both insect and mammalian cells, restoring the original TTAA target sequence upon excision. It also retains the insertion activity in mammalian cells with a plasmid to chromosome transposition rate about 10-fold higher than random integration. Plasmid rescue assays revealed that the TTAA target sequence was duplicated at the junctions of the insertion site. Deletion of the terminal sequences including the sub-terminal repeats decreased the transposition activity of the 708-residue-long transposase, while the transposition activity of the short form of transposase was not affected. With its low sequence similarity to piggyBac, PLE-wu will contribute to the understanding the mechanism of PLE transposition, as well as design of new transposon systems with higher activity. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca)

OpenAIRE

Liu, Wei; Zhao, Yonghui; Liu, Zhaoliang; Zhang, Ying; Lian, Zhengxing; Li, Ning

2006-01-01

Abstract Background The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda was constructed in this study. Results This BAC library contains 198,844 clones with an average insert size of 108 kb, which represents approximately seven equivalents o...

A nucleolus-predominant piggyBac transposase, NP-mPB, mediates elevated transposition efficiency in mammalian cells.

Science.gov (United States)

Hong, Jin-Bon; Chou, Fu-Ju; Ku, Amy T; Fan, Hsiang-Hsuan; Lee, Tung-Lung; Huang, Yung-Hsin; Yang, Tsung-Lin; Su, I-Chang; Yu, I-Shing; Lin, Shu-Wha; Chien, Chung-Liang; Ho, Hong-Nerng; Chen, You-Tzung

2014-01-01

PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase) codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP) signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB). Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3-4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells.

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

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Blackmon Barbara P

2011-07-01

Full Text Available Abstract Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus

International Nuclear Information System (INIS)

Jang Songhun; Zhou Fang; Xia Laixin; Zhao Wei; Cheng Hanhua; Zhou Rongjia

2006-01-01

A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes

An efficient approach to BAC based assembly of complex genomes.

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Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; Batley, Jacqueline; Šimková, Hana; Doležel, Jaroslav; Edwards, David

2016-01-01

There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.

A BAC-based transgenic mouse specifically expresses an inducible Cre in the urothelium.

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Tian Huai Shen

Full Text Available Cre-loxp mediated conditional knockout strategy has played critical roles for revealing functions of many genes essential for development, as well as the causal relationships between gene mutations and diseases in the postnatal adult mice. One key factor of this strategy is the availability of mice with tissue- or cell type-specific Cre expression. However, the success of the traditional molecular cloning approach to generate mice with tissue specific Cre expression often depends on luck. Here we provide a better alternative by using bacterial artificial chromosome (BAC-based recombineering to insert iCreERT2 cDNA at the ATG start of the Upk2 gene. The BAC-based transgenic mice express the inducible Cre specifically in the urothelium as demonstrated by mRNA expression and staining for LacZ expression after crossing with a Rosa26 reporter mouse. Taking into consideration the size of the gene of interest and neighboring genes included in a BAC, this method should be widely applicable for generation of mice with tissue specific gene expression or deletions in a more specific manner than previously reported.

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes

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Gallus, Susanne; Janke, Axel

2017-01-01

Abstract Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. PMID:28985298

Thirty-six Cases of Pseudobulbar Palsy Treated by Needling with Prompt and Deep Insertion

Institute of Scientific and Technical Information of China (English)

Chen Hong

2006-01-01

@@ Pseudobulbar palsy refers to bulbar paralysis due to the upper motor neuron injury, which is one of the severe complications of cerebrovascular diseases.The author has treated 36 cases of the disease with acupuncture by a prompt and deep insertion technique, and achieved satisfactory therapeutic results. A report follows.

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.

Science.gov (United States)

Lammers, Fritjof; Gallus, Susanne; Janke, Axel; Nilsson, Maria A

2017-10-01

Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Application of Deep Cryogenic Treatment to Uncoated Tungsten Carbide Inserts in the Turning of AISI 304 Stainless Steel

Science.gov (United States)

Özbek, Nursel Altan; Çİçek, Adem; Gülesİn, Mahmut; Özbek, Onur

2016-12-01

This study investigated the effects of deep cryogenic treatment (DCT) on the wear performance of uncoated tungsten carbide inserts. AISI 304 austenitic stainless steel, widely used in industry, was selected as the workpiece material. Cutting experiments showed that the amount of wear significantly increased with increasing cutting speed. In addition, it was found that DCT contributed to the wear resistance of the turning inserts. The treated turning inserts were less worn by 48 and 38 pct in terms of crater wear and notch wear, respectively, whereas they exhibited up to 18 pct superior wear performance in terms of flank wear. This was attributed to the precipitation of new and finer η-carbides and their homogeneous distribution in the microstructure of the tungsten carbide material after deep cryogenic treatment. Analyses via image processing, hardness measurements, and SEM observations confirmed these findings.

Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy

Science.gov (United States)

2011-01-01

Background DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery. Results We have observed that (1) the Tol2 transposase (but not piggyBac) is highly sensitive to molecular engineering; (2) the piggyBac donor with only the 40 bp 3'-and 67 bp 5'-terminal repeat domain is sufficient for effective transposition; and (3) a small amount of piggyBac transposases results in robust transposition suggesting the piggyBac transpospase is highly active. Performing genome-wide target profiling on data sets obtained by retrieving chromosomal targeting sequences from individual clones, we have identified several piggyBac and Tol2 hotspots and observed that (4) piggyBac and Tol2 display a clear difference in targeting preferences in the human genome. Finally, we have observed that (5) only sites with a particular sequence context can be targeted by either piggyBac or Tol2. Conclusions The non-overlapping targeting preference of piggyBac and Tol2 makes them complementary research tools for manipulating mammalian genomes. PiggyBac is the most promising transposon-based vector system for achieving site-specific targeting of therapeutic genes due to the flexibility of its transposase for being molecularly engineered. Insights from this study will provide a basis for engineering piggyBac transposases to achieve site-specific therapeutic gene targeting. PMID:21447194

Fight Bac! | Partnership for Food Safety Education

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Fight Bac! Fight Bac! Fight Bac! Partnership for Food Safety Education Supporting consumers to & Symptoms Food Safety Glossary Food Safety Education Food Safety Education Month 2017 Don't Wing Spanish Resources Food Safety Education Food Safety Education Month 2017 Don't Wing It The Story of Your

Sequencing of BAC pools by different next generation sequencing platforms and strategies

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Scholz Uwe

2011-10-01

Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening

Institute of Scientific and Technical Information of China (English)

SU Ai-guo; LI Shuang-shuang; LIU Guo-zheng; LEI Bin-bin; KANG Ding-ming; LI Zhao-hu; MA Zhi-ying; HUA Jin-ping

2014-01-01

The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artiifcial chromosome (BAC) library. Thirty-ifve primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and veriifed for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be ampliifed, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

Construction of a llama bacterial artificial chromosome library with approximately 9-fold genome equivalent coverage.

Science.gov (United States)

Airmet, K W; Hinckley, J D; Tree, L T; Moss, M; Blumell, S; Ulicny, K; Gustafson, A K; Weed, M; Theodosis, R; Lehnardt, M; Genho, J; Stevens, M R; Kooyman, D L

2012-01-01

The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be 2.4 × 10⁹ bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.

Efficacy of two antiseptic regimens on skin colonization of insertion sites for two different catheter types: a randomized, clinical trial.

Science.gov (United States)

Lutz, Juergen Thomas; Diener, Isabel Victoria; Freiberg, Kerstin; Zillmann, Robert; Shah-Hosseini, Kija; Seifert, Harald; Berger-Schreck, Bettina; Wisplinghoff, Hilmar

2016-12-01

Catheter-related bloodstream infections affect patients in surgical and intensive care settings worldwide, causing complications, aggravation of existing symptoms and increased length of stay. The trial aimed at comparing two registered skin antiseptics with respect to their residual and therefore infection-preventing effects. In a parallel, monocentric, prospective, triple-blind, randomized trial the difference in bacterial recolonization of catheter skin sites in central venous (CVC) and epidural catheters (EC) was investigated by comparing two alcoholic-based skin disinfectants. Patients receiving planned surgeries or intensive care were eligible for the trial. Those in the trial group received skin disinfection with the additive octenidine dihydrochloride (OCT) (n = 51), those in the control group were treated with benzalkonium chloride as additive (BAC) (n = 59) prior to catheter insertion. Randomization was carried out by assigning patients to groups week-wise. Endpoints of the investigation were skin colonization of the catheter site counted in colony forming units per swab at three time points: (1) prior to catheter insertion, on untreated skin; (2) directly after catheter insertion, prior to sterile coverage; (3) 48 h after catheter insertion. The hypothesis was tested by a Wilcoxon test with a two-sided alpha = 5 %. From second to third swab, recolonization of the catheter-surrounding skin was significantly lower in the trial group for both sorts of catheters: delta 2-3 OCT group: 0.72 (95 % CI: 0.42; 1.02); delta 2-3 BAC group: 1.97 (95 % CI: 1.45; 2.50); p < 0.001. None of the patients enrolled developed a catheter-related blood stream infection (CRBSI) during follow-up. Previous studies have shown that skin colonization is strongly associated with the occurrence of CRBSI. This randomized controlled trial supports the observations made in previous trials that octenidine dihydrochloride in disinfectants is more effective than agents

Upper extremity deep venous thrombosis after port insertion: What are the risk factors?

Science.gov (United States)

Tabatabaie, Omidreza; Kasumova, Gyulnara G; Kent, Tara S; Eskander, Mariam F; Fadayomi, Ayotunde B; Ng, Sing Chau; Critchlow, Jonathan F; Tawa, Nicholas E; Tseng, Jennifer F

2017-08-01

Totally implantable venous access devices (ports) are widely used, especially for cancer chemotherapy. Although their use has been associated with upper extremity deep venous thrombosis, the risk factors of upper extremity deep venous thrombosis in patients with a port are not studied adequately. The Healthcare Cost and Utilization Project's Florida State Ambulatory Surgery and Services Database was queried between 2007 and 2011 for patients who underwent outpatient port insertion, identified by Current Procedural Terminology code. Patients were followed in the State Ambulatory Surgery and Services Database, State Inpatient Database, and State Emergency Department Database for upper extremity deep venous thrombosis occurrence. The cohort was divided into a test cohort and a validation cohort based on the year of port placement. A multivariable logistic regression model was developed to identify risk factors for upper extremity deep venous thrombosis in patients with a port. The model then was tested on the validation cohort. Of the 51,049 patients in the derivation cohort, 926 (1.81%) developed an upper extremity deep venous thrombosis. On multivariate analysis, independently significant predictors of upper extremity deep venous thrombosis included age deep venous thrombosis (odds ratio = 1.77), all-cause 30-day revisit (odds ratio = 2.36), African American race (versus white; odds ratio = 1.86), and other nonwhite races (odds ratio = 1.35). Additionally, compared with genitourinary malignancies, patients with gastrointestinal (odds ratio = 1.55), metastatic (odds ratio = 1.76), and lung cancers (odds ratio = 1.68) had greater risks of developing an upper extremity deep venous thrombosis. This study identified major risk factors of upper extremity deep venous thrombosis. Further studies are needed to evaluate the appropriateness of thromboprophylaxis in patients at greater risk of upper extremity deep venous thrombosis. Copyright © 2017 Elsevier Inc

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

Directory of Open Access Journals (Sweden)

Ritland Carol

2009-08-01

Full Text Available Abstract Background Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs and full-length (FLcDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. Results We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR and a cytochrome P450 (CYP720B4 from a non-arrayed genomic BAC library of white spruce (Picea glauca. Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR and 94 kbp (CYP720B4 long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs, high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. Conclusion We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene

Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome.

Science.gov (United States)

Hamberger, Björn; Hall, Dawn; Yuen, Mack; Oddy, Claire; Hamberger, Britta; Keeling, Christopher I; Ritland, Carol; Ritland, Kermit; Bohlmann, Jörg

2009-08-06

Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR) and a cytochrome P450 (CYP720B4) from a non-arrayed genomic BAC library of white spruce (Picea glauca). Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR) and 94 kbp (CYP720B4) long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs), high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene families can be isolated in a gene-specific fashion. The

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

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Jinfeng Chen

2017-01-01

Full Text Available Background Transposable element (TE polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools. Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD of TE insertions allowing it to report TE polymorphism loci with single base pair precision. Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be

Molecular and FISH analyses of a 53-kbp intact DNA fragment inserted by biolistics in wheat (Triticum aestivum L.) genome.

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Partier, A; Gay, G; Tassy, C; Beckert, M; Feuillet, C; Barret, P

2017-10-01

A large, 53-kbp, intact DNA fragment was inserted into the wheat ( Triticum aestivum L.) genome. FISH analyses of individual transgenic events revealed multiple insertions of intact fragments. Transferring large intact DNA fragments containing clusters of resistance genes or complete metabolic pathways into the wheat genome remains a challenge. In a previous work, we showed that the use of dephosphorylated cassettes for wheat transformation enabled the production of simple integration patterns. Here, we used the same technology to produce a cassette containing a 44-kb Arabidopsis thaliana BAC, flanked by one selection gene and one reporter gene. This 53-kb linear cassette was integrated in the bread wheat (Triticum aestivum L.) genome by biolistic transformation. Our results showed that transgenic plants harboring the entire cassette were generated. The inheritability of the cassette was demonstrated in the T1 and T2 generation. Surprisingly, FISH analysis performed on T1 progeny of independent events identified double genomic insertions of intact fragments in non-homoeologous positions. Inheritability of these double insertions was demonstrated by FISH analysis of the T1 generation. Relative conclusions that can be drawn from molecular or FISH analysis are discussed along with future prospects of the engineering of large fragments for wheat transformation or genome editing.

Design and testing of microfabricated surgical tools for large animal probe insertion

Energy Technology Data Exchange (ETDEWEB)

Jorgensen, Shelly [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-08-05

Neural probes provide therapeutic stimulation for neuropsychiatric disorders or record neural activity to investigate the workings of the brain. Researchers utilize 6 mm long temporary silicon stiffeners attached with biodissolvable adhesive to insert flexible neural probes into rat brains, but increasing the probe length fivefold makes inserting large animal probes a significant challenge because of an increased potential for buckling. This study compared the insertion success rates of 6 mm and 30 mm long silicon stiffeners that were 80 μm wide and 30 μm thick, and ascertained the material thickness and modulus of elasticity that would provide successful insertion for a 30 mm probe. Using a microdrive, stiffeners were inserted into an agarose brain phantom at controlled insertion speeds while being video-recorded. Twenty-five percent of the 30 mm silicon stiffeners fully inserted at speeds approximately four times higher than the target rate of 0.13 mm/s, while 100 percent of the 6 mm silicon stiffeners inserted successfully at target speed. Critical buckling loads (P_cr) were calculated for the 6 mm and 30 mm silicon stiffeners, and for 30 mm diamond and tungsten stiffeners, with thicknesses varying from 30-80 μm. Increasing the thickness of the material by 10 μm, 20 μm and 30 μm improved the P_cr by 2.4, 4.7 and 8.2 times, respectively, independent of the material, and substituting diamond for silicon multiplied the buckling capacity by 5.0 times. Stiffeners made of silicon for large animal probe insertion are not strong enough to withstand buckling upon insertion without a significant increase in thickness. Replacing silicon with diamond and increasing the thickness of the stiffener to 50 μm would afford a stiffener with the same P_cr capacity as the 6 mm silicon stiffener that had a 100 percent insertion success rate. Experiments should continue with diamond to determine a minimum thickness that will ensure successful

Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

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Asamizu, Erika; Shirasawa, Kenta; Hirakawa, Hideki; Sato, Shusei; Tabata, Satoshi; Yano, Kentaro; Ariizumi, Tohru; Shibata, Daisuke; Ezura, Hiroshi

2012-01-01

A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. PMID:23227037

Generation of a BAC-based physical map of the melon genome

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Puigdomènech Pere

2010-05-01

Full Text Available Abstract Background Cucumis melo (melon belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high intra-specific genetic variation, morphologic diversity and a small genome size (450 Mb, which make this species suitable for a great variety of molecular and genetic studies that can lead to the development of tools for breeding varieties of the species. A number of genetic and genomic resources have already been developed, such as several genetic maps and BAC genomic libraries. These tools are essential for the construction of a physical map, a valuable resource for map-based cloning, comparative genomics and assembly of whole genome sequencing data. However, no physical map of any Cucurbitaceae has yet been developed. A project has recently been started to sequence the complete melon genome following a whole-genome shotgun strategy, which makes use of massive sequencing data. A BAC-based melon physical map will be a useful tool to help assemble and refine the draft genome data that is being produced. Results A melon physical map was constructed using a 5.7 × BAC library and a genetic map previously developed in our laboratories. High-information-content fingerprinting (HICF was carried out on 23,040 BAC clones, digesting with five restriction enzymes and SNaPshot labeling, followed by contig assembly with FPC software. The physical map has 1,355 contigs and 441 singletons, with an estimated physical length of 407 Mb (0.9 × coverage of the genome and the longest contig being 3.2 Mb. The anchoring of 845 BAC clones to 178 genetic markers (100 RFLPs, 76 SNPs and 2 SSRs also allowed the genetic positioning of 183 physical map contigs/singletons, representing 55 Mb (12% of the melon genome, to individual chromosomal loci. The melon FPC database is available for download at http://melonomics.upv.es/static/files/public/physical_map/. Conclusions Here we report the construction

Outcomes of inferior vena cava filter insertion in patients with lower extremity deep vein thrombosis for prevention of pulmonary thromboembolism: A single center retrospective analysis

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Park, Byung Jin; Kim, Jae Kyu; Yim, Nam Yeol; Kim, Hyoung Ook [Dept. of Radiology, Chonnam National University Hospital, Gwangju (Korea, Republic of); Kang, Yang Jun [Dept. of Radiology, Chonnam National University Hwasun Hospital, Hwasun (Korea, Republic of)

2017-07-15

To evaluate the mid- and long-term outcomes of inferior vena cava (IVC) filter insertion in patients with underlying deep vein thrombosis for prevention of pulmonary thromboembolism, based on a single center experience. A total of 166 IVC filter insertion procedures in 160 patients, between February 2004 and December 2014, were retrospectively reviewed. Severity of deep vein thrombosis, indwelling time of the IVC filter, retrieval rate, and complication rate depending on the type of IVC filter were analyzed based on the patients' radiologic findings and medical records. IVC filter insertion procedures were successfully performed in all patients. Among the 99 attempts at filter retrieval, 91 trials succeeded (91.9%, 91/99) and 8 trials failed. Indwelling time of the IVC filter showed a positive correlation with failure of filter retrieval (p = 0.01). There was no procedure-related complication after all IVC filter insertion procedures. Eight delayed complications (5.0%, 8/160 patients with IVC filter insertion) were observed [caval thrombosis below the IVC filter (n = 7) and IVC penetration (n = 1)]. Günther Tulip filter was associated with a significant incidence of complication (p = 0.036). IVC filter insertion in patients with lower extremity deep vein thrombosis for prevention of pulmonary thromboembolism can be regarded as a safe treatment modality with an acceptable complication rate.

Outcomes of inferior vena cava filter insertion in patients with lower extremity deep vein thrombosis for prevention of pulmonary thromboembolism: A single center retrospective analysis

International Nuclear Information System (INIS)

Park, Byung Jin; Kim, Jae Kyu; Yim, Nam Yeol; Kim, Hyoung Ook; Kang, Yang Jun

2017-01-01

To evaluate the mid- and long-term outcomes of inferior vena cava (IVC) filter insertion in patients with underlying deep vein thrombosis for prevention of pulmonary thromboembolism, based on a single center experience. A total of 166 IVC filter insertion procedures in 160 patients, between February 2004 and December 2014, were retrospectively reviewed. Severity of deep vein thrombosis, indwelling time of the IVC filter, retrieval rate, and complication rate depending on the type of IVC filter were analyzed based on the patients' radiologic findings and medical records. IVC filter insertion procedures were successfully performed in all patients. Among the 99 attempts at filter retrieval, 91 trials succeeded (91.9%, 91/99) and 8 trials failed. Indwelling time of the IVC filter showed a positive correlation with failure of filter retrieval (p = 0.01). There was no procedure-related complication after all IVC filter insertion procedures. Eight delayed complications (5.0%, 8/160 patients with IVC filter insertion) were observed [caval thrombosis below the IVC filter (n = 7) and IVC penetration (n = 1)]. Günther Tulip filter was associated with a significant incidence of complication (p = 0.036). IVC filter insertion in patients with lower extremity deep vein thrombosis for prevention of pulmonary thromboembolism can be regarded as a safe treatment modality with an acceptable complication rate

Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage

DEFF Research Database (Denmark)

Batth, Tanveer S; Olsen, Jesper V

2016-01-01

Protein phosphorylation, a process in which kinases modify serines, threonines, and tyrosines with phosphoryl groups is of major importance in eukaryotic biology. Protein phosphorylation events are key initiators of signaling responses which determine cellular outcomes after environmental...... and metabolic stimuli, and are thus highly regulated. Therefore, studying the mechanism of regulation by phosphorylation, and pinpointing the exact site of phosphorylation on proteins is of high importance. This protocol describes in detail a phosphoproteomics workflow for ultra-deep coverage by fractionating...

Computer Identification of Symptomatic Deep Venous Thrombosis Associated with Peripherally Inserted Central Catheters

Science.gov (United States)

Evans, R. Scott; Linford, Lorraine H.; Sharp, Jamie H.; White, Gayle; Lloyd, James F.; Weaver, Lindell K.

2007-01-01

Peripherally inserted central catheters (PICCs) are considered a safe method to provide long-term antibiotic therapy, chemotherapy and nutrition support. Deep venous thrombosis (DVT) is a complication that requires early PICC removal, may extend hospitalization and can result in pulmonary embolism. PICC insertion teams strive to understand risk factors and develop methods to prevent DVTs. However, they can only manage what they can measure. At LDS Hospital, identification of PICC associated DVTs was dependent on verbal notification or manual surveillance of more than a thousand free-text vascular reports. Accurate DVT rates were not known which hindered prevention. We describe the development of a computer application (PICC-DVT monitor) to identify PICC associated DVTs each day. A one-year evaluation of the monitor by the PICC team and a review of 445 random vascular reports found a positive predictive value of 98%, sensitivity of 94%, specificity of 100% and a PICC team associated DVT rate of 2.8%. PMID:18693831

Computer identification of symptomatic deep venous thrombosis associated with peripherally inserted venous catheters.

Science.gov (United States)

Evans, R Scott; Linford, Lorraine H; Sharp, Jamie H; White, Gayle; Lloyd, James F; Weaver, Lindell K

2007-10-11

Peripherally inserted central catheters (PICCs) are considered a safe method to provide long-term antibiotic therapy, chemotherapy and nutrition support. Deep venous thrombosis (DVT) is a complication that requires early PICC removal, may extend hospitalization and can result in pulmonary embolism. PICC insertion teams strive to understand risk factors and develop methods to prevent DVTs. However, they can only manage what they can measure. At LDS Hospital, identification of PICC associated DVTs was dependent on verbal notification or manual surveillance of more than a thousand free-text vascular reports. Accurate DVT rates were not known which hindered prevention. We describe the development of a computer application (PICC-DVT monitor) to identify PICC associated DVTs each day. A one-year evaluation of the monitor by the PICC team and a review of 445 random vascular reports found a positive predictive value of 98%, sensitivity of 94%, specificity of 100% and a PICC team associated DVT rate of 2.8%.

Management of facial burns with a collagen/glycosaminoglycan skin substitute-prospective experience with 12 consecutive patients with large, deep facial burns.

Science.gov (United States)

Klein, Matthew B; Engrav, Loren H; Holmes, James H; Friedrich, Jeffrey B; Costa, Beth A; Honari, Shari; Gibran, Nicole S

2005-05-01

Management of deep facial burns remains one of the greatest challenges in burn care. We have developed a protocol over the past 20 years for management of facial burns that includes excision and coverage with thick autograft. However, the results were not perfect. Deformities of the eyelids, nose and mouth as well as the prominence of skin graft junctures demonstrated the need to explore novel approaches. Integra has been used with success in the management of burns of the trunk and extremities. The purpose of this study was to prospectively evaluate the aesthetic outcome of the use of Integra for deep facial burns. Twelve consecutive patients underwent excision of large, deep facial burns and placement of Integra. Integra provides excellent color and minimally visible skin graft junctures. The texture is good but not as supple as thick autograft. Integra is not well suited for use in the coverage of eyelid burns due to the need to wait 2 weeks for adequate vascularization. In summary, thick autograft remains the gold standard for deep facial burns. However, for patients with extensive burns and limited donor sites, Integra provides an acceptable alternative.

De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley

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Scholz Uwe

2009-11-01

Full Text Available Abstract Background De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L. is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable. Results To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes. By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies. Conclusion The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.

Comparative analysis of catfish BAC end sequences with the zebrafish genome

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Abernathy Jason

2009-12-01

Full Text Available Abstract Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of 43,000 BAC end sequences and their applications for comparative genome analysis in catfish. Using these and the additional 20,000 existing BAC end sequences as a resource along with linkage mapping and existing physical map, conserved syntenic regions were identified between the catfish and zebrafish genomes. A total of 10,943 catfish BAC end sequences (17.3% had significant BLAST hits to the zebrafish genome (cutoff value ≤ e-5, of which 3,221 were unique gene hits, providing a platform for comparative mapping based on locations of these genes in catfish and zebrafish. Genetic linkage mapping of microsatellites associated with contigs allowed identification of large conserved genomic segments and construction of super scaffolds. Conclusion BAC end sequences and their associated polymorphic markers are great resources for comparative genome analysis in catfish. Highly conserved chromosomal regions were identified to exist between catfish and zebrafish. However, it appears that the level of conservation at local genomic regions are high while a high level of chromosomal shuffling and rearrangements exist between catfish and zebrafish genomes. Orthologous regions established through comparative analysis should facilitate both structural and functional genome analysis in catfish.

New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits

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Feltus Frank A

2011-07-01

Full Text Available Abstract Background Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18 to duodecaploid (12X = 108. Like in other large, repeat-rich plant genomes, this genomic complexity will hinder whole genome sequencing efforts. An extensive physical map providing enough information to resolve the homoeologous genomes would provide the necessary framework for accurate assembly of the switchgrass genome. Results A switchgrass BAC library constructed by partial digestion of nuclear DNA with EcoRI contains 147,456 clones covering the effective genome approximately 10 times based on a genome size of 3.2 Gigabases (~1.6 Gb effective. Restriction digestion and PFGE analysis of 234 randomly chosen BACs indicated that 95% of the clones contained inserts, ranging from 60 to 180 kb with an average of 120 kb. Comparative sequence analysis of two homoeologous genomic regions harboring orthologs of the rice OsBRI1 locus, a low-copy gene encoding a putative protein kinase and associated with biomass, revealed that orthologous clones from homoeologous chromosomes can be unambiguously distinguished from each other and correctly assembled to respective fingerprint contigs. Thus, the data obtained not only provide genomic resources for further analysis of switchgrass genome, but also improve efforts for an accurate genome sequencing strategy. Conclusions The construction of the first switchgrass BAC library and comparative analysis of

A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs

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Gong Shiaochin

2009-03-01

Full Text Available Abstract Background Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. Results We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1 subclone genes of interest into BAC linking vectors, (2 insert desired reporter genes into respective genes and (3 link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. Conclusion The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs.

Science.gov (United States)

Maye, Peter; Stover, Mary Louise; Liu, Yaling; Rowe, David W; Gong, Shiaochin; Lichtler, Alexander C

2009-03-13

Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP) reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1) subclone genes of interest into BAC linking vectors, (2) insert desired reporter genes into respective genes and (3) link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data

KAUST Repository

Allam, Amin

2015-07-14

Motivation: Next-generation sequencing generates large amounts of data affected by errors in the form of substitutions, insertions or deletions of bases. Error correction based on the high-coverage information, typically improves de novo assembly. Most existing tools can correct substitution errors only; some support insertions and deletions, but accuracy in many cases is low. Results: We present Karect, a novel error correction technique based on multiple alignment. Our approach supports substitution, insertion and deletion errors. It can handle non-uniform coverage as well as moderately covered areas of the sequenced genome. Experiments with data from Illumina, 454 FLX and Ion Torrent sequencing machines demonstrate that Karect is more accurate than previous methods, both in terms of correcting individual-bases errors (up to 10% increase in accuracy gain) and post de novo assembly quality (up to 10% increase in NGA50). We also introduce an improved framework for evaluating the quality of error correction.

Vector modifications to eliminate transposase expression following piggyBac-mediated transgenesis

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Chakraborty, Syandan; Ji, HaYeun; Chen, Jack; Gersbach, Charles A.; Leong, Kam W.

2014-01-01

Transgene insertion plays an important role in gene therapy and in biological studies. Transposon-based systems that integrate transgenes by transposase-catalyzed “cut-and-paste” mechanism have emerged as an attractive system for transgenesis. Hyperactive piggyBac transposon is particularly promising due to its ability to integrate large transgenes with high efficiency. However, prolonged expression of transposase can become a potential source of genotoxic effects due to uncontrolled transposition of the integrated transgene from one chromosomal locus to another. In this study we propose a vector design to decrease post-transposition expression of transposase and to eliminate the cells that have residual transposase expression. We design a single plasmid construct that combines the transposase and the transpositioning transgene element to share a single polyA sequence for termination. Consequently, the separation of the transposase element from the polyA sequence after transposition leads to its deactivation. We also co-express Herpes Simplex Virus thymidine kinase (HSV-tk) with the transposase. Therefore, cells having residual transposase expression can be eliminated by the administration of ganciclovir. We demonstrate the utility of this combination transposon system by integrating and expressing a model therapeutic gene, human coagulation Factor IX, in HEK293T cells. PMID:25492703

Genetic stability of pestivirus genomes cloned into BACs

DEFF Research Database (Denmark)

Rasmussen, Thomas Bruun; Reimann, Ilona; Uttenthal, Åse

pestivirus genomes to demonstrate the suitability of the BAC vector for harbouring pestivirus genomes. Two BAC clones, comprising the complete genomes of BDV Gifhorn (pBeloGif3) and CSFV Paderborn (pBeloPader10) were passaged 15 times in E.coli representing at least 360 bacteria generations. From 15th...

454 sequencing of pooled BAC clones on chromosome 3H of barley

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Yamaji Nami

2011-05-01

Full Text Available Abstract Background Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp. Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. Results We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. Conclusions We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.

Large-scale Labeled Datasets to Fuel Earth Science Deep Learning Applications

Science.gov (United States)

Maskey, M.; Ramachandran, R.; Miller, J.

2017-12-01

Deep learning has revolutionized computer vision and natural language processing with various algorithms scaled using high-performance computing. However, generic large-scale labeled datasets such as the ImageNet are the fuel that drives the impressive accuracy of deep learning results. Large-scale labeled datasets already exist in domains such as medical science, but creating them in the Earth science domain is a challenge. While there are ways to apply deep learning using limited labeled datasets, there is a need in the Earth sciences for creating large-scale labeled datasets for benchmarking and scaling deep learning applications. At the NASA Marshall Space Flight Center, we are using deep learning for a variety of Earth science applications where we have encountered the need for large-scale labeled datasets. We will discuss our approaches for creating such datasets and why these datasets are just as valuable as deep learning algorithms. We will also describe successful usage of these large-scale labeled datasets with our deep learning based applications.

Inferior vena cava filter insertion through the popliteal vein: enabling the percutaneous endovenous intervention of deep vein thrombosis with a single venous access approach in a single session

Science.gov (United States)

Kim, Hyoung Ook; Kim, Jae Kyu; Park, Jin Gyoon; Yim, Nam Yeol; Kang, Yang Jun; Jung, Hye Doo

2016-01-01

PURPOSE We aimed to evaluate the efficiency of placing an inferior vena cava (IVC) filter through the same popliteal vein access site used for percutaneous endovenous intervention in patients with extensive lower extremity deep vein thrombosis. METHODS This retrospective study included 21 patients who underwent IVC filter insertion through the popliteal vein over a three-year period. Patient medical records were reviewed for the location of the deep vein thrombosis, result of filter removal, and total number of endovascular procedures needed for filter insertion and recanalization of the lower extremity venous system. Follow-up lower extremity computed tomography (CT) venography was also reviewed in each patient to assess the degree of filter tilt in the IVC. RESULTS All patients had extensive lower extremity deep vein thrombosis involving the iliac vein and/or femoral vein. Seventeen patients showed deep vein thrombosis of the calf veins. In all patients, IVC filter insertion and the recanalization procedure were performed during a single procedure through the single popliteal vein access site. In the 17 patients undergoing follow-up CT, the mean tilt angle of the filter was 7.14°±4.48° in the coronal plane and 8.77°±5.49° in the sagittal plane. Filter retrieval was successful in 16 of 17 patients (94.1%) in whom filter retrieval was attempted. CONCLUSION Transpopliteal IVC filter insertion is an efficient technique that results in low rates of significant filter tilt and enables a single session procedure using a single venous access site for filter insertion and percutaneous endovenous intervention. PMID:27559713

GenMapDB: a database of mapped human BAC clones

OpenAIRE

Morley, Michael; Arcaro, Melissa; Burdick, Joshua; Yonescu, Raluca; Reid, Thomas; Kirsch, Ilan R.; Cheung, Vivian G.

2001-01-01

GenMapDB (http://genomics.med.upenn.edu/genmapdb) is a repository of human bacterial artificial chromosome (BAC) clones mapped by our laboratory to sequence-tagged site markers. Currently, GenMapDB contains over 3000 mapped clones that span 19 chromosomes, chromosomes 2, 4, 5, 9–22, X and Y. This database provides positional information about human BAC clones from the RPCI-11 human male BAC library. It also contains restriction fragment analysis data and end sequen...

An all-in-one, Tet-On 3G inducible PiggyBac system for human pluripotent stem cells and derivatives.

Science.gov (United States)

Randolph, Lauren N; Bao, Xiaoping; Zhou, Chikai; Lian, Xiaojun

2017-05-08

Human pluripotent stem cells (hPSCs) offer tremendous promise in tissue engineering and cell-based therapies due to their unique combination of two properties: pluripotency and unlimited proliferative capacity. However, directed differentiation of hPSCs to clinically relevant cell lineages is needed to achieve the goal of hPSC-based therapies. This requires a deep understanding of how cell signaling pathways converge on the nucleus to control differentiation and the ability to dissect gene function in a temporal manner. Here, we report the use of the PiggyBac transposon and a Tet-On 3G drug-inducible gene expression system to achieve versatile inducible gene expression in hPSC lines. Our new system, XLone, offers improvement over previous Tet-On systems with significantly reduced background expression and increased sensitivity to doxycycline. Transgene expression in hPSCs is tightly regulated in response to doxycycline treatment. In addition, the PiggyBac elements in our XLone construct provide a rapid and efficient strategy for generating stable transgenic hPSCs. Our inducible gene expression PiggyBac transposon system should facilitate the study of gene function and directed differentiation in human stem cells.

Conversion of BAC Clones into Binary BAC (BIBAC) Vectors and Their Delivery into Basidiomycete Fungal Cells Using Agrobacterium tumefaciens

KAUST Repository

Ali, Shawkat

2014-09-19

The genetic transformation of certain organisms, required for gene function analysis or complementation, is often not very efficient, especially when dealing with large gene constructs or genomic fragments. We have adapted the natural DNA transfer mechanism from the soil pathogenic bacterium Agrobacterium tumefaciens, to deliver intact large DNA constructs to basidiomycete fungi of the genus Ustilago where they stably integrated into their genome. To this end, Bacterial Artificial Chromosome (BAC) clones containing large fungal genomic DNA fragments were converted via a Lambda phage-based recombineering step to Agrobacterium transfer-competent binary vectors (BIBACs) with a Ustilago-specific selection marker. The fungal genomic DNA fragment was subsequently successfully delivered as T-DNA through Agrobacterium-mediated transformation into Ustilago species where an intact copy stably integrated into the genome. By modifying the recombineering vector, this method can theoretically be adapted for many different fungi.

Time to Detection with BacT/Alert FA Plus Compared to BacT/Alert FA Blood Culture Media.

Science.gov (United States)

Nutman, A; Fisher Even-Tsur, S; Shapiro, G; Braun, T; Schwartz, D; Carmeli, Y

2016-09-01

Rapid identification of the causative pathogen in patients with bacteremia allows adjustment of antibiotic therapy and improves patient outcomes. We compared in vitro and real-life time to detection (TTD) of two blood culture media, BacT/Alert FA (FA) and BacT/Alert FA Plus (FA Plus), for the nine most common species of bacterial pathogens recovered from blood samples. Experimental data from simulated cultures was compared with microbiology records of TTD for both culture media with growth of the species of interest in clinical blood cultures. In the experimental conditions, median TTD was 3.8 hours (23.9 %) shorter using FA Plus media. The magnitude of reduction differed between species. Similarly, in real life data, FA Plus had shorter TTD than FA media; however, the difference between culture media was smaller, and median TTD was only 1 hour (8.5 %) less. We found shorter TTD with BacT/Alert FA Plus culture media, both experimentally and in real-life conditions and unrelated to antibiotic neutralization, highlighting the importance of appropriate blood culture media selection.

78 FR 54996 - Information Reporting by Applicable Large Employers on Health Insurance Coverage Offered Under...

Science.gov (United States)

2013-09-09

... Information Reporting by Applicable Large Employers on Health Insurance Coverage Offered Under Employer... credit to help individuals and families afford health insurance coverage purchased through an Affordable... or group health insurance coverage offered by an employer to the employee that is (1) a governmental...

Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase.

Directory of Open Access Journals (Sweden)

Guillaume Manat

Full Text Available Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2 catalyze the dephosphorylation of C55-PP molecules on the same (outer side of the plasma membrane.

Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains.

Science.gov (United States)

Kurushima, Jun; Ike, Yasuyoshi; Tomita, Haruyoshi

2016-09-01

Bacteriocin 41 (Bac41) is the plasmid-encoded bacteriocin produced by the opportunistic pathogen Enterococcus faecalis Its genetic determinant consists of bacL1 (effector), bacL2 (regulator), bacA (effector), and bacI (immunity). The secreted effectors BacL1 and BacA coordinate to induce the lytic cell death of E. faecalis Meanwhile, the immunity factor BacI provides self-resistance to the Bac41 producer, E. faecalis, against the action of BacL1 and BacA. In this study, we demonstrated that more than half of the 327 clinical strains of E. faecalis screened had functional Bac41 genes. Analysis of the genetic structure of the Bac41 genes in the DNA sequences of the E. faecalis strains revealed that the Bac41-like genes consist of a relatively conserved region and a variable region located downstream from bacA Based on similarities in the variable region, the Bac41-like genes could be classified into type I, type IIa, and type IIb. Interestingly, the distinct Bac41 types had specific immunity factors for self-resistance, BacI1 or BacI2, and did not show cross-immunity to the other type of effector. We also demonstrated experimentally that the specificity of the immunity was determined by the combination of the C-terminal region of BacA and the presence of the unique BacI1 or BacI2 factor. These observations suggested that Bac41-like bacteriocin genes are extensively disseminated among E. faecalis strains in the clinical environment and can be grouped into at least three types. It was also indicated that the partial diversity results in specificity of self-resistance which may offer these strains a competitive advantage. Bacteriocins are antibacterial effectors produced by bacteria. In general, a bacteriocin-coding gene is accompanied by a cognate immunity gene that confers self-resistance on the bacteriocin-producing bacterium itself. We demonstrated that one of the bacteriocins, Bac41, is disseminated among E. faecalis clinical strains and the Bac41 subtypes with

A first generation BAC-based physical map of the rainbow trout genome

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Thorgaard Gary H

2009-10-01

Full Text Available Abstract Background Rainbow trout (Oncorhynchus mykiss are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species. Results The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF method. The clones were assembled into physical map contigs using the finger-printing contig (FPC program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1 comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2 anchoring large contigs to the microsatellite-based genetic linkage map. Conclusion The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome

Numerical simulation of the insert chemistry of the hollow cathode from the deep space 1 ion engine 30,000 Hrs life test

OpenAIRE

Coletti, Michele; Grubisic, Angelo; Gabriel, Stephen

2007-01-01

A model for the insert chemistry developed by the authors and based on the knowledge of the BaO – CaO – Al2O3 ternary system the ELT discharge cathode insert from the Deep Space 1 life test has been simulated. The computed data show a good agreement with the experimental one; the agreement increase with the imposition of boundary conditions closer to the experimental evidence. Tungsten deposition effect have been introduced into the model using experimental data and further improving the agre...

A Bac Library and Paired-PCR Approach to Mapping and Completing the Genome Sequence of Sulfolobus Solfataricus P2

DEFF Research Database (Denmark)

She, Qunxin; Confalonieri, F.; Zivanovic, Y.

2000-01-01

The original strategy used in the Sulfolobus solfatnricus genome project was to sequence non overlapping, or minimally overlapping, cosmid or lambda inserts without constructing a physical map. However, after only about two thirds of the genome sequence was completed, this approach became counter......-productive because there was a high sequence bias in the cosmid and lambda libraries. Therefore, a new approach was devised for linking the sequenced regions which may be generally applicable. BAC libraries were constructed and terminal sequences of the clones were determined and used for both end mapping and PCR...

Solving Large-Scale TSP Using a Fast Wedging Insertion Partitioning Approach

Directory of Open Access Journals (Sweden)

Zuoyong Xiang

2015-01-01

Full Text Available A new partitioning method, called Wedging Insertion, is proposed for solving large-scale symmetric Traveling Salesman Problem (TSP. The idea of our proposed algorithm is to cut a TSP tour into four segments by nodes’ coordinate (not by rectangle, such as Strip, FRP, and Karp. Each node is located in one of their segments, which excludes four particular nodes, and each segment does not twist with other segments. After the partitioning process, this algorithm utilizes traditional construction method, that is, the insertion method, for each segment to improve the quality of tour, and then connects the starting node and the ending node of each segment to obtain the complete tour. In order to test the performance of our proposed algorithm, we conduct the experiments on various TSPLIB instances. The experimental results show that our proposed algorithm in this paper is more efficient for solving large-scale TSPs. Specifically, our approach is able to obviously reduce the time complexity for running the algorithm; meanwhile, it will lose only about 10% of the algorithm’s performance.

Frameless Stereotactic Insertion of Viewsite Brain Access System with Microscope-Mounted Tracking Device for Resection of Deep Brain Lesions: Technical Report.

Science.gov (United States)

White, Tim; Chakraborty, Shamik; Lall, Rohan; Fanous, Andrew A; Boockvar, John; Langer, David J

2017-02-04

The surgical management of deep brain tumors is often challenging due to the limitations of stereotactic needle biopsies and the morbidity associated with transcortical approaches. We present a novel microscopic navigational technique utilizing the Viewsite Brain Access System (VBAS) (Vycor Medical, Boca Raton, FL, USA) for resection of a deep parietal periventricular high-grade glioma as well as another glioma and a cavernoma with no related morbidity. The approach utilized a navigational tracker mounted on a microscope, which was set to the desired trajectory and depth. It allowed gentle continuous insertion of the VBAS directly to a deep lesion under continuous microscopic visualization, increasing safety by obviating the need to look up from the microscope and thus avoiding loss of trajectory. This technique has broad value for the resection of a variety of deep brain lesions.

The complexity of Rhipicephalus (Boophilus microplus genome characterised through detailed analysis of two BAC clones

Directory of Open Access Journals (Sweden)

Valle Manuel

2011-07-01

Full Text Available Abstract Background Rhipicephalus (Boophilus microplus (Rmi a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as Drosophila and Anopheles are too taxonomically distant for a reference in tick genomic sequence analysis. This study focuses on the de-novo assembly of two R. microplus BAC sequences from the understudied R microplus genome. Based on available R. microplus sequenced resources and comparative analysis, tick genomic structure and functional predictions identify complex gene structures and genomic targets expressed during tick-cattle interaction. Results In our BAC analyses we have assembled, using the correct positioning of BAC end sequences and transcript sequences, two challenging genomic regions. Cot DNA fractions compared to the BAC sequences confirmed a highly repetitive BAC sequence BM-012-E08 and a low repetitive BAC sequence BM-005-G14 which was gene rich and contained short interspersed elements (SINEs. Based directly on the BAC and Cot data comparisons, the genome wide frequency of the SINE Ruka element was estimated. Using a conservative approach to the assembly of the highly repetitive BM-012-E08, the sequence was de-convoluted into three repeat units, each unit containing an 18S, 5.8S and 28S ribosomal RNA (rRNA encoding gene sequence (rDNA, related internal transcribed spacer and complex intergenic region. In the low repetitive BM-005-G14, a novel gene complex was found between to 2 genes on the same strand. Nested in the second intron of a large 9 Kb papilin gene was a helicase gene. This helicase overlapped in two exonic regions with the papilin. Both these genes were shown expressed in different tick life stage important in ectoparasite interaction with the host. Tick specific sequence

Bioinspired microneedle insertion for deep and precise skin penetration with low force: Why the application of mechanophysical stimuli should be considered.

Science.gov (United States)

Kim, Jonghun; Park, Sungmin; Nam, Gyungmok; Choi, Young; Woo, Seungpyo; Yoon, Sang-Hee

2018-02-01

A mosquito is known to precisely and easily insert its proboscis to the human skin by pressing down a labium and vibrating a fascicle bundle. Its advanced skin-piercing mechanisms indicate that skin resistance to the insertion of needle-like objects can be changed by the application of mechanophysical stimuli. Here, we characterize the effect of the application of mechanophysical stimuli on skin resistance to microneedle insertion to find clues for inserting a microneedle in a deep and precise fashion with low force. Microneedles with a diameter of 60-140µm are inserted at a velocity of 0.1-2.0mm/s to full-thickness porcine skins while either uniaxial/equibiaxial stretch of 0-20% or mechanical vibration at a frequency of 1 to 1000Hz and an amplitude of 1-10µm is applied to the skins as static or dynamic mechanophysical stimulus, respectively. The values of force and depth at two events of skin puncture and maximum penetration are measured to explore changes in skin resistance induced by the application of external stimuli. The static mechanophysical stimulus applied to the skin mainly affects the precision of microneedle insertion; the application of dynamic mechanophysical stimulus controls the value and deviation of skin resistance to microneedle insertion. The application of mechanophysical stimuli, inspired from a mosquito, therefore allows a microneedle to be deeply and easily inserted to the skin in a controlled way. The findings will have broad impacts on microneedle-mediated applications and lead to an in-depth understanding of skin biomechanics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bacterial contamination of platelet components not detected by BacT/ALERT®.

Science.gov (United States)

Abela, M A; Fenning, S; Maguire, K A; Morris, K G

2018-02-01

To investigate the possible causes for false negative results in BacT/ALERT ® 3D Signature System despite bacterial contamination of platelet units. The Northern Ireland Blood Transfusion Service (NIBTS) routinely extends platelet component shelf life to 7 days. Components are sampled and screened for bacterial contamination using an automated microbial detection system, the BacT/ALERT ® 3D Signature System. We report on three platelet components with confirmed bacterial contamination, which represent false negative BacT/ALERT ® results and near-miss serious adverse events. NIBTS protocols for risk reduction of bacterial contamination of platelet components are described. The methodology for bacterial detection using BacT/ALERT ® is outlined. Laboratory tests, relevant patient details and relevant follow-up information are analysed. In all three cases, Staphylococcus aureus was isolated from the platelet residue and confirmed on terminal sub-culture using BacT/ALERT ® . In two cases, S. aureus with similar genetic makeup was isolated from the donors. Risk reduction measures for bacterial contamination of platelet components are not always effective. Automated bacterial culture detection does not eliminate the risk of bacterial contamination. Visual inspection of platelet components prior to release, issue and administration remains an important last line of defence. © 2017 British Blood Transfusion Society.

Towards Semantic Web Services on Large, Multi-Dimensional Coverages

Science.gov (United States)

Baumann, P.

2009-04-01

Observed and simulated data in the Earth Sciences often come as coverages, the general term for space-time varying phenomena as set forth by standardization bodies like the Open GeoSpatial Consortium (OGC) and ISO. Among such data are 1-d time series, 2-D surface data, 3-D surface data time series as well as x/y/z geophysical and oceanographic data, and 4-D metocean simulation results. With increasing dimensionality the data sizes grow exponentially, up to Petabyte object sizes. Open standards for exploiting coverage archives over the Web are available to a varying extent. The OGC Web Coverage Service (WCS) standard defines basic extraction operations: spatio-temporal and band subsetting, scaling, reprojection, and data format encoding of the result - a simple interoperable interface for coverage access. More processing functionality is available with products like Matlab, Grid-type interfaces, and the OGC Web Processing Service (WPS). However, these often lack properties known as advantageous from databases: declarativeness (describe results rather than the algorithms), safe in evaluation (no request can keep a server busy infinitely), and optimizable (enable the server to rearrange the request so as to produce the same result faster). WPS defines a geo-enabled SOAP interface for remote procedure calls. This allows to webify any program, but does not allow for semantic interoperability: a function is identified only by its function name and parameters while the semantics is encoded in the (only human readable) title and abstract. Hence, another desirable property is missing, namely an explicit semantics which allows for machine-machine communication and reasoning a la Semantic Web. The OGC Web Coverage Processing Service (WCPS) language, which has been adopted as an international standard by OGC in December 2008, defines a flexible interface for the navigation, extraction, and ad-hoc analysis of large, multi-dimensional raster coverages. It is abstract in that it

The influence of patient positioning in breast CT on breast tissue coverage and patient comfort

Energy Technology Data Exchange (ETDEWEB)

Roessler, A.C.; Althoff, F.; Kalender, W. [Erlangen Univ. (Germany). Inst. of Medical Physics; Wenkel, E. [University Hospital of Erlangen (Germany). Radiological Inst.

2015-02-15

The presented study aimed at optimizing a patient table design for breast CT (BCT) systems with respect to breast tissue coverage and patient comfort. Additionally, the benefits and acceptance of an immobilization device for BCT using underpressure were evaluated. Three different study parts were carried out. In a positioning study women were investigated on an MRI tabletop with exchangeable inserts (flat and cone-shaped with different opening diameters) to evaluate their influence on breast coverage and patient comfort in various positioning alternatives. Breast length and volume were calculated to compare positioning modalities including various opening diameters and forms. In the second study part, an underpressure system was tested for its functionality and comfort on a stereotactic biopsy table mimicking a future CT scanner table. In the last study part, this system was tested regarding breast tissue coverage. Best results for breast tissue coverage were shown for cone-shaped table inserts with an opening of 180 mm. Flat inserts did not provide complete coverage of breast tissue. The underpressure system showed robust function and tended to pull more breast tissue into the field of view. Patient comfort was rated good for all table inserts, with highest ratings for cone-shaped inserts. Cone-shaped tabletops appeared to be adequate for BCT systems and to allow imaging of almost the complete breast. An underpressure system proved promising for the fixation of the breast during imaging and increased coverage. Patient comfort appears to be adequate.

A controlled comparison of the BacT/ALERT® 3D and VIRTUO™ microbial detection systems.

Science.gov (United States)

Totty, H; Ullery, M; Spontak, J; Viray, J; Adamik, M; Katzin, B; Dunne, W M; Deol, P

2017-10-01

The performance of the next-generation BacT/ALERT® VIRTUO™ Microbial Detection System (VIRTUO™, bioMérieux Inc., Hazelwood, MO) was compared to the BacT/ALERT® 3D Microbial Detection System (3D, bioMérieux Inc., Durham, NC) using BacT/ALERT® FA Plus (FA Plus), BacT/ALERT® PF Plus (PF Plus), BacT/ALERT® FN Plus (FN Plus), BacT/ALERT® Standard Aerobic (SA), and BacT/ALERT® Standard Anaerobic (SN) blood culture bottles (bioMérieux Inc., Durham, NC). A seeded limit of detection (LoD) study was performed for each bottle type in both systems. The LoD studies demonstrated that both systems were capable of detecting organisms at nearly identical levels [detection (TTD) between the systems using a panel of clinically relevant microorganisms inoculated at or near the LoD with 0, 4, or 10 mL of healthy human blood. VIRTUO™ exhibited a faster TTD by an average of 3.5 h, as well as demonstrated a significantly improved detection rate of 99.9% compared to 98.8% with 3D (p-value <0.05).

AN EFFICIENT METHOD FOR DEEP WEB CRAWLER BASED ON ACCURACY -A REVIEW

OpenAIRE

Pranali Zade1, Dr.S.W.Mohod2

2018-01-01

As deep web grows at a very fast pace, there has been increased interest in techniques that help efficiently locate deep-web interfaces. However, due to the large volume of web resources and the dynamic nature of deep web, achieving wide coverage and high efficiency is a challenging issue. We propose a three-stage framework, for efficient harvesting deep web interfaces. Project experimental results on a set of representative domains show the agility and accuracy of our proposed crawler framew...

Efficient Expression of Acetylcholine-Binding Protein from Aplysia californica in Bac-to-Bac System

Directory of Open Access Journals (Sweden)

Bo Lin

2014-01-01

Full Text Available The Bac-to-Bac baculovirus expression system can efficiently produce recombinant proteins, but the system may have to be optimized to achieve high-level expression for different candidate proteins. We reported here the efficient expression of acetylcholine-binding proteins from sea hares Aplysia californica (Ac-AChBP and a convenient method to monitor protein expression level in this expression system. Three key factors affecting expression of Ac-AChBP were optimized for maximizing the yield, which included the cell density, volume of the infecting baculovirus inoculums, and the culturing time of postinfection. We have found it to reach a high yield of ∼5 mg/L, which needs 55 h incubation after infection at the cell density of 2 × 106 cells/mL with an inoculum volume ratio of 1 : 100. The optimized expression system in this study was also applied for expressing another protein Ls-AChBP from Lymnaea stagnalis successfully. Therefore, this established method is helpful to produce high yields of AChBP proteins for X-ray crystallographic structural and functional studies.

Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane.

Science.gov (United States)

Elazar, Assaf; Weinstein, Jonathan; Biran, Ido; Fridman, Yearit; Bibi, Eitan; Fleishman, Sarel Jacob

2016-01-29

Insertion of helix-forming segments into the membrane and their association determines the structure, function, and expression levels of all plasma membrane proteins. However, systematic and reliable quantification of membrane-protein energetics has been challenging. We developed a deep mutational scanning method to monitor the effects of hundreds of point mutations on helix insertion and self-association within the bacterial inner membrane. The assay quantifies insertion energetics for all natural amino acids at 27 positions across the membrane, revealing that the hydrophobicity of biological membranes is significantly higher than appreciated. We further quantitate the contributions to membrane-protein insertion from positively charged residues at the cytoplasm-membrane interface and reveal large and unanticipated differences among these residues. Finally, we derive comprehensive mutational landscapes in the membrane domains of Glycophorin A and the ErbB2 oncogene, and find that insertion and self-association are strongly coupled in receptor homodimers.

The canine sarcoglycan delta gene: BAC clone contig assembly, chromosome assignment and interrogation as a candidate gene for dilated cardiomyopathy in Dobermann dogs.

Science.gov (United States)

Stabej, P; Leegwater, P A J; Imholz, S; Versteeg, S A; Zijlstra, C; Stokhof, A A; Domanjko-Petriè, A; van Oost, B A

2005-01-01

Dilated cardiomyopathy (DCM) is a common disease of the myocardium recognized in human, dog and experimental animals. Genetic factors are responsible for a large proportion of cases in humans, and 17 genes with DCM causing mutations have been identified. The genetic origin of DCM in the Dobermann dogs has been suggested, but no disease genes have been identified to date. In this paper, we describe the characterization and evaluation of the canine sarcoglycan delta (SGCD), a gene implicated in DCM in human and hamster. Bacterial artificial chromosomes (BACs) containing the canine SGCD gene were isolated with probes for exon 3 and exons 4-8 and were characterized by Southern blot analysis. BAC end sequences were obtained for four BACs. Three of the BACs overlapped and could be ordered relative to each other and the end sequences of all four BACs could be anchored on the preliminary assembly of the dog genome sequence (www. ensembl.org). One of the BACs of the partial contig was localized by fluorescent in situ hybridization to canine chromosome 4q22, in agreement with the dog genome sequence. Two highly informative polymorphic microsatellite markers in intron 7 of the SGCD gene were identified. In 25 DCM-affected and 13 non DCM-affected dogs seven different haplotypes could be distinguished. However, no association between any of the SGCD variants and the disease locus was apparent.

A simple statistical signal loss model for deep underground garage

DEFF Research Database (Denmark)

Nguyen, Huan Cong; Gimenez, Lucas Chavarria; Kovacs, Istvan

2016-01-01

In this paper we address the channel modeling aspects for a deep-indoor scenario with extreme coverage conditions in terms of signal losses, namely underground garage areas. We provide an in-depth analysis in terms of path loss (gain) and large scale signal shadowing, and a propose simple...... propagation model which can be used to predict cellular signal levels in similar deep-indoor scenarios. The proposed frequency-independent floor attenuation factor (FAF) is shown to be in range of 5.2 dB per meter deep....

Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant.

Directory of Open Access Journals (Sweden)

Qing Ye

Full Text Available The bacterial artificial chromosome (BAC system is widely used in isolation of large genomic fragments of interest. Construction of a routine BAC library requires several months for picking clones and arraying BACs into superpools in order to employ 4D-PCR to screen positive BACs, which might be time-consuming and laborious. The major histocompatibility complex (MHC is a cluster of genes involved in the vertebrate immune system, and the classical avian MHC-B locus is a minimal essential one, occupying a 100-kb genomic region. In this study, we constructed a more effective reverse-4D BAC library for the golden pheasant, which first creates sub-libraries and then only picks clones of positive sub-libraries, and identified several MHC clones within thirty days. The full sequencing of a 97-kb reverse-4D BAC demonstrated that the golden pheasant MHC-B locus contained 20 genes and showed good synteny with that of the chicken. The notable differences between these two species were the numbers of class II B loci and NK genes and the inversions of the TAPBP gene and the TAP1-TAP2 region. Furthermore, the inverse TAP2-TAP1 was unique in the golden pheasant in comparison with that of chicken, turkey, and quail. The newly defined genomic structure of the golden pheasant MHC will give an insight into the evolutionary history of the avian MHC.

Aerobic biodegradation of a sulfonated phenylazonaphthol dye by a bacterial community immobilized in a multistage packed-bed BAC reactor.

Science.gov (United States)

Ruiz-Arias, Alfredo; Juárez-Ramírez, Cleotilde; de los Cobos-Vasconcelos, Daniel; Ruiz-Ordaz, Nora; Salmerón-Alcocer, Angélica; Ahuatzi-Chacón, Deifilia; Galíndez-Mayer, Juvencio

2010-11-01

A microbial community able to aerobically degrade the azo dye Acid Orange 7 was selected from riparian or lacustrine sediments collected at sites receiving textile wastewaters. Three bacterial strains, pertaining to the genera Pseudomonas, Arthrobacter, and Rhizobium, constitute the selected community. The biodegradation of AO7 was carried out in batch-suspended cell culture and in a continuously operated multistage packed-bed BAC reactor. The rapid decolorization observed in batch culture, joined to a delay of about 24 h in COD removal and cell growth, suggests that enzymes involved in biodegradation of the aromatic amines generated after AO7 azo-bond cleavage (1-amino-2-naphthol [1-A2N] and 4-aminobenzenesulfonic acid [4-ABS]), are inducible in this microbial consortium. After this presumptive induction period, the accumulated byproducts, measured through COD, were partially metabolized and transformed in cell mass. At all azo dye loading rates used, complete removal of AO7 and 1-A2N was obtained in the multistage packed-bed BAC reactor (PBR).; however, the overall COD (eta ( COD )) and 4-ABS (eta ( ABS )) removal efficiencies obtained in steady state continuous culture were about 90%. Considering the toxicity of 1-A2N, its complete removal has particular relevance. In the first stages of the packed-bed BAC reactor (Fig. 4a-c), major removal was observed. In the last stage, only a slight removal of COD and 4-ABS was obtained. Comparing to several reported studies, the continuously operated multistage packed-bed BAC reactor showed similar or superior results. In addition, the operation of large-packed-bed BAC reactors could be improved by using several shallow BAC bed stages, because the pressure drop caused by bed compaction of a support material constituted by small and fragile particles can be reduced.

Effects of nitrogen ion irradiation on endoglucanase activity and gene mutation of Bacillus subtilis Bac01

International Nuclear Information System (INIS)

Lv Jie; Mao Peihong; Jin Xiang; Yu Long; Ying Hanjie

2009-01-01

Bacillus subtilis Bac01 was mutated by 15 keV N + ions of 1.5xl0 16 cm -2 . The mutant strain Bac11 with high yield of endoglucanase was isolated using carboxymethylcellulose sodium and congo red indicative plates. It exhibited higher endoglucanase activity (381.89IU) than the original strain Bac01 (93.33IU). Two 1,500 bp endoglucanase gene fragments were obtained with PCR amplification from B. subtilis Bac01 and mutant strain Bac11. BLAST comparison result indicated that 10 nucleotides mutated. Bioinformatics methods were used to analyze the two predicted amino acid sequences, and it was found that 5 amino acid residues changed, being all in the cellulose-binding domain of endoglucanase. (authors)

Comparison of biological activated carbon (BAC) and membrane bioreactor (MBR) for pollutants removal in drinking water treatment.

Science.gov (United States)

Tian, J Y; Chen, Z L; Liang, H; Li, X; Wang, Z Z; Li, G B

2009-01-01

Biological activated carbon (BAC) and membrane bioreactor (MBR) were systematically compared for the drinking water treatment from slightly polluted raw water under the same hydraulic retention time (HRT) of 0.5 h. MBR exhibited excellent turbidity removal capacity due to the separation of the membrane; while only 60% of influent turbidity was intercepted by BAC. Perfect nitrification was achieved by MBR with the 89% reduction in ammonia; by contrast, BAC only eliminated a moderate amount of influent ammonia (by 54.5%). However, BAC was able to remove more dissolved organic matter (DOM, especially for organic molecules of 3,000 approximately 500 Daltons) and corresponding disinfection by-product formation potential (DBPFP) in raw water than MBR. Unfortunately, particulate organic matter (POM) was detected in the BAC effluent. On the other hand, BAC and MBR displayed essentially the same capacity for biodegradable organic matter (BOM) removal. Fractionation of DOM showed that the removal efficiencies of hydrophobic neutrals, hydrophobic acids, weakly hydrophobic acids and hydrophilic organic matter through BAC treatment were 11.7%, 8.8%, 13.9% and 4.8% higher than that through MBR; while MBR achieved 13.8% higher hydrophobic bases removal as compared with BAC.

HD-MTL: Hierarchical Deep Multi-Task Learning for Large-Scale Visual Recognition.

Science.gov (United States)

Fan, Jianping; Zhao, Tianyi; Kuang, Zhenzhong; Zheng, Yu; Zhang, Ji; Yu, Jun; Peng, Jinye

2017-02-09

In this paper, a hierarchical deep multi-task learning (HD-MTL) algorithm is developed to support large-scale visual recognition (e.g., recognizing thousands or even tens of thousands of atomic object classes automatically). First, multiple sets of multi-level deep features are extracted from different layers of deep convolutional neural networks (deep CNNs), and they are used to achieve more effective accomplishment of the coarseto- fine tasks for hierarchical visual recognition. A visual tree is then learned by assigning the visually-similar atomic object classes with similar learning complexities into the same group, which can provide a good environment for determining the interrelated learning tasks automatically. By leveraging the inter-task relatedness (inter-class similarities) to learn more discriminative group-specific deep representations, our deep multi-task learning algorithm can train more discriminative node classifiers for distinguishing the visually-similar atomic object classes effectively. Our hierarchical deep multi-task learning (HD-MTL) algorithm can integrate two discriminative regularization terms to control the inter-level error propagation effectively, and it can provide an end-to-end approach for jointly learning more representative deep CNNs (for image representation) and more discriminative tree classifier (for large-scale visual recognition) and updating them simultaneously. Our incremental deep learning algorithms can effectively adapt both the deep CNNs and the tree classifier to the new training images and the new object classes. Our experimental results have demonstrated that our HD-MTL algorithm can achieve very competitive results on improving the accuracy rates for large-scale visual recognition.

Bac on the Border

OpenAIRE

Umberger, Emily

2007-01-01

Although now on the Tohono O'odom reservation in the modern US Southwest, when the Franciscan church of San Xavier del Bac was built (1780-97), its location was the northern frontier of New Spain. From the outset the church stood out from other northern New Spanish missions in its elaborate decoration, and it still stands out because its contents remain intact, despite changes through time. This essay serves as an introduction to the church as a subject of art historical study. It highlights ...

Rapid molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus L., based on large Y-chromosomal insertions.

Science.gov (United States)

Bakker, Theo C M; Giger, Thomas; Frommen, Joachim G; Largiadèr, Carlo R

2017-08-01

There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences. Three molecular PCR-based sex tests were developed, in which the first, the second or both insertions were covered. In five European populations (from DE, CH, NL, GB) of three-spined sticklebacks, tests with both insertions combined showed two clearly separated bands on agarose minigels in males and one band in females. The tests with the separate insertions gave similar results. Thus, the new molecular sexing method gave rapid and reliable results for sexing three-spined sticklebacks and is an improvement and/or alternative to existing methods.

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

Science.gov (United States)

Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S S; Kudrna, David A; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A; Luo, Meizhong

2013-11-01

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

Report on the Deep Argo Implementation Workshop. Hobart, May 5-7th 2015

OpenAIRE

Zilberman, Nathalie; Maze, Guillaume

2015-01-01

Deep-ocean (> 2000 m) hydrographic observations are limited to sparse ship-board hydrographic sections repeated every decade and short-lived moored arrays of confined spatial coverage. Upper-ocean (< 2000 m) sampling, largely carried out by the conventional Argo array, has much higher resolution in space and time. The need for more intensive sampling in the deep ocean has been widely recognized by the scientific community. The development of deep profiling Argo floats, a new generation of aut...

Investigation of decolorization of textile wastewater in an anaerobic/aerobic biological activated carbon system (A/A BAC).

Science.gov (United States)

Pasukphun, N; Vinitnantharat, S; Gheewala, S

2010-04-01

The aim of this study is to investigate the decolorization in anaerobic/aerobic biological activated carbon (A/A BAC) system. The experiment was divided into 2 stages; stage I is batch test for preliminary study of dye removal equilibrium time. The preliminary experiment (stage I) provided the optimal data for experimental design of A/A BAC system in SBR (stage II). Stage II is A/A BAC system imitated Sequencing Batch Reactor (SBR) which consist of 5 main periods; fill, react, settle, draw and idle. React period include anaerobic phase followed by aerobic phase. The BAC main media; Granular Activated Carbon (GAC), Mixed Cultures (MC) and Biological Activated Carbon (BAC) were used for dye and organic substances removal in three different solutions; Desizing Agent Solution (DAS), dye Solution (DS) and Synthetic Textile Wastewater (STW). Results indicate that GAC adsorption plays role in dye removal followed by BAC and MC activities, respectively. In the presence desizing agent, decolorization by MC was improved because desizing agent acts as co-substrates for microorganisms. It was found that 50% of dye removal efficiency was achieved in Fill period by MC. GC/MS analysis was used to identify dye intermediate from decolorization. Dye intermediate containing amine group was found in the solution and on BAC surfaces. The results demonstrated that combination of MC and BAC in the system promotes decolorization and dye intermediate removal. In order to improve dye removal efficiency in an A/A BAC system, replacement of virgin GAC, sufficient co-substrates supply and the appropriate anaerobic: aerobic period should be considered.

Large-eddy simulation of maritime deep tropical convection

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Peter A Bogenschutz

2009-12-01

Full Text Available This study represents an attempt to apply Large-Eddy Simulation (LES resolution to simulate deep tropical convection in near equilibrium for 24 hours over an area of about 205 x 205 km2, which is comparable to that of a typical horizontal grid cell in a global climate model. The simulation is driven by large-scale thermodynamic tendencies derived from mean conditions during the GATE Phase III field experiment. The LES uses 2048 x 2048 x 256 grid points with horizontal grid spacing of 100 m and vertical grid spacing ranging from 50 m in the boundary layer to 100 m in the free troposphere. The simulation reaches a near equilibrium deep convection regime in 12 hours. The simulated vertical cloud distribution exhibits a trimodal vertical distribution of deep, middle and shallow clouds similar to that often observed in Tropics. A sensitivity experiment in which cold pools are suppressed by switching off the evaporation of precipitation results in much lower amounts of shallow and congestus clouds. Unlike the benchmark LES where the new deep clouds tend to appear along the edges of spreading cold pools, the deep clouds in the no-cold-pool experiment tend to reappear at the sites of the previous deep clouds and tend to be surrounded by extensive areas of sporadic shallow clouds. The vertical velocity statistics of updraft and downdraft cores below 6 km height are compared to aircraft observations made during GATE. The comparison shows generally good agreement, and strongly suggests that the LES simulation can be used as a benchmark to represent the dynamics of tropical deep convection on scales ranging from large turbulent eddies to mesoscale convective systems. The effect of horizontal grid resolution is examined by running the same case with progressively larger grid sizes of 200, 400, 800, and 1600 m. These runs show a reasonable agreement with the benchmark LES in statistics such as convective available potential energy, convective inhibition

Aspects of coverage in medical DNA sequencing

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Wilson Richard K

2008-05-01

Full Text Available Abstract Background DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but many design specifications have yet to be conclusively established. Perhaps the most fundamental of these is the redundancy required to detect sequence variations, which bears directly upon genomic coverage and the consequent resolving power for discerning somatic mutations. Results We address the medical sequencing coverage problem via an extension of the standard mathematical theory of haploid coverage. The expected diploid multi-fold coverage, as well as its generalization for aneuploidy are derived and these expressions can be readily evaluated for any project. The resulting theory is used as a scaling law to calibrate performance to that of standard BAC sequencing at 8× to 10× redundancy, i.e. for expected coverages that exceed 99% of the unique sequence. A differential strategy is formalized for tumor/normal studies wherein tumor samples are sequenced more deeply than normal ones. In particular, both tumor alleles should be detected at least twice, while both normal alleles are detected at least once. Our theory predicts these requirements can be met for tumor and normal redundancies of approximately 26× and 21×, respectively. We explain why these values do not differ by a factor of 2, as might intuitively be expected. Future technology developments should prompt even deeper sequencing of tumors, but the 21× value for normal samples is essentially a constant. Conclusion Given the assumptions of standard coverage theory, our model gives pragmatic estimates for required redundancy. The differential strategy should be an efficient means of identifying potential somatic mutations for further study.

Application of EDTA-functionalized bamboo activated carbon (BAC) for Pb(II) and Cu(II) removal from aqueous solutions

Science.gov (United States)

Lv, Dan; Liu, Yu; Zhou, Jiasheng; Yang, Kunlun; Lou, Zimo; Baig, Shams Ali; Xu, Xinhua

2018-01-01

In this study, a novel bamboo activated carbon (BAC) with ethylene diamine tetraacetic acid (EDTA) functionality was prepared by direct grafting in the presence of tetraethyl orthosilicate (TEOS) as a crosslinking agent. The BAC@SiO2-EDTA was characterized by SEM, TEM, TGA, FTIR, XPS and its adsorption property for removal of Pb(II) and Cu(II) under various experimental conditions was also investigated. The characterization results reflected that EDTA was successfully assembled on the surface of the BAC and average pore size increased from 4.10 to 4.83 nm as BAC grafted with EDTA. Adsorption data fitted very well in Langmuir isotherm model and pseudo-second-order kinetic model. As compared with the raw BAC, the maximum adsorption capacities of BAC@SiO2-EDTA for the Pb(II) and Cu(II) increased from 45.45 to 123.45 mg g-1 and from 6.85 to 42.19 mg g-1, since the existence of EDTA on modified BAC promoted the formation of chemical complex. The removal of heavy metal ions mainly depended on the complexation with EDTA and the electrostatic attractions with negatively charged surface of BAC@SiO2-EDTA. The adsorption of Pb(II)/Cu(II) on the BAC@SiO2-EDTA was pH dependent and pH 5-6 was considered an optimum. However, lower temperature favored the adsorption and the maximum adsorption was recorded at 20 °C. In addition, BAC@SiO2-EDTA had an excellent reusability with about 40% decline in the adsorption capacity for Pb(II) after fifth reuse. Insignificant influences of co-existing cations and natural organic matter (NOM) were found on the adsorption of Pb(II) and Cu(II). All the results demonstrate that BAC@SiO2-EDTA is a potential adsorbent for metal ions in wastewater.

Sensitivity and applicability of the Brazilian version of the Brief Assessment of Cognition in Schizophrenia (BACS

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João Vinícius Salgado

Full Text Available Abstract Cognitive assessment in schizophrenia has traditionally used batteries that are long and complex or differ widely in their content. The Brief Assessment of Cognition in Schizophrenia (BACS has been developed to cover the main cognitive deficits of schizophrenia as well as to be easily and briefly administered, portable, sensitive and reliable. Objectives: To investigate the applicability and sensitivity of the Brazilian Version of the BACS (Brazilian-BACS. Methods: Performance of 20 stable patients with schizophrenia on the Brazilian-BACS was compared to 20 matched healthy controls. Results: Applying the Brazilian-BACS required 43.4±8.4 minutes for patients and 40.5±5.7 minutes for controls (p=0.17. All tests demonstrated significant differences between controls and patients (P<0.01. Pearson's correlation analysis and Cronbach's a evidenced a high internal consistency for patient performance. The cognitive deficit in the patients was approximately 1.5 standard deviations below controls. These results were consistent with those reported in the validation of the original version and in meta-analyses of similar studies. Conclusions: The Brazilian-BACS displayed good applicability and sensitivity in assessing the major cognitive constructs that are impaired in schizophrenia. Thus, the Brazilian-BACS seems to be a promising tool for assessing cognition in patients with schizophrenia in Brazil.

Using Bacterial Artificial Chromosomes in Leukemia Research: The Experience at the University Cytogenetics Laboratory in Brest, France

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Etienne De Braekeleer

2011-01-01

Full Text Available The development of the bacterial artificial chromosome (BAC system was driven in part by the human genome project in order to construct genomic DNA libraries and physical maps for genomic sequencing. The availability of BAC clones has become a valuable tool for identifying cancer genes. We report here our experience in identifying genes located at breakpoints of chromosomal rearrangements and in defining the size and boundaries of deletions in hematological diseases. The methodology used in our laboratory consists of a three-step approach using conventional cytogenetics followed by FISH with commercial probes, then BAC clones. One limitation to the BAC system is that it can only accommodate inserts of up to 300 kb. As a consequence, analyzing the extent of deletions requires a large amount of material. Array comparative genomic hybridization (array-CGH using a BAC/PAC system can be an alternative. However, this technique has limitations also, and it cannot be used to identify candidate genes at breakpoints of chromosomal rearrangements such as translocations, insertions, and inversions.

A PiggyBac-mediated approach for muscle gene transfer or cell therapy

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Déborah Ley

2014-11-01

Full Text Available An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies.

A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L

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Abbo Shahal

2010-09-01

Full Text Available Abstract Background Chickpea (Cicer arietinum L. is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. Results We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 × of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR and QTL8 for days to first flower (DTF, thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. Conclusion The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus, will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.

Loss of locality in gravitational correlators with a large number of insertions

Science.gov (United States)

Ghosh, Sudip; Raju, Suvrat

2017-09-01

We review lessons from the AdS/CFT correspondence that indicate that the emergence of locality in quantum gravity is contingent upon considering observables with a small number of insertions. Correlation functions, where the number of insertions scales with a power of the central charge of the CFT, are sensitive to nonlocal effects in the bulk theory, which arise from a combination of the effects of the bulk Gauss law and a breakdown of perturbation theory. To examine whether a similar effect occurs in flat space, we consider the scattering of massless particles in the bosonic string and the superstring in the limit, where the number of external particles, n, becomes very large. We use estimates of the volume of the Weil-Petersson moduli space of punctured Riemann surfaces to argue that string amplitudes grow factorially in this limit. We verify this factorial behavior through an extensive numerical analysis of string amplitudes at large n. Our numerical calculations rely on the observation that, in the large n limit, the string scattering amplitude localizes on the Gross-Mende saddle points, even though individual particle energies are small. This factorial growth implies the breakdown of string perturbation theory for n ˜(M/plE ) d -2 in d dimensions, where E is the typical individual particle energy. We explore the implications of this breakdown for the black hole information paradox. We show that the loss of locality suggested by this breakdown is precisely sufficient to resolve the cloning and strong subadditivity paradoxes.

Usage of a rotational flap for coverage of a large central forehead defect

Directory of Open Access Journals (Sweden)

El-Sabbagh, Ahmed Hassan

2017-02-01

Full Text Available Background: The forehead is a donor site for facial reconstruction but has no generous donor site for its coverage. All options of the reconstructive ladder can be used. A large rotation flap was used to reconstruct a big central forehead defect following failed previous repair in an elderly diabetic patient after a motor car accident. Case presentation: A 64-year-old diabetic man presented with an extensive central forehead defect after failed previous repair following a motor car accident. Coverage of the defect was performed using a flap based around the ear on one side in a rotation movement. An accepted functional and esthetic result was achieved after 3 months of Conclusion: A rotation flap based on arteries around the ear can be used for coverage of a difficult lesion in the central forehead. Level of evidence: Level V, therapeutic study

Failure mechanism and supporting measures for large deformation of Tertiary deep soft rock

Institute of Scientific and Technical Information of China (English)

Guo Zhibiao; Wang Jiong; Zhang Yuelin

2015-01-01

The Shenbei mining area in China contains typical soft rock from the Tertiary Period. As mining depths increase, deep soft rock roadways are damaged by large deformations and constantly need to be repaired to meet safety requirements, which is a great security risk. In this study, the characteristics of deformation and failure of typical roadway were analyzed, and the fundamental reason for the roadway deformation was that traditional support methods and materials cannot control the large deformation of deep soft rock. Deep soft rock support technology was developed based on constant resistance energy absorption using constant resistance large deformation bolts. The correlative deformation mechanisms of surrounding rock and bolt were analyzed to understand the principle of constant resistance energy absorption. The new technology works well on-site and provides a new method for the excavation of roadways in Tertiary deep soft rock.

Differential CT features of infectious pneumonia versus bronchioloalveolar carcinoma (BAC) mimicking pneumonia

International Nuclear Information System (INIS)

Kim, Tae Hoon; Kim, Sang Jin; Ryu, Young Hoon; Chung, Soo Yoon; Seo, Jae Seung; Kim, Young Jin; Choi, Byoung Wook; Lee, Sun Hwa; Cho, Sang Ho

2006-01-01

The purpose of this study was to evaluate retrospectively the differential CT features of bronchioloalveolar carcinoma (BAC) mimicking pneumonia and infectious pneumonia at the lung periphery. CT images were reviewed in 47 patients with focal areas of parenchymal opacification at the lung periphery. We evaluated the presence of ground-glass attenuation, marginal conspicuity of the lesion, CT angiogram sign, air-bronchogram sign, a bubble-like low-attenuation area within the lesion, presence of pleural thickening and retraction associated with the lesion, presence of pleural effusion and extra-pleural fatty hypertrophy, presence of bronchial wall thickening proximal to the lesion, and air-trapping in the normal lung near the lesion. BAC (n=18) depicted the presence of a bubble-like low-attenuation area within the lesion, whereas infectious pneumonia (n=29) represented the pleural thickening associated with the lesion and bronchial wall thickening proximal to the lesion (P 0.05). The focal areas of the parenchymal opacification on the CT images may suggest infectious pneumonia rather than BAC when they show bronchial wall thickening proximal to the lesion and pleural thickening associated with the lesion, whereas BAC is characterized as the presence of a bubble-like low attenuation area within the tumor. (orig.)

Differential CT features of infectious pneumonia versus bronchioloalveolar carcinoma (BAC) mimicking pneumonia

Energy Technology Data Exchange (ETDEWEB)

Kim, Tae Hoon [Yonsei University College of Medicine, Department of Radiology, Seoul (Korea); Yongdong Severance Hospital, Department of Radiology, Seoul (Korea); Kim, Sang Jin; Ryu, Young Hoon; Chung, Soo Yoon; Seo, Jae Seung; Kim, Young Jin; Choi, Byoung Wook [Yonsei University College of Medicine, Department of Radiology, Seoul (Korea); Lee, Sun Hwa [NeoDin Medical Institute, Department of Clinical Pathology, Seoul (Korea); Cho, Sang Ho [Yonsei University College of Medicine, Department of Pathology, Seoul (Korea)

2006-08-15

The purpose of this study was to evaluate retrospectively the differential CT features of bronchioloalveolar carcinoma (BAC) mimicking pneumonia and infectious pneumonia at the lung periphery. CT images were reviewed in 47 patients with focal areas of parenchymal opacification at the lung periphery. We evaluated the presence of ground-glass attenuation, marginal conspicuity of the lesion, CT angiogram sign, air-bronchogram sign, a bubble-like low-attenuation area within the lesion, presence of pleural thickening and retraction associated with the lesion, presence of pleural effusion and extra-pleural fatty hypertrophy, presence of bronchial wall thickening proximal to the lesion, and air-trapping in the normal lung near the lesion. BAC (n=18) depicted the presence of a bubble-like low-attenuation area within the lesion, whereas infectious pneumonia (n=29) represented the pleural thickening associated with the lesion and bronchial wall thickening proximal to the lesion (P<0.05). The other CT findings showed no significant differences (P>0.05). The focal areas of the parenchymal opacification on the CT images may suggest infectious pneumonia rather than BAC when they show bronchial wall thickening proximal to the lesion and pleural thickening associated with the lesion, whereas BAC is characterized as the presence of a bubble-like low attenuation area within the tumor. (orig.)

Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea

DEFF Research Database (Denmark)

Treusch, Alexander H; Kletzin, Arnulf; Raddatz, Guenter

2004-01-01

Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large-insert fosmid libraries in total...... (approximately 1% each) have been captured in our libraries. The diversity of putative protein-encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms. A huge variety of genomic fragments has been captured...

Insulated piggyBac vectors for insect transgenesis

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Horn Carsten

2006-06-01

Full Text Available Abstract Background Germ-line transformation of insects is now a widely used method for analyzing gene function and for the development of genetically modified strains suitable for pest control programs. The most widely used transposable element for the germ-line transformation of insects is piggyBac. The site of integration of the transgene can influence gene expression due to the effects of nearby transcription enhancers or silent heterochromatic regions. Position effects can be minimized by flanking a transgene with insulator elements. The scs/scs' and gypsy insulators from Drosophila melanogaster as well as the chicken β-globin HS4 insulator function in both Drosophila and mammalian cells. Results To minimize position effects we have created a set of piggyBac transformation vectors that contain either the scs/scs', gypsy or chicken β-globin HS4 insulators. The vectors contain either fluorescent protein or eye color marker genes and have been successfully used for germ-line transformation of Drosophila melanogaster. A set of the scs/scs' vectors contains the coral reef fluorescent protein marker genes AmCyan, ZsGreen and DsRed that have not been optimized for translation in human cells. These marker genes are controlled by a combined GMR-3xP3 enhancer/promoter that gives particularly strong expression in the eyes. This is also the first report of the use of the ZsGreen and AmCyan reef fluorescent proteins as transformation markers in insects. Conclusion The insulated piggyBac vectors should protect transgenes against position effects and thus facilitate fine control of gene expression in a wide spectrum of insect species. These vectors may also be used for transgenesis in other invertebrate species.

[Construction of a recombinant HVT virus expressing the HA gene of avian influenza virus H5N1 via Rde/ET recombination system].

Science.gov (United States)

Lan, Desong; Shi, Xingming; Wang, Yunfeng; Liu, Changjun; Wang, Mei; Cui, Hongyu; Tian, Guobin; Li, Jisong; Tong, Guangzhi

2009-01-01

In recent years,manipulation of large herpesvirus genomes has been facilitated by using bacterial artificial chromosome (BAC) vectors. We have previously reported the construction of the BAC clones (HVT BACs) of herpesvirus of turkey (HVT). With these BAC clones in hand,we manipulated the genome of HVT by utilizing Red/ET recombination system, and developed a biologically safe live vaccine based on the HVT BACs. In this two-step approach, we first transformed the plasmid pRedET into the DH10B competent cells that carried the HVT BACs,and added inducer L-arabinose into the cells. We prepared the cells into competent cells and electroporated the linear rpsL-neo counter-selection/selection cassette flanked by the 50 bp long homology arms into the cells. So the functional cassette was inserted into the U(S)2 locus. Only colonies carrying the modified BAC would survive Kanamycin selection on the agar plates. The successful integration of the rpsL-neo cassette was monitored by PCR and Streptomycin selection, for the insertion of rpsL-neo cassette cells will become Streptomycin sensitive. Secondly, in the same way, we replaced the rpsL-neo cassette with the hemagglutinin (HA) gene of (HPAIV) A/Goose/ Guangdong/1/96(H5N1) flanked by the same homology arms. Only colonies which lost the rpsL-neo cassette will grow on Streptomycin containing plates. Finally, we obtained many colonies of which the HA gene of the AIV was inserted into the U(S)2 locus to be modified of HVT. And we reconstituted one recombinant virus from transfecting one of these BAC clones DNA into chick embryo fibroblasts (CEFs). We achieved one rescued recombinant virus which designated as rHVT-HA3. The H5 subtype HA gene expression in this recombinant virus rHVT-HA3 was confirmed by immunofluorescence assay.

Construction and Screening of Marine Metagenomic Large Insert Libraries.

Science.gov (United States)

Weiland-Bräuer, Nancy; Langfeldt, Daniela; Schmitz, Ruth A

2017-01-01

The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.

BAC-Dkk3-EGFP Transgenic Mouse: An In Vivo Analytical Tool for Dkk3 Expression

Directory of Open Access Journals (Sweden)

Yuki Muranishi

2012-01-01

Full Text Available Dickkopf (DKK family proteins are secreted modulators of the Wnt signaling pathway and are capable of regulating the development of many organs and tissues. We previously identified Dkk3 to be a molecule predominantly expressed in the mouse embryonic retina. However, which cell expresses Dkk3 in the developing and mature mouse retina remains to be elucidated. To examine the precise expression of the Dkk3 protein, we generated BAC-Dkk3-EGFP transgenic mice that express EGFP integrated into the Dkk3 gene in a BAC plasmid. Expression analysis using the BAC-Dkk3-EGFP transgenic mice revealed that Dkk3 is expressed in retinal progenitor cells (RPCs at embryonic stages and in Müller glial cells in the adult retina. Since Müller glial cells may play a potential role in retinal regeneration, BAC-Dkk3-EGFP mice could be useful for retinal regeneration studies.

Deep Hashing Based Fusing Index Method for Large-Scale Image Retrieval

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Lijuan Duan

2017-01-01

Full Text Available Hashing has been widely deployed to perform the Approximate Nearest Neighbor (ANN search for the large-scale image retrieval to solve the problem of storage and retrieval efficiency. Recently, deep hashing methods have been proposed to perform the simultaneous feature learning and the hash code learning with deep neural networks. Even though deep hashing has shown the better performance than traditional hashing methods with handcrafted features, the learned compact hash code from one deep hashing network may not provide the full representation of an image. In this paper, we propose a novel hashing indexing method, called the Deep Hashing based Fusing Index (DHFI, to generate a more compact hash code which has stronger expression ability and distinction capability. In our method, we train two different architecture’s deep hashing subnetworks and fuse the hash codes generated by the two subnetworks together to unify images. Experiments on two real datasets show that our method can outperform state-of-the-art image retrieval applications.

Single-molecule study of full-length NaChBac by planar lipid bilayer recording.

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Andrew Jo

Full Text Available Planar lipid bilayer device, alternatively known as BLM, is a powerful tool to study functional properties of conducting membrane proteins such as ion channels and porins. In this work, we used BLM to study the prokaryotic voltage-gated sodium channel (Nav NaChBac in a well-defined membrane environment. Navs are an essential component for the generation and propagation of electric signals in excitable cells. The successes in the biochemical, biophysical and crystallographic studies on prokaryotic Navs in recent years has greatly promoted the understanding of the molecular mechanism that underlies these proteins and their eukaryotic counterparts. In this work, we investigated the single-molecule conductance and ionic selectivity behavior of NaChBac. Purified NaChBac protein was first reconstituted into lipid vesicles, which is subsequently incorporated into planar lipid bilayer by fusion. At single-molecule level, we were able to observe three distinct long-lived conductance sub-states of NaChBac. Change in the membrane potential switches on the channel mainly by increasing its opening probability. In addition, we found that individual NaChBac has similar permeability for Na+, K+, and Ca2+. The single-molecule behavior of the full-length protein is essentially highly stochastic. Our results show that planar lipid bilayer device can be used to study purified ion channels at single-molecule level in an artificial environment, and such studies can reveal new protein properties that are otherwise not observable in in vivo ensemble studies.

KAIKObase: An integrated silkworm genome database and data mining tool

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Nagaraju Javaregowda

2009-10-01

Full Text Available Abstract Background The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, B. mori has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for B. mori were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups. Description Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size among the sequenced insect genomes and provided a high degree of nucleotide coverage (88% of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from two-dimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a Bombyx trap database was constructed for documenting insertion positions and expression data of transposon insertion lines. Conclusion For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the

Measuring brain activity cycling (BAC) in long term EEG monitoring of preterm babies

International Nuclear Information System (INIS)

Stevenson, Nathan J; Palmu, Kirsi; Wikström, Sverre; Hellström-Westas, Lena; Vanhatalo, Sampsa

2014-01-01

Measuring fluctuation of vigilance states in early preterm infants undergoing long term intensive care holds promise for monitoring their neurological well-being. There is currently, however, neither objective nor quantitative methods available for this purpose in a research or clinical environment. The aim of this proof-of-concept study was, therefore, to develop quantitative measures of the fluctuation in vigilance states or brain activity cycling (BAC) in early preterm infants. The proposed measures of BAC were summary statistics computed on a frequency domain representation of the proportional duration of spontaneous activity transients (SAT%) calculated from electroencephalograph (EEG) recordings. Eighteen combinations of three statistics and six frequency domain representations were compared to a visual interpretation of cycling in the SAT% signal. Three high performing measures (band energy/periodogram: R = 0.809, relative band energy/nonstationary frequency marginal: R = 0.711, g-statistic/nonstationary frequency marginal: R = 0.638) were then compared to a grading of sleep wake cycling based on the visual interpretation of the amplitude-integrated EEG trend. These measures of BAC are conceptually straightforward, correlate well with the visual scores of BAC and sleep wake cycling, are robust enough to cope with the technically compromised monitoring data available in intensive care units, and are recommended for further validation in prospective studies. (paper)

Bioreactor scale up and protein product quality characterization of piggyBac transposon derived CHO pools.

Science.gov (United States)

Rajendra, Yashas; Balasubramanian, Sowmya; Peery, Robert B; Swartling, James R; McCracken, Neil A; Norris, Dawn L; Frye, Christopher C; Barnard, Gavin C

2017-03-01

Chinese hamster ovary (CHO) cells remain the most popular host for the production of biopharmaceutical drugs, particularly monoclonal antibodies (mAbs), bispecific antibodies, and Fc-fusion proteins. Creating and characterizing the stable CHO clonally-derived cell lines (CDCLs) needed to manufacture these therapeutic proteins is a lengthy and laborious process. Therefore, CHO pools have increasingly been used to rapidly produce protein to support and enable preclinical drug development. We recently described the generation of CHO pools yielding mAb titers as high as 7.6 g/L in a 16 day bioprocess using piggyBac transposon-mediated gene integration. In this study, we wanted to understand why the piggyBac pool titers were significantly higher (2-10 fold) than the control CHO pools. Higher titers were the result of a combination of increased average gene copy number, significantly higher messenger RNA levels and the homogeneity (i.e. less diverse population distribution) of the piggyBac pools, relative to the control pools. In order to validate the use of piggyBac pools to support preclinical drug development, we then performed an in-depth product quality analysis of purified protein. The product quality of protein obtained from the piggyBac pools was very similar to the product quality profile of protein obtained from the control pools. Finally, we demonstrated the scalability of these pools from shake flasks to 36L bioreactors. Overall, these results suggest that gram quantities of therapeutic protein can be rapidly obtained from piggyBac CHO pools without significantly changing product quality attributes. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:534-540, 2017. © 2017 American Institute of Chemical Engineers.

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

Science.gov (United States)

Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

2011-04-01

Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

Investigation of Secondary Neutron Production in Large Space Vehicles for Deep Space

Science.gov (United States)

Rojdev, Kristina; Koontz, Steve; Reddell, Brandon; Atwell, William; Boeder, Paul

2016-01-01

Future NASA missions will focus on deep space and Mars surface operations with large structures necessary for transportation of crew and cargo. In addition to the challenges of manufacturing these large structures, there are added challenges from the space radiation environment and its impacts on the crew, electronics, and vehicle materials. Primary radiation from the sun (solar particle events) and from outside the solar system (galactic cosmic rays) interact with materials of the vehicle and the elements inside the vehicle. These interactions lead to the primary radiation being absorbed or producing secondary radiation (primarily neutrons). With all vehicles, the high-energy primary radiation is of most concern. However, with larger vehicles, there is more opportunity for secondary radiation production, which can be significant enough to cause concern. In a previous paper, we embarked upon our first steps toward studying neutron production from large vehicles by validating our radiation transport codes for neutron environments against flight data. The following paper will extend the previous work to focus on the deep space environment and the resulting neutron flux from large vehicles in this deep space environment.

The relationship of normal body temperature, end-expired breath temperature, and BAC/BrAC ratio in 98 physically fit human test subjects.

Science.gov (United States)

Cowan, J Mack; Burris, James M; Hughes, James R; Cunningham, Margaret P

2010-06-01

The relationship between normal body temperature, end-expired breath temperature, and blood alcohol concentration (BAC)/breath alcohol concentration (BrAC) ratio was studied in 98 subjects (84 men, 14 women). Subjects consumed alcohol sufficient to produce a BrAC of at least 0.06 g/210 L 45-75 min after drinking. Breath samples were analyzed using an Intoxilyzer 8000 specially equipped to measure breath temperature. Venous blood samples and body temperatures were then taken. The mean body temperature of the men (36.6 degrees C) was lower than the women (37.0 degrees C); however, their mean breath temperatures were virtually identical (men: 34.5 degrees C; women: 34.6 degrees C). The BAC exceeded the BrAC for every subject. BAC/BrAC ratios were calculated from the BAC and BrAC analytical results. There was no difference in the BAC/BrAC ratios for men (1:2379) and women (1:2385). The correlation between BAC and BrAC was high (r = 0.938, p body temperature and end-expired breath temperature, body temperature and BAC/BrAC ratio, and breath temperature and BAC/BrAC ratio were much lower. Neither normal body temperature nor end-expired breath temperature was strongly associated with BAC/BrAC ratio.

Insertion sequences enrichment in extreme Red sea brine pool vent

KAUST Repository

Elbehery, Ali H. A.

2016-12-03

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world’s largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

Insurance Coverage Policies for Personalized Medicine

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Andrew Hresko

2012-10-01

Full Text Available Adoption of personalized medicine in practice has been slow, in part due to the lack of evidence of clinical benefit provided by these technologies. Coverage by insurers is a critical step in achieving widespread adoption of personalized medicine. Insurers consider a variety of factors when formulating medical coverage policies for personalized medicine, including the overall strength of evidence for a test, availability of clinical guidelines and health technology assessments by independent organizations. In this study, we reviewed coverage policies of the largest U.S. insurers for genomic (disease-related and pharmacogenetic (PGx tests to determine the extent that these tests were covered and the evidence basis for the coverage decisions. We identified 41 coverage policies for 49 unique testing: 22 tests for disease diagnosis, prognosis and risk and 27 PGx tests. Fifty percent (or less of the tests reviewed were covered by insurers. Lack of evidence of clinical utility appears to be a major factor in decisions of non-coverage. The inclusion of PGx information in drug package inserts appears to be a common theme of PGx tests that are covered. This analysis highlights the variability of coverage determinations and factors considered, suggesting that the adoption of personal medicine will affected by numerous factors, but will continue to be slowed due to lack of demonstrated clinical benefit.

Biases in Drosophila melanogaster protein trap screens

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Müller Ilka

2009-05-01

utility of P-element vectors for protein trap screens has largely been exhausted, and that approximately 2,800 genes may still be amenable using piggyBac vectors. Thus protein trap strategies based on current approaches are unlikely to offer true genome-wide coverage. We suggest that either transposons with reduced insertion bias or recombineering-based targeting techniques will be required for comprehensive genome coverage in Drosophila.

Large-scale Exploration of Neuronal Morphologies Using Deep Learning and Augmented Reality.

Science.gov (United States)

Li, Zhongyu; Butler, Erik; Li, Kang; Lu, Aidong; Ji, Shuiwang; Zhang, Shaoting

2018-02-12

Recently released large-scale neuron morphological data has greatly facilitated the research in neuroinformatics. However, the sheer volume and complexity of these data pose significant challenges for efficient and accurate neuron exploration. In this paper, we propose an effective retrieval framework to address these problems, based on frontier techniques of deep learning and binary coding. For the first time, we develop a deep learning based feature representation method for the neuron morphological data, where the 3D neurons are first projected into binary images and then learned features using an unsupervised deep neural network, i.e., stacked convolutional autoencoders (SCAEs). The deep features are subsequently fused with the hand-crafted features for more accurate representation. Considering the exhaustive search is usually very time-consuming in large-scale databases, we employ a novel binary coding method to compress feature vectors into short binary codes. Our framework is validated on a public data set including 58,000 neurons, showing promising retrieval precision and efficiency compared with state-of-the-art methods. In addition, we develop a novel neuron visualization program based on the techniques of augmented reality (AR), which can help users take a deep exploration of neuron morphologies in an interactive and immersive manner.

Validation of the French version of the BACS (the brief assessment of cognition in schizophrenia) among 50 French schizophrenic patients.

Science.gov (United States)

Bralet, Marie-Cécile; Falissard, Bruno; Neveu, Xavier; Lucas-Ross, Margaret; Eskenazi, Anne-Marie; Keefe, Richard S E

2007-09-01

Schizophrenic patients demonstrate impairments in several key dimensions of cognition. These impairments are correlated with important aspects of functional outcome. While assessment of these cognition disorders is increasingly becoming a part of clinical and research practice in schizophrenia, there is no standard and easily administered test battery. The BACS (Brief Assessment of Cognition in Schizophrenia) has been validated in English language [Keefe RSE, Golberg TE, Harvey PD, Gold JM, Poe MP, Coughenour L. The Brief Assessment of Cognition in Schizophrenia: reliability, sensibility, and comparison with a standard neurocognitive battery. Schizophr. Res 2004;68:283-97], and was found to be as sensitive to cognitive dysfunction as a standard battery of tests, with the advantage of requiring less than 35 min to complete. We developed a French adaptation of the BACS and this study tested its ease of administration and concurrent validity. Correlation analyses between the BACS (version A) and a standard battery were performed. A sample of 50 stable schizophrenic patients received the French Version A of the BACS in a first session, and in a second session a standard battery. All the patients completed each of the subtests of the French BACS . The mean duration of completion for the BACS French version was 36 min (S.D.=5.56). A correlation analysis between the BACS (version A) global score and the standard battery global score showed a significant result (r=0.81, p<0.0001). The correlation analysis between the BACS (version A) sub-scores and the standard battery sub-scores showed significant results for verbal memory, working memory, verbal fluency, attention and speed of information processing and executive functions (p<0.001) and for motor speed (p<0.05). The French Version of the BACS is easier to use in French schizophrenic patients compared to a standard battery (administration shorter and completion rate better) and its good psychometric properties suggest

The need for blood alcohol concentration (BAC) legislation in Nigeria

African Journals Online (AJOL)

Dr Patrick O Erah

Tropical Journal of Pharmaceutical Research, June 2004; 3 (1): 319-327. © Pharmacotherapy Group, ... 1Department of Restorative Dentistry, Clinical therapeutic Unit, University of Benin, Benin City, .... An international survey of BAC is quite.

SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

Science.gov (United States)

2014-01-01

Background Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated. Results We analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites. Conclusions Since active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome. PMID:24958239

Large lattice relaxation deep levels in neutron-irradiated GaN

International Nuclear Information System (INIS)

Li, S.; Zhang, J.D.; Beling, C.D.; Wang, K.; Wang, R.X.; Gong, M.; Sarkar, C.K.

2005-01-01

Deep level transient spectroscopy (DLTS) and deep level optical spectroscopy (DLOS) measurements have been carried out in neutron-irradiated n-type hydride-vapor-phase-epitaxy-grown GaN. A defect center characterized by a DLTS line, labeled as N1, is observed at E C -E T =0.17 eV. Another line, labeled as N2, at E C -E T =0.23 eV, seems to be induced at the same rate as N1 under irradiation and may be identified with E1. Other defects native to wurtzite GaN such as the C and E2 lines appear to enhance under neutron irradiation. The DLOS results show that the defects N1 and N2 have large Frank-Condon shifts of 0.64 and 0.67 eV, respectively, and hence large lattice relaxations. The as-grown and neutron-irradiated samples all exhibit the persistent photoconductivity effect commonly seen in GaN that may be attributed to DX centers. The concentration of the DX centers increases significantly with neutron dosage and is helpful in sustaining sample conductivity at low temperatures, thus making possible DLTS measurements on N1 an N2 in the radiation-induced deep-donor defect compensated material which otherwise are prevented by carrier freeze-out

Evaluation of a high resolution silicon PET insert module

Energy Technology Data Exchange (ETDEWEB)

Grkovski, Milan, E-mail: milan.grkovski@ijs.si [Jožef Stefan Institute, Ljubljana (Slovenia); Memorial Sloan Kettering Cancer Center, New York, NY (United States); Brzezinski, Karol [IFIC/CSIC, Valencia (Spain); Cindro, Vladimir [Jožef Stefan Institute, Ljubljana (Slovenia); Clinthorne, Neal H. [University of Michigan, Ann Arbor, MI (United States); Kagan, Harris [Ohio State University, Columbus, OH (United States); Lacasta, Carlos [IFIC/CSIC, Valencia (Spain); Mikuž, Marko [Jožef Stefan Institute, Ljubljana (Slovenia); Solaz, Carles [IFIC/CSIC, Valencia (Spain); Studen, Andrej [Jožef Stefan Institute, Ljubljana (Slovenia); Weilhammer, Peter [Ohio State University, Columbus, OH (United States); Žontar, Dejan [Jožef Stefan Institute, Ljubljana (Slovenia)

2015-07-11

Conventional PET systems can be augmented with additional detectors placed in close proximity of the region of interest. We developed a high resolution PET insert module to evaluate the added benefit of such a combination. The insert module consists of two back-to-back 1 mm thick silicon sensors, each segmented into 1040 1 mm{sup 2} pads arranged in a 40 by 26 array. A set of 16 VATAGP7.1 ASICs and a custom assembled data acquisition board were used to read out the signal from the insert module. Data were acquired in slice (2D) geometry with a Jaszczak phantom (rod diameters of 1.2–4.8 mm) filled with {sup 18}F-FDG and the images were reconstructed with ML-EM method. Both data with full and limited angular coverage from the insert module were considered and three types of coincidence events were combined. The ratio of high-resolution data that substantially improves quality of the reconstructed image for the region near the surface of the insert module was estimated to be about 4%. Results from our previous studies suggest that such ratio could be achieved at a moderate technological expense by using an equivalent of two insert modules (an effective sensor thickness of 4 mm)

Large-scale transportation network congestion evolution prediction using deep learning theory.

Science.gov (United States)

Ma, Xiaolei; Yu, Haiyang; Wang, Yunpeng; Wang, Yinhai

2015-01-01

Understanding how congestion at one location can cause ripples throughout large-scale transportation network is vital for transportation researchers and practitioners to pinpoint traffic bottlenecks for congestion mitigation. Traditional studies rely on either mathematical equations or simulation techniques to model traffic congestion dynamics. However, most of the approaches have limitations, largely due to unrealistic assumptions and cumbersome parameter calibration process. With the development of Intelligent Transportation Systems (ITS) and Internet of Things (IoT), transportation data become more and more ubiquitous. This triggers a series of data-driven research to investigate transportation phenomena. Among them, deep learning theory is considered one of the most promising techniques to tackle tremendous high-dimensional data. This study attempts to extend deep learning theory into large-scale transportation network analysis. A deep Restricted Boltzmann Machine and Recurrent Neural Network architecture is utilized to model and predict traffic congestion evolution based on Global Positioning System (GPS) data from taxi. A numerical study in Ningbo, China is conducted to validate the effectiveness and efficiency of the proposed method. Results show that the prediction accuracy can achieve as high as 88% within less than 6 minutes when the model is implemented in a Graphic Processing Unit (GPU)-based parallel computing environment. The predicted congestion evolution patterns can be visualized temporally and spatially through a map-based platform to identify the vulnerable links for proactive congestion mitigation.

ORF Alignment: NC_002128 [GENIUS II[Archive

Lifescience Database Archive (English)

Full Text Available ing protein SopA [Large-insert cloning vector ... pSMART VC] gb|AAR05665.1| stabilization of plasmid ... ... protein A [Salmonella typhimurium] gb|AAO61293.1| ParA ... [BAC cloning vector pEBAC190G

Viral Bacterial Artificial Chromosomes: Generation, Mutagenesis, and Removal of Mini-F Sequences

Directory of Open Access Journals (Sweden)

B. Karsten Tischer

2012-01-01

Full Text Available Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.

Analysis of large optical ground stations for deep-space optical communications

Science.gov (United States)

Garcia-Talavera, M. Reyes; Rivera, C.; Murga, G.; Montilla, I.; Alonso, A.

2017-11-01

Inter-satellite and ground to satellite optical communications have been successfully demonstrated over more than a decade with several experiments, the most recent being NASA's lunar mission Lunar Atmospheric Dust Environment Explorer (LADEE). The technology is in a mature stage that allows to consider optical communications as a high-capacity solution for future deep-space communications [1][2], where there is an increasing demand on downlink data rate to improve science return. To serve these deep-space missions, suitable optical ground stations (OGS) have to be developed providing large collecting areas. The design of such OGSs must face both technical and cost constraints in order to achieve an optimum implementation. To that end, different approaches have already been proposed and analyzed, namely, a large telescope based on a segmented primary mirror, telescope arrays, and even the combination of RF and optical receivers in modified versions of existing Deep-Space Network (DSN) antennas [3][4][5]. Array architectures have been proposed to relax some requirements, acting as one of the key drivers of the present study. The advantages offered by the array approach are attained at the expense of adding subsystems. Critical issues identified for each implementation include their inherent efficiency and losses, as well as its performance under high-background conditions, and the acquisition, pointing, tracking, and synchronization capabilities. It is worth noticing that, due to the photon-counting nature of detection, the system performance is not solely given by the signal-to-noise ratio parameter. To start with the analysis, first the main implications of the deep space scenarios are summarized, since they are the driving requirements to establish the technical specifications for the large OGS. Next, both the main characteristics of the OGS and the potential configuration approaches are presented, getting deeper in key subsystems with strong impact in the

Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

Directory of Open Access Journals (Sweden)

Wang Jintu

2011-04-01

Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

Science.gov (United States)

2011-01-01

Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

Germ-line transformation of the Queensland fruit fly, Bactrocera tryoni, using a piggyBac vector in the presence of endogenous piggyBac elements

Science.gov (United States)

We report the stable genetic transformation of the Queensland fruit fly Bactrocera tryoni using a piggyBac vector marked with either the fluorescent protein DsRed or EGFP.A transformation frequency of 5–10% was obtained.Inheritance of the transgenes has remained stable over eight generations despite...

Incidence of thrombosis in children with tunneled central venous access devices versus peripherally inserted central catheters (PICCs).

Science.gov (United States)

Kanin, Maralee; Young, Guy

2013-11-01

The recent proliferation of deep vein thrombosis in children has been attributed to the increased use of central venous catheters, specifically tunneled lines and peripherally inserted central catheters. A formal comparison of the incidence rate for deep vein thrombosis between tunneled lines and peripherally inserted central catheters has not been undertaken. Children inclusion. Data were extracted from the hospital discharge database which includes data on all procedures and up to 20 diagnoses per admission. Diagnoses and procedures were identified by International Classification of Disease, Ninth Revision coding. Patients were excluded if they received more than one central line. Data collected included type of central line, deep vein thrombosis event, and underlying medical illnesses classified according to chronic complex conditions. Over the seven year study period there was an overall rate of 73 deep vein thromboses per 10,000 hospital discharges. Of the 6915 eligible subjects, 181 had a deep vein thrombosis for an overall incidence rate of 2.6%. There were 152 thrombi (2.6%) in subjects with peripherally inserted central catheters and 29 thrombi (3.1%) in subjects with tunneled lines [OR=.83 (0.55, 1.29), p=0.38]. Despite the relative ease and simplicity of use of peripherally inserted central catheters leading to a substantial rise in their use, this study demonstrates that such lines pose a substantial risk for venous thrombosis and no difference in incidence was detected between such lines and tunneled lines. © 2013.

Response of deep and shallow tropical maritime cumuli to large-scale processes

Science.gov (United States)

Yanai, M.; Chu, J.-H.; Stark, T. E.; Nitta, T.

1976-01-01

The bulk diagnostic method of Yanai et al. (1973) and a simplified version of the spectral diagnostic method of Nitta (1975) are used for a more quantitative evaluation of the response of various types of cumuliform clouds to large-scale processes, using the same data set in the Marshall Islands area for a 100-day period in 1956. The dependence of the cloud mass flux distribution on radiative cooling, large-scale vertical motion, and evaporation from the sea is examined. It is shown that typical radiative cooling rates in the tropics tend to produce a bimodal distribution of mass spectrum exhibiting deep and shallow clouds. The bimodal distribution is further enhanced when the large-scale vertical motion is upward, and a nearly unimodal distribution of shallow clouds prevails when the relative cooling is compensated by the heating due to the large-scale subsidence. Both deep and shallow clouds are modulated by large-scale disturbances. The primary role of surface evaporation is to maintain the moisture flux at the cloud base.

A novel method of microneedle array fabrication using inclined deep x-ray exposure

International Nuclear Information System (INIS)

Moon, Sang Jun; Jin, Chun Yan; Lee, Seung S

2006-01-01

We report a novel fabrication method for the microneedle array with a 3-dimensional feature and its replication method; 'Hot-pressing' process with bio-compatible material, PLLA (Poly L-LActide). Using inclined deep X-ray exposure technique, we fabricate a band type microneedle array with a single body on the same material basement. Since the single body feature does not make adhesion problem with the microneedle shank and basement during peel-off step of a mold, the PMMA (Poly-Methyl-MethAcrylate) microneedle array mold insert can be used for mold process which is used with the soft material mold, PDMS (Poly-Di- Methyl-Siloxane). The side inclined deep X-ray exposure also makes complex 3-dimensional features by the regions which are not exposed during twice successive exposure steps. In addition, the successive exposure does not need an additional mask alignment after the first side exposure. The fabricated band type microneedle array mold inserts are assembled for large area patch type out-of-plane microneedle array. The bio-compatible microneedle array can be fabricated to the laboratory scale mass production by the single body PMMA mold insert and 'Hot-pressing' process

A novel method of microneedle array fabrication using inclined deep x-ray exposure

Energy Technology Data Exchange (ETDEWEB)

Moon, Sang Jun; Jin, Chun Yan; Lee, Seung S [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology (KAIST), 373-1, Guseong-dong, Yuseong-dong, Daejeon (Korea, Republic of)

2006-04-01

We report a novel fabrication method for the microneedle array with a 3-dimensional feature and its replication method; 'Hot-pressing' process with bio-compatible material, PLLA (Poly L-LActide). Using inclined deep X-ray exposure technique, we fabricate a band type microneedle array with a single body on the same material basement. Since the single body feature does not make adhesion problem with the microneedle shank and basement during peel-off step of a mold, the PMMA (Poly-Methyl-MethAcrylate) microneedle array mold insert can be used for mold process which is used with the soft material mold, PDMS (Poly-Di- Methyl-Siloxane). The side inclined deep X-ray exposure also makes complex 3-dimensional features by the regions which are not exposed during twice successive exposure steps. In addition, the successive exposure does not need an additional mask alignment after the first side exposure. The fabricated band type microneedle array mold inserts are assembled for large area patch type out-of-plane microneedle array. The bio-compatible microneedle array can be fabricated to the laboratory scale mass production by the single body PMMA mold insert and 'Hot-pressing' process.

Large-scale transportation network congestion evolution prediction using deep learning theory.

Directory of Open Access Journals (Sweden)

Xiaolei Ma

Full Text Available Understanding how congestion at one location can cause ripples throughout large-scale transportation network is vital for transportation researchers and practitioners to pinpoint traffic bottlenecks for congestion mitigation. Traditional studies rely on either mathematical equations or simulation techniques to model traffic congestion dynamics. However, most of the approaches have limitations, largely due to unrealistic assumptions and cumbersome parameter calibration process. With the development of Intelligent Transportation Systems (ITS and Internet of Things (IoT, transportation data become more and more ubiquitous. This triggers a series of data-driven research to investigate transportation phenomena. Among them, deep learning theory is considered one of the most promising techniques to tackle tremendous high-dimensional data. This study attempts to extend deep learning theory into large-scale transportation network analysis. A deep Restricted Boltzmann Machine and Recurrent Neural Network architecture is utilized to model and predict traffic congestion evolution based on Global Positioning System (GPS data from taxi. A numerical study in Ningbo, China is conducted to validate the effectiveness and efficiency of the proposed method. Results show that the prediction accuracy can achieve as high as 88% within less than 6 minutes when the model is implemented in a Graphic Processing Unit (GPU-based parallel computing environment. The predicted congestion evolution patterns can be visualized temporally and spatially through a map-based platform to identify the vulnerable links for proactive congestion mitigation.

BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple.

Science.gov (United States)

Han, Yuepeng; Chagné, David; Gasic, Ksenija; Rikkerink, Erik H A; Beever, Jonathan E; Gardiner, Susan E; Korban, Schuyler S

2009-03-01

A genome-wide BAC physical map of the apple, Malus x domestica Borkh., has been recently developed. Here, we report on integrating the physical and genetic maps of the apple using a SNP-based approach in conjunction with bin mapping. Briefly, BAC clones located at ends of BAC contigs were selected, and sequenced at both ends. The BAC end sequences (BESs) were used to identify candidate SNPs. Subsequently, these candidate SNPs were genetically mapped using a bin mapping strategy for the purpose of mapping the physical onto the genetic map. Using this approach, 52 (23%) out of 228 BESs tested were successfully exploited to develop SNPs. These SNPs anchored 51 contigs, spanning approximately 37 Mb in cumulative physical length, onto 14 linkage groups. The reliability of the integration of the physical and genetic maps using this SNP-based strategy is described, and the results confirm the feasibility of this approach to construct an integrated physical and genetic maps for apple.

Comparison of 'time to detection' values between BacT/ALERT VIRTUO and BacT/ALERT 3D instruments for clinical blood culture samples.

Science.gov (United States)

Congestrì, Francesco; Pedna, Maria Federica; Fantini, Michela; Samuelli, Michela; Schiavone, Pasqua; Torri, Arianna; Bertini, Stefania; Sambri, Vittorio

2017-09-01

The early detection of bacteraemia and fungemia is of paramount importance to guide antimicrobial therapy in septic patients. In this study the 'time to detection' (TTD) value for the new blood culture system BacT/ALERT VIRTUO (VIRTUO) was evaluated in 1462 positive clinical bottles and compared with the TTD for 1601 positive clinical bottles incubated in the BacT/ALERT 3D system (BTA-3D). The most representative microorganisms isolated from bottles incubated in both blood culture systems were divided into eight categories (in order of frequency): coagulase-negative staphylococci (CoNS), Escherichia coli, Enterobacteriaceae (other than E. coli), Staphylococcus aureus, Enterococcus spp, viridans group streptococci, Pseudomonas aeruginosa, and Candida spp. The comparison of TTD values for the two blood culture systems strongly indicated that growth of the first five groups listed above was detected earlier with VIRTUO than with BTA-3D (p culture system can reduce the TTD for more than 75% of isolated microorganisms. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The need for blood alcohol concentration (BAC) legislation in Nigeria

African Journals Online (AJOL)

The pharmacology, clinical and sports implications of indulgence in alcohol and the debate on its legal status are highlighted in this article. The information presented could offer both clinical and safety benefits to psychomotor tasks executors and road safety professionals. Keywords: Blood alcohol concentration (BAC), ...

Third-Generation Sequencing and Analysis of Four Complete Pig Liver Esterase Gene Sequences in Clones Identified by Screening BAC Library.

Science.gov (United States)

Zhou, Qiongqiong; Sun, Wenjuan; Liu, Xiyan; Wang, Xiliang; Xiao, Yuncai; Bi, Dingren; Yin, Jingdong; Shi, Deshi

2016-01-01

Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing. After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification. Specific primers were then selected based on the PCR amplification results. A three-step PCR screening method was used to identify PLE-positive clones by screening a Rongchang pig BAC library and PacBio third-generation sequencing was performed. BLAST comparisons and other bioinformatics methods were applied for sequence analysis. Five PLE-positive BAC clones, designated BAC-10, BAC-70, BAC-75, BAC-119 and BAC-206, were identified. Sequence analysis yielded the complete sequences of four PLE genes, PLE1, PLE-B9, PLE-C4, and PLE-G2. Complete PLE gene sequences were defined as those containing regulatory sequences, exons, and introns. It was found that, not only did the PLE exon sequences of the four genes show a high degree of homology, but also that the intron sequences were highly similar. Additionally, the regulatory region of the genes contained two 720bps reverse complement sequences that may have an important function in the regulation of PLE gene expression. This is the first report to confirm the complete sequences of four PLE genes. In addition, the study demonstrates that each PLE isoform is encoded by a single gene and that the various genes exhibit a high degree of sequence homology, suggesting that the PLE family evolved from a single ancestral gene. Obtaining the complete sequences of these PLE genes provides the necessary foundation for

The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood

Science.gov (United States)

Rothman, Richard E.; Peterson, Stephen; Carroll, Karen C.; Zhang, Sean X.; Avornu, Gideon D.; Rounds, Megan A.; Carolan, Heather E.; Toleno, Donna M.; Moore, David; Hall, Thomas A.; Massire, Christian; Richmond, Gregory S.; Gutierrez, Jose R.; Sampath, Rangarajan; Ecker, David J.; Blyn, Lawrence B.

2016-01-01

Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States. PMID:27384540

Genome-wide BAC-end sequencing of Musa acuminata DH Pahang reveals further insights into the genome organization of banana

NARCIS (Netherlands)

Arnago, R.E.; Togawa, R.C.; Carpentier, S.C.; Lintel Hekkert, te B.; Kema, G.H.J.; Souza, M.T.

2011-01-01

Banana and plantain (Musa spp.) are grown in more than 120 countries in tropical and subtropical regions and constitute an important staple food for millions of people. A Musa acuminata ssp. malaccencis DH Pahang bacterial artificial chromosome (BAC) library (MAMB) was submitted for BAC-end

Generation of BAC transgenic epithelial organoids.

Directory of Open Access Journals (Sweden)

Gerald Schwank

Full Text Available Under previously developed culture conditions, mouse and human intestinal epithelia can be cultured and expanded over long periods. These so-called organoids recapitulate the three-dimensional architecture of the gut epithelium, and consist of all major intestinal cell types. One key advantage of these ex vivo cultures is their accessibility to live imaging. So far the establishment of transgenic fluorescent reporter organoids has required the generation of transgenic mice, a laborious and time-consuming process, which cannot be extended to human cultures. Here we present a transfection protocol that enables the generation of recombinant mouse and human reporter organoids using BAC (bacterial artificial chromosome technology.

An efficient approach to BAC based assembly of complex genomes

Czech Academy of Sciences Publication Activity Database

Visendi, P.; Berkman, P.J.; Hayashi, S.; Golicz, A.A.; Bayer, P.E.; Ruperao, P.; Hurgobin, B.; Montenegro, J.; Chan, C.K.K.; Staňková, Helena; Batley, J.; Šimková, Hana; Doležel, Jaroslav; Edwards, D.

2016-01-01

Roč. 12, JAN 20 (2016), s. 2 ISSN 1746-4811 R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GAP501/12/2554 Institutional support: RVO:61389030 Keywords : Next-generation sequencing * SASSY * BAC Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.510, year: 2016

Characterization of Extracellular Penicilin G Acylase Produced by A New Local Strain of Bacillus subtilis BAC4

Directory of Open Access Journals (Sweden)

SUPARTONO

2008-06-01

Full Text Available Penicillin G acylase (PGA which catalyses penicillin G hydrolysis reaction is a key enzyme for the industrial production of penicilin G derivatives used in therapeutics. A new local strain of Bacillus subtilis BAC4 was found capable of producing extracellular PGA. However, characteristics of this extracellular PGA are not known. The goal of this research was to characterize the extracellular PGA produced by B. subtilis BAC4. Enzyme production was carried out by batch fermentation, followed by enzyme purification and characterization of the PGA. The PGA activity was determined by the Kornfeld method, with optimal activity for hydrolysing penicillin G observed at 43 °C and pH 8.5. The activation energy of penicillin G hydrolysis by the PGA of B. subtilis BAC4 was determined as 4.9 kcal.mol−1 and Vmax and Km values were found to be 0.7 μmole.min−1.mg−1 and 3.5 mM respectively. PGA catalytic activity was competitively inhibited by phenylacetic acid with an inhibition constant, Ki(PAA, of 347.2 mM. It was concluded that the extracellular PGA of B. subtilis BAC4 can hydrolyse penicillin G efficiently.

Characterization of Extracellular Penicilin G Acylase Produced by A New Local Strain of Bacillus subtilis BAC4

Directory of Open Access Journals (Sweden)

SUPARTONO

2008-06-01

Full Text Available Penicillin G acylase (PGA which catalyses penicillin G hydrolysis reaction is a key enzyme for the industrial production of penicilin G derivatives used in therapeutics. A new local strain of Bacillus subtilis BAC4 was found capable of producing extracellular PGA. However, characteristics of this extracellular PGA are not known. The goal of this research was to characterize the extracellular PGA produced by B. subtilis BAC4. Enzyme production was carried out by batch fermentation, followed by enzyme purification and characterization of the PGA. The PGA activity was determined by the Kornfeld method, with optimal activity for hydrolysing penicillin G observed at 43 oC and pH 8.5. The activation energy of penicillin G hydrolysis by the PGA of B. subtilis BAC4 was determined as 4.9 kcal.mol-1 and Vmax and Km values were found to be 0.7 µmole.min-1.mg-1 and 3.5 mM respectively. PGA catalytic activity was competitively inhibited by phenylacetic acid with an inhibition constant, Ki(PAA, of 347.2 mM. It was concluded that the extracellular PGA of B. subtilis BAC4 can hydrolyse penicillin G efficiently.

Deep whole-genome sequencing of 90 Han Chinese genomes.

Science.gov (United States)

Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

2017-09-01

Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

Deep coverage of the beer proteome.

Science.gov (United States)

Grochalová, Martina; Konečná, Hana; Stejskal, Karel; Potěšil, David; Fridrichová, Danuše; Srbová, Eva; Ornerová, Kateřina; Zdráhal, Zbyněk

2017-06-06

We adopted an approach based on peptide immobilized pH gradient-isoelectric focusing (IPG-IEF) separation, coupled with LC-MS/MS, in order to maximize coverage of the beer proteome. A lager beer brewed using traditional Czech technology was degassed, desalted and digested. Tryptic peptides were separated by isoelectric focusing on an immobilized pH gradient strip and, after separation, the gel strip was divided into seven equally sized parts. Peptides extracted from gel fractions were analyzed by LC-MS/MS. This approach resulted in a three-fold increase in the number of proteins identified (over 1700) when compared to analysis of unfractionated beer processed by a filter-aided sample preparation (FASP). Over 1900 protein groups (PGs) in total were identified by both approaches. The study significantly extends knowledge about the beer proteome and demonstrates its complexity. Detailed knowledge of the protein content, especially gluten proteins, will enhance the evaluation of potential health risks related to beer consumption (coeliac disease) and will contribute to improving beer quality. Copyright © 2017 Elsevier B.V. All rights reserved.

Combining shallow and deep processing for a robust, fast, deep-linguistic dependency parser

OpenAIRE

Schneider, G

2004-01-01

This paper describes Pro3Gres, a fast, robust, broad-coverage parser that delivers deep-linguistic grammatical relation structures as output, which are closer to predicate-argument structures and more informative than pure constituency structures. The parser stays as shallow as is possible for each task, combining shallow and deep-linguistic methods by integrating chunking and by expressing the majority of long-distance dependencies in a context-free way. It combines statistical and rule-base...

Climate, carbon cycling, and deep-ocean ecosystems.

Science.gov (United States)

Smith, K L; Ruhl, H A; Bett, B J; Billett, D S M; Lampitt, R S; Kaufmann, R S

2009-11-17

Climate variation affects surface ocean processes and the production of organic carbon, which ultimately comprises the primary food supply to the deep-sea ecosystems that occupy approximately 60% of the Earth's surface. Warming trends in atmospheric and upper ocean temperatures, attributed to anthropogenic influence, have occurred over the past four decades. Changes in upper ocean temperature influence stratification and can affect the availability of nutrients for phytoplankton production. Global warming has been predicted to intensify stratification and reduce vertical mixing. Research also suggests that such reduced mixing will enhance variability in primary production and carbon export flux to the deep sea. The dependence of deep-sea communities on surface water production has raised important questions about how climate change will affect carbon cycling and deep-ocean ecosystem function. Recently, unprecedented time-series studies conducted over the past two decades in the North Pacific and the North Atlantic at >4,000-m depth have revealed unexpectedly large changes in deep-ocean ecosystems significantly correlated to climate-driven changes in the surface ocean that can impact the global carbon cycle. Climate-driven variation affects oceanic communities from surface waters to the much-overlooked deep sea and will have impacts on the global carbon cycle. Data from these two widely separated areas of the deep ocean provide compelling evidence that changes in climate can readily influence deep-sea processes. However, the limited geographic coverage of these existing time-series studies stresses the importance of developing a more global effort to monitor deep-sea ecosystems under modern conditions of rapidly changing climate.

Variation in the insertion of the palmaris longus tendon

Science.gov (United States)

Sunil, Vinutha; Rajanna, Shubha; Gitanjali; Kadaba, Jayanthi

2015-01-01

The palmaris longus is harvested as a tendon graft in various surgical procedures. We herein report the variations in the insertion of the palmaris longus tendon. During a routine dissection, a rare variation in the insertion of the palmaris longus tendon was observed. In the left forearm, the palmaris longus tendon bifurcated, while in the right forearm, the palmaris longus tendon trifurcated, giving rise to an accessory muscle, which passed superficial to the ulnar artery and ulnar nerve. The accessory muscle was supplied by a deep branch of the ulnar nerve, and the ulnar artery was observed to be tortuous. During reconstructive surgeries, surgeons should bear in mind the accessory muscle. Also, since the palmaris longus muscle provides a very useful graft in tendon surgery, every surgeon should be aware of the variations in the insertion of the palmaris longus tendon. PMID:25640108

Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

Directory of Open Access Journals (Sweden)

King Graham J

2010-10-01

Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads.

Directory of Open Access Journals (Sweden)

Jovan Rebolledo-Mendez

Full Text Available The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight's half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects' and Twilight's genome or due to errors in the reference. EquCab2 is regarded as "The Twilight Assembly." The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies

Multicenter Clinical Evaluation of BacT/Alert Virtuo Blood Culture System.

Science.gov (United States)

Jacobs, Michael R; Mazzulli, Tony; Hazen, Kevin C; Good, Caryn E; Abdelhamed, Ayman M; Lo, Pauline; Shum, Bianche; Roman, Katharine P; Robinson, Danielle C

2017-08-01

BacT/Alert Virtuo is an advanced, automated blood culture system incorporating improved automation and an enhanced detection algorithm to shorten time to detection. A multicenter study of the investigational Virtuo system (bioMérieux, Inc., Durham, NC) compared to BacT/Alert 3D (BTA3D) for detection of bacteremia/fungemia in four bottle types, SA and FA Plus (aerobic) and SN and FN Plus (anaerobic), was performed in a clinical setting with patient samples in a matched system design clinical trial. Blood was added to paired aerobic or anaerobic bottles, with the volume in each bottle in each pair required to be ≤10 ml and with the volumes required to be within 30% of each other. Of 5,709 bottle sets (52.5% aerobic pairs and 47.5% anaerobic pairs), 430 (7.5%) were positive for bacterial or fungal growth, with 342 (6.0%) clinically significant and 83 (1.5%) contaminated. A total of 3,539 sets (62.0%) were volume compliant, with 203 sets (5.7%) clinically significant. The positivity rates for volume-compliant bottle pairs determined by the two systems were comparable, with 68.7% of clinically significant isolates detected by both instruments, 15.7% by Virtuo only, and 15.7% by BTA3D only. Virtuo detected microbial growth nearly 2 h sooner overall than BTA3D (mean, 15.9 h versus 17.7 h). Shorter time to detection by Virtuo was related to organism group, with the time to detection being significantly shorter for enteric Gram-negative bacilli and enterococci (means, 3.6 h and 2.3 h shorter, respectively). This large clinical study demonstrated that the Virtuo blood culture system produced results comparable to those seen with the long-established BTA3D system, with significantly shorter time to detection. Copyright © 2017 Jacobs et al.

Earthquakes drive large-scale submarine canyon development and sediment supply to deep-ocean basins.

Science.gov (United States)

Mountjoy, Joshu J; Howarth, Jamie D; Orpin, Alan R; Barnes, Philip M; Bowden, David A; Rowden, Ashley A; Schimel, Alexandre C G; Holden, Caroline; Horgan, Huw J; Nodder, Scott D; Patton, Jason R; Lamarche, Geoffroy; Gerstenberger, Matthew; Micallef, Aaron; Pallentin, Arne; Kane, Tim

2018-03-01

Although the global flux of sediment and carbon from land to the coastal ocean is well known, the volume of material that reaches the deep ocean-the ultimate sink-and the mechanisms by which it is transferred are poorly documented. Using a globally unique data set of repeat seafloor measurements and samples, we show that the moment magnitude ( M w ) 7.8 November 2016 Kaikōura earthquake (New Zealand) triggered widespread landslides in a submarine canyon, causing a powerful "canyon flushing" event and turbidity current that traveled >680 km along one of the world's longest deep-sea channels. These observations provide the first quantification of seafloor landscape change and large-scale sediment transport associated with an earthquake-triggered full canyon flushing event. The calculated interevent time of ~140 years indicates a canyon incision rate of 40 mm year -1 , substantially higher than that of most terrestrial rivers, while synchronously transferring large volumes of sediment [850 metric megatons (Mt)] and organic carbon (7 Mt) to the deep ocean. These observations demonstrate that earthquake-triggered canyon flushing is a primary driver of submarine canyon development and material transfer from active continental margins to the deep ocean.

Using Flipped Classroom Approach to Explore Deep Learning in Large Classrooms

Science.gov (United States)

Danker, Brenda

2015-01-01

This project used two Flipped Classroom approaches to stimulate deep learning in large classrooms during the teaching of a film module as part of a Diploma in Performing Arts course at Sunway University, Malaysia. The flipped classes utilized either a blended learning approach where students first watched online lectures as homework, and then…

Effect of mercaptoethylamine on DNA degradation in thermophilic bacteria Bac. stearothermophilus exposed to. gamma. -, UV-radiation or methylnitrosourea

Energy Technology Data Exchange (ETDEWEB)

Fomenko, L A; Kuznetsovea, E A; Gaziev, A I

1984-07-01

The effect of mercaptoethylamine (MEA) on degradation of DNA in thermophilic bacteria Bac. stear. exposed to ..gamma..-, UV-rays or methylnitrosourea (MNU) was studied. Using centrifugation on alkaline and neutral sucrose gradients, it was shown that MEA inhibits the accumulation of breaks in the DNA of Bac. stear. It also lowers the level of DNA degradation in toluene-treated cells of Bac. stear. under the action of the intrinsic nuclease, reduces the activity of the endonuclease specific for apurinic DNA, as well as that of S/sub 1/-nuclease and DNase-I in vitro. The inhibition in the accumulation of DNA breaks is assumed to be due to a decrease of the endonuclease activity in the cells of thermophilic bacteria.

Effect of mercaptoethylamine on DNA degradation in thermophilic bacteria Bac. stearothermophilus exposed to γ-, UV-radiation or methylnitrosourea

International Nuclear Information System (INIS)

Fomenko, L.A.; Kuznetsovea, E.A.; Gaziev, A.I.

1984-01-01

The effect of mercaptoethylamine (MEA) on degradation of DNA in thermophilic bacteria Bac. stear. exposed to γ-, UV-rays or methylnitrosourea (MNU) was studied. Using centrifugation on alkaline and neutral sucrose gradients, it was shown that MEA inhibits the accumulation of breaks in the DNA of Bac. stear. It also lowers the level of DNA degradation in toluene-treated cells of Bac. stear. under the action of the intrinsic nuclease, reduces the activity of the endonuclease specific for apurinic DNA, as well as that of S 1 -nuclease and DNase-I in vitro. The inhibition in the accumulation of DNA breaks is assumed to be due to a decrease of the endonuclease activity in the cells of thermophilic bacteria. (orig.)

Large scale anisotropy studies with the Auger Observatory

International Nuclear Information System (INIS)

Santos, E.M.; Letessier-Selvon, A.

2006-01-01

With the increasing Auger surface array data sample of the highest energy cosmic rays, large scale anisotropy studies at this part of the spectrum become a promising path towards the understanding of the origin of ultra-high energy cosmic particles. We describe the methods underlying the search for distortions in the cosmic rays arrival directions over large angular scales, that is, bigger than those commonly employed in the search for correlations with point-like sources. The widely used tools, known as coverage maps, are described and some of the issues involved in their calculations are presented through Monte Carlo based studies. Coverage computation requires a deep knowledge on the local detection efficiency, including the influence of weather parameters like temperature and pressure. Particular attention is devoted to a new proposed method to extract the coverage, based upon the assumption of time factorization of an extensive air shower detector acceptance. We use Auger monitoring data to test the goodness of such a hypothesis. We finally show the necessity of using more than one coverage to extract any possible anisotropic pattern on the sky, by pointing to some of the biases present in commonly used methods based, for example, on the scrambling of the UTC arrival times for each event. (author)

Genic regions of a large salamander genome contain long introns and novel genes

Directory of Open Access Journals (Sweden)

Bryant Susan V

2009-01-01

Full Text Available Abstract Background The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp were isolated and sequenced to characterize the structure of genic regions. Results Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86% of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases! Conclusion This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.

State Blood Alcohol Concentration (BAC) Testing and Reporting for Drivers Involved in Fatal Crashes : Current Practices, Results, and Strategies, 1997-2009

Science.gov (United States)

2012-08-01

This report documents current State blood alcohol concentration (BAC) testing and reporting practices and results for drivers involved in fatal crashes. It summarizes known BAC results by State for the years 1997 to 2009 for both fatally injured and ...

Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes.

Science.gov (United States)

Kukekova, Anna V; Vorobieva, Nadegda V; Beklemisheva, Violetta R; Johnson, Jennifer L; Temnykh, Svetlana V; Yudkin, Dmitry V; Trut, Lyudmila N; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D; Acland, Gregory M; Graphodatsky, Alexander S

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.

Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

Science.gov (United States)

Seoane-Zonjic, Pedro; Cañas, Rafael A; Bautista, Rocío; Gómez-Maldonado, Josefa; Arrillaga, Isabel; Fernández-Pozo, Noé; Claros, M Gonzalo; Cánovas, Francisco M; Ávila, Concepción

2016-02-27

In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82% of the gene structures, and a high proportion (85%) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members. The experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a

The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome.

Science.gov (United States)

Cook, R Kimberley; Christensen, Stacey J; Deal, Jennifer A; Coburn, Rachel A; Deal, Megan E; Gresens, Jill M; Kaufman, Thomas C; Cook, Kevin R

2012-01-01

Chromosomal deletions are used extensively in Drosophila melanogaster genetics research. Deletion mapping is the primary method used for fine-scale gene localization. Effective and efficient deletion mapping requires both extensive genomic coverage and a high density of molecularly defined breakpoints across the genome. A large-scale resource development project at the Bloomington Drosophila Stock Center has improved the choice of deletions beyond that provided by previous projects. FLP-mediated recombination between FRT-bearing transposon insertions was used to generate deletions, because it is efficient and provides single-nucleotide resolution in planning deletion screens. The 793 deletions generated pushed coverage of the euchromatic genome to 98.4%. Gaps in coverage contain haplolethal and haplosterile genes, but the sizes of these gaps were minimized by flanking these genes as closely as possible with deletions. In improving coverage, a complete inventory of haplolethal and haplosterile genes was generated and extensive information on other haploinsufficient genes was compiled. To aid mapping experiments, a subset of deletions was organized into a Deficiency Kit to provide maximal coverage efficiently. To improve the resolution of deletion mapping, screens were planned to distribute deletion breakpoints evenly across the genome. The median chromosomal interval between breakpoints now contains only nine genes and 377 intervals contain only single genes. Drosophila melanogaster now has the most extensive genomic deletion coverage and breakpoint subdivision as well as the most comprehensive inventory of haploinsufficient genes of any multicellular organism. The improved selection of chromosomal deletion strains will be useful to nearly all Drosophila researchers.

Large deep neural networks for MS lesion segmentation

Science.gov (United States)

Prieto, Juan C.; Cavallari, Michele; Palotai, Miklos; Morales Pinzon, Alfredo; Egorova, Svetlana; Styner, Martin; Guttmann, Charles R. G.

2017-02-01

Multiple sclerosis (MS) is a multi-factorial autoimmune disorder, characterized by spatial and temporal dissemination of brain lesions that are visible in T2-weighted and Proton Density (PD) MRI. Assessment of lesion burden and is useful for monitoring the course of the disease, and assessing correlates of clinical outcomes. Although there are established semi-automated methods to measure lesion volume, most of them require human interaction and editing, which are time consuming and limits the ability to analyze large sets of data with high accuracy. The primary objective of this work is to improve existing segmentation algorithms and accelerate the time consuming operation of identifying and validating MS lesions. In this paper, a Deep Neural Network for MS Lesion Segmentation is implemented. The MS lesion samples are extracted from the Partners Comprehensive Longitudinal Investigation of Multiple Sclerosis (CLIMB) study. A set of 900 subjects with T2, PD and a manually corrected label map images were used to train a Deep Neural Network and identify MS lesions. Initial tests using this network achieved a 90% accuracy rate. A secondary goal was to enable this data repository for big data analysis by using this algorithm to segment the remaining cases available in the CLIMB repository.

A PILOT FOR A VERY LARGE ARRAY H I DEEP FIELD

International Nuclear Information System (INIS)

Fernández, Ximena; Van Gorkom, J. H.; Schiminovich, David; Hess, Kelley M.; Pisano, D. J.; Kreckel, Kathryn; Momjian, Emmanuel; Popping, Attila; Oosterloo, Tom; Chomiuk, Laura; Verheijen, M. A. W.; Henning, Patricia A.; Bershady, Matthew A.; Wilcots, Eric M.; Scoville, Nick

2013-01-01

High-resolution 21 cm H I deep fields provide spatially and kinematically resolved images of neutral hydrogen at different redshifts, which are key to understanding galaxy evolution across cosmic time and testing predictions of cosmological simulations. Here we present results from a pilot for an H I deep field done with the Karl G. Jansky Very Large Array (VLA). We take advantage of the newly expanded capabilities of the telescope to probe the redshift interval 0 < z < 0.193 in one observation. We observe the COSMOS field for 50 hr, which contains 413 galaxies with optical spectroscopic redshifts in the imaged field of 34' × 34' and the observed redshift interval. We have detected neutral hydrogen gas in 33 galaxies in different environments spanning the probed redshift range, including three without a previously known spectroscopic redshift. The detections have a range of H I and stellar masses, indicating the diversity of galaxies we are probing. We discuss the observations, data reduction, results, and highlight interesting detections. We find that the VLA's B-array is the ideal configuration for H I deep fields since its long spacings mitigate radio frequency interference. This pilot shows that the VLA is ready to carry out such a survey, and serves as a test for future H I deep fields planned with other Square Kilometer Array pathfinders.

A PILOT FOR A VERY LARGE ARRAY H I DEEP FIELD

Energy Technology Data Exchange (ETDEWEB)

Fernandez, Ximena; Van Gorkom, J. H.; Schiminovich, David [Department of Astronomy, Columbia University, New York, NY 10027 (United States); Hess, Kelley M. [Department of Astronomy, Astrophysics, Cosmology and Gravity Centre, University of Cape Town, Private Bag X3, Rondebosch 7701 (South Africa); Pisano, D. J. [Department of Physics, West Virginia University, P.O. Box 6315, Morgantown, WV 26506 (United States); Kreckel, Kathryn [Max Planck Institute for Astronomy, Koenigstuhl 17, D-69117 Heidelberg (Germany); Momjian, Emmanuel [National Radio Astronomy Observatory, Socorro, NM 87801 (United States); Popping, Attila [International Centre for Radio Astronomy Research (ICRAR), The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009 (Australia); Oosterloo, Tom [Netherlands Institute for Radio Astronomy (ASTRON), Postbus 2, NL-7990 AA Dwingeloo (Netherlands); Chomiuk, Laura [Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824 (United States); Verheijen, M. A. W. [Kapteyn Astronomical Institute, University of Groningen, Postbus 800, NL-9700 AV Groningen (Netherlands); Henning, Patricia A. [Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131 (United States); Bershady, Matthew A.; Wilcots, Eric M. [Department of Astronomy, University of Wisconsin-Madison, Madison, WI 53706 (United States); Scoville, Nick, E-mail: ximena@astro.columbia.edu [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States)

2013-06-20

High-resolution 21 cm H I deep fields provide spatially and kinematically resolved images of neutral hydrogen at different redshifts, which are key to understanding galaxy evolution across cosmic time and testing predictions of cosmological simulations. Here we present results from a pilot for an H I deep field done with the Karl G. Jansky Very Large Array (VLA). We take advantage of the newly expanded capabilities of the telescope to probe the redshift interval 0 < z < 0.193 in one observation. We observe the COSMOS field for 50 hr, which contains 413 galaxies with optical spectroscopic redshifts in the imaged field of 34' Multiplication-Sign 34' and the observed redshift interval. We have detected neutral hydrogen gas in 33 galaxies in different environments spanning the probed redshift range, including three without a previously known spectroscopic redshift. The detections have a range of H I and stellar masses, indicating the diversity of galaxies we are probing. We discuss the observations, data reduction, results, and highlight interesting detections. We find that the VLA's B-array is the ideal configuration for H I deep fields since its long spacings mitigate radio frequency interference. This pilot shows that the VLA is ready to carry out such a survey, and serves as a test for future H I deep fields planned with other Square Kilometer Array pathfinders.

Defining “Binge” Drinking as Five Drinks per Occasion or Drinking to a 0.08% BAC: Which is More Sensitive to Risk?

Science.gov (United States)

Fillmore, Mark T.; Jude, Rebecca

2011-01-01

Heavy episodic or “binge” drinking is commonly defined as drinking 4–5 drinks per occasion (5/4 definition) or drinking that results in a blood alcohol concentration (BAC) of 0.08%. The present study compared the validity of each binge definition as an indicator of at-risk, problem drinking. 251 college students were classified as non-binge drinkers or as binge drinkers based on the 5/4 definition or the 0.08% BAC definition. The two definitions of binge drinking were examined in terms of their sensitivity and specificity as indicators of alcohol-related problems as determined by scores on the Alcohol Use Disorders Identification Test (AUDIT). Over half the sample (56%) were at-risk drinkers according to the AUDIT. The 0.08% definition detected only one-half of these individuals. Gender differences were also evident. Female binge drinkers actually achieved significantly higher estimated BACs per episode than their male binge drinking counterparts. The findings suggest that drinking to a sub-threshold BAC (i.e., risk independent of the BAC achieved during drinking episodes. The findings also highlight the importance of considering frequency of consumption in determining risky drinking versus relying solely on quantity measures. PMID:21838847

Major technological innovations introduced in the large antennas of the Deep Space Network

Science.gov (United States)

Imbriale, W. A.

2002-01-01

The NASA Deep Space Network (DSN) is the largest and most sensitive scientific, telecommunications and radio navigation network in the world. Its principal responsibilities are to provide communications, tracking, and science services to most of the world's spacecraft that travel beyond low Earth orbit. The network consists of three Deep Space Communications Complexes. Each of the three complexes consists of multiple large antennas equipped with ultra sensitive receiving systems. A centralized Signal Processing Center (SPC) remotely controls the antennas, generates and transmits spacecraft commands, and receives and processes the spacecraft telemetry.

Enhanced biodegradation of petrochemical wastewater using ozonation and BAC advanced treatment system

Energy Technology Data Exchange (ETDEWEB)

Lin, Chi-Kang; Tsai, Tsung-Yueh; Liu, Jiunn-Ching; Chen, Mei-Chen [Energy and Resources Labs., ITRI, Hsinchu (Taiwan)

2001-07-01

The characteristics of degradation/conversion of bio-refractory and the growth of a biofilm are investigated in laboratory-scale pre-ozonation and lifted moving-bed biological activated carbon (BAC) advanced treatment processes treating phenol, benzoic acid, aminobenzoic acid and petrochemical industry wastewater which contains acrylonitrile butadiene styrene (ABS). The optimal reaction time and ozone dosage of pre-ozonation for bio-refractory conversion were determined to be 30 min and 100-200mg O{sub 3}/hr, respectively. After pre-ozonation of 30 min treatment, BOD{sub 5}/COD ratio of influent and effluent increased apparently from 20 to 35%, approximately. However, the change of pH in pre-ozonation was inconspicuous. The optimal flow rate of influent and air were controlled at 1.6 1/h and 120-l50nl/min in lifted moving-bed BAC advanced treatment reactor. A COD removal efficiency of 85-95% and 70-90% may be maintained by using an organic loading of 3.2-6.3kg COD/m{sup 3} day and 0.6-1.6 kg-COD/m{sup 3} day with an HRT of 6.0 h as secondary and advanced treatment system, respectively. The time required for the BAC bed to be regenerated by a thermal regeneration is prolonged 4-5 times more than that of GAC system. It can be estimated that the enhanced COD removal capability of the biofilm was not only due to the increase in the COD removal capability of acclimated bacteria, but also due to species succession of bacteria in bio-film ecosystem. (Author)

The host antimicrobial peptide Bac71-35 binds to bacterial ribosomal proteins and inhibits protein synthesis.

Science.gov (United States)

Mardirossian, Mario; Grzela, Renata; Giglione, Carmela; Meinnel, Thierry; Gennaro, Renato; Mergaert, Peter; Scocchi, Marco

2014-12-18

Antimicrobial peptides (AMPs) are molecules from innate immunity with high potential as novel anti-infective agents. Most of them inactivate bacteria through pore formation or membrane barrier disruption, but others cross the membrane without damages and act inside the cells, affecting vital processes. However, little is known about their intracellular bacterial targets. Here we report that Bac71-35, a proline-rich AMP belonging to the cathelicidin family, can reach high concentrations (up to 340 μM) inside the E. coli cytoplasm. The peptide specifically and completely inhibits in vitro translation in the micromolar concentration range. Experiments of incorporation of radioactive precursors in macromolecules with E. coli cells confirmed that Bac71-35 affects specifically protein synthesis. Ribosome coprecipitation and crosslinking assays showed that the peptide interacts with ribosomes, binding to a limited subset of ribosomal proteins. Overall, these results indicate that the killing mechanism of Bac71-35 is based on a specific block of protein synthesis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Crystal structures and electronic properties of BaC2 isomers by theoretical study based on DFT

Institute of Scientific and Technical Information of China (English)

2008-01-01

Band structures and electronic properties of two BaC2 isomers were calculated by using density func-tional theory(DFT) properly.The ionic bond features are all typical between cation(Ba) and anion clusters(C2) in both structures of the isomers.However,a much stronger covalent bond exists in anion clusters which can be seen by inspecting the electron distribution contour that has a dull bell like shape between two carbon atoms.The shortest distance between Ba2+ and C22? and the bond length in anion clusters are different in these isomers of BaC2,which are 0.2945 nm and 0.1185 nm for the structure with the I4/mmm space group and 0.2744 and 0.1136 nm with the C2/c type,respectively.Band structures were clarified by combining the DOS to indicate the ionic bonding features more clearly.Population analysis provided further evidence on these ideas.Thermodynamical calculation results reveal that the transition temperature of these two polymorphs of BaC2 locates near 132 K,which is consistent with the recent experimental results.

Fanning the flames? : How media coverage of a price war impacts retailers, consumers and investors

NARCIS (Netherlands)

van Heerde, H.J.; Gijsbrechts, E.; Pauwels, K.

2015-01-01

This paper explores how media coverage of a price war impacts customer, retailer and investor reactions over time. Based on data covering a Dutch supermarket price war (2003–2005), the authors find that price reductions, and especially deep ones, trigger media coverage of the price conflict. This

Spatial attributes of the four-helix bundle group of bacteriocins – The high-resolution structure of BacSp222 in solution

KAUST Repository

Nowakowski, Michał

2017-11-01

BacSp222 is a multifunctional bacteriocin produced by Staphylococcus pseudintermedius strain 222, an opportunistic pathogen of domestic animals. At micromolar concentrations, BacSp222 kills Gram-positive bacteria and is cytotoxic toward mammalian cells, while at nanomolar doses, it acts as an immunomodulatory factor, enhancing nitric oxide release in macrophage-like cell lines. The bacteriocin is a cationic, N-terminally formylated, 50-amino-acid-long linear peptide that is rich in tryptophan residues.In this study, the solution structure of BacSp222 was determined and compared to the currently known structures of similar bacteriocins. BacSp222 was isolated from a liquid culture medium in a uniformly 13C- and 15N-labeled form, and NMR data were collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns.Although the amino acid sequence of BacSp222 has no significant similarity to any known peptide or protein, a 3D structure similarity search indicates a close relation to other four-helix bundle-motif bacteriocins, such as aureocin A53, lacticin Q and enterocins 7A/7B. Assuming similar functions, biology, structure and physicochemical properties, we propose to distinguish the four-helix bundle bacteriocins as a new Type A in subclass IId of bacteriocins, containing linear, non-pediocin-like peptides.

Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses.

Science.gov (United States)

Clark, Shaunna L; McClay, Joseph L; Adkins, Daniel E; Aberg, Karolina A; Kumar, Gaurav; Nerella, Sri; Xie, Linying; Collins, Ann L; Crowley, James J; Quakenbush, Corey R; Hillard, Christopher E; Gao, Guimin; Shabalin, Andrey A; Peterson, Roseann E; Copeland, William E; Silberg, Judy L; Maes, Hermine; Sullivan, Patrick F; Costello, Elizabeth J; van den Oord, Edwin J

2016-05-01

Genome-wide association study meta-analyses have robustly implicated three loci that affect susceptibility for smoking: CHRNA5\\CHRNA3\\CHRNB4, CHRNB3\\CHRNA6 and EGLN2\\CYP2A6. Functional follow-up studies of these loci are needed to provide insight into biological mechanisms. However, these efforts have been hampered by a lack of knowledge about the specific causal variant(s) involved. In this study, we prioritized variants in terms of the likelihood they account for the reported associations. We employed targeted capture of the CHRNA5\\CHRNA3\\CHRNB4, CHRNB3\\CHRNA6, and EGLN2\\CYP2A6 loci and flanking regions followed by next-generation deep sequencing (mean coverage 78×) to capture genomic variation in 363 individuals. We performed single locus tests to determine if any single variant accounts for the association, and examined if sets of (rare) variants that overlapped with biologically meaningful annotations account for the associations. In total, we investigated 963 variants, of which 71.1% were rare (minor allele frequency < 0.01), 6.02% were insertion/deletions, and 51.7% were catalogued in dbSNP141. The single variant results showed that no variant fully accounts for the association in any region. In the variant set results, CHRNB4 accounts for most of the signal with significant sets consisting of directly damaging variants. CHRNA6 explains most of the signal in the CHRNB3\\CHRNA6 locus with significant sets indicating a regulatory role for CHRNA6. Significant sets in CYP2A6 involved directly damaging variants while the significant variant sets suggested a regulatory role for EGLN2. We found that multiple variants implicating multiple processes explain the signal. Some variants can be prioritized for functional follow-up. © The Author 2015. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Coverage matters: insurance and health care

National Research Council Canada - National Science Library

Board on Health Care Services Staff; Institute of Medicine Staff; Institute of Medicine; National Academy of Sciences

2001-01-01

...? How does the system of insurance coverage in the U.S. operate, and where does it fail? The first of six Institute of Medicine reports that will examine in detail the consequences of having a large uninsured population, Coverage Matters...

Fish food in the deep sea: revisiting the role of large food-falls.

Directory of Open Access Journals (Sweden)

Nicholas D Higgs

Full Text Available The carcasses of large pelagic vertebrates that sink to the seafloor represent a bounty of food to the deep-sea benthos, but natural food-falls have been rarely observed. Here were report on the first observations of three large 'fish-falls' on the deep-sea floor: a whale shark (Rhincodon typus and three mobulid rays (genus Mobula. These observations come from industrial remotely operated vehicle video surveys of the seafloor on the Angola continental margin. The carcasses supported moderate communities of scavenging fish (up to 50 individuals per carcass, mostly from the family Zoarcidae, which appeared to be resident on or around the remains. Based on a global dataset of scavenging rates, we estimate that the elasmobranch carcasses provided food for mobile scavengers over extended time periods from weeks to months. No evidence of whale-fall type communities was observed on or around the carcasses, with the exception of putative sulphide-oxidising bacterial mats that outlined one of the mobulid carcasses. Using best estimates of carcass mass, we calculate that the carcasses reported here represent an average supply of carbon to the local seafloor of 0.4 mg m(-2d(-1, equivalent to ∼ 4% of the normal particulate organic carbon flux. Rapid flux of high-quality labile organic carbon in fish carcasses increases the transfer efficiency of the biological pump of carbon from the surface oceans to the deep sea. We postulate that these food-falls are the result of a local concentration of large marine vertebrates, linked to the high surface primary productivity in the study area.

The first generation of a BAC-based physical map of Brassica rapa

Directory of Open Access Journals (Sweden)

Lee Soo

2008-06-01

Full Text Available Abstract Background The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. Results A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. Conclusion The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.

Case report: accessory head of the deep forearm flexors

Science.gov (United States)

JONES, M.; ABRAHAMS, P. H.; SAÑUDO, J. R.

1997-01-01

In 1813 Gantzer described 2 accessory muscles in the human forearm which bear his name (Wood, 1868; Macalister, 1875) and these have subsequently been reported with variable attachments (Wood, 1868; Macalister, 1875; Turner, 1879; Schäfer & Thane, 1894; Le Double, 1897; Dykes & Anson, 1944; Mangini, 1960; Malhotra et al. 1982; Kida, 1988; Tountas & Bergman, 1993). The accessory heads of the deep flexors of the forearm (Gantzer's muscles) have been described as 2 different small bellies which insert either into FPL or FDP. There are no previous reports which have mentioned the existence of an accessory muscle which inserts into both of the 2 deep flexors of the forearm as in the case presented here. PMID:9306208

Sur la filabilité d'une laine teinte en bac-ouvert et d'une laine teinte à la continue

NARCIS (Netherlands)

Werker, W.; Mulder, D.; Stomph, J.; Schartman, A.F.

1966-01-01

Afin de constater, si la teinture selon le procédé à la continue ou selon le procédé en bac-ouvert influence les résultats dans Ia filature, on a teint deux lots homogènes à 18OO kg par lot en quatre parties: 450 kg, procédé à la continue, teints en rouge, 450 kg, procédé bac-ouvert, teints en

A Study of the Large Deformation Mechanism and Control Techniques for Deep Soft Rock Roadways

Directory of Open Access Journals (Sweden)

Xiaojie Yang

2018-04-01

Full Text Available Large deformation control of deep soft rock roadways has been a major problem in mining activities worldwide. This paper considers the supporting problem related to large deformation of a deep soft rock roadway in Chao’hua coal mine. The discrete element simulation method (UDEC software is adopted to simulate a tailgate of panel 31041 in Chao’hua coal mine. The failure patterns of unsupported and primary supported roadway are simulated, and these reveal the characteristics of deformation, stress and crack propagation. The excavation of roadway leads to high deviator stress, which exceeds the peak strength of shallow surrounding rock and causes it to enter the post-failure stage. Tensile failures then initiate and develop around the roadway, which causes the fragmentation, dilation and separation of shallow surrounding rock. The compressive capacity of the primary support system is low, which results in serious contraction in the full section of the roadway. An improved control scheme is put forward for the support of a tailgate. The underground test results confirm that the improved support system effectively controlled large deformation of the surrounding rocks, which can provide references for support in the design of roadways excavated in deep soft stratum.

Early Mission Maneuver Operations for the Deep Space Climate Observatory Sun-Earth L1 Libration Point Mission

Science.gov (United States)

Roberts, Craig; Case, Sara; Reagoso, John; Webster, Cassandra

2015-01-01

The Deep Space Climate Observatory mission launched on February 11, 2015, and inserted onto a transfer trajectory toward a Lissajous orbit around the Sun-Earth L1 libration point. This paper presents an overview of the baseline transfer orbit and early mission maneuver operations leading up to the start of nominal science orbit operations. In particular, the analysis and performance of the spacecraft insertion, mid-course correction maneuvers, and the deep-space Lissajous orbit insertion maneuvers are discussed, com-paring the baseline orbit with actual mission results and highlighting mission and operations constraints..

Multicenter surgical experience evaluation on the Mid-Scala electrode and insertion tools.

Science.gov (United States)

Gazibegovic, Dzemal; Bero, Eva M

2017-02-01

The HiFocus Mid-Scala electrode is intended to improve hearing for individuals with severe-to-profound hearing loss by providing extended electrical coverage of the cochlea while minimizing trauma related to insertion. The electrode is appropriate for use with a wide range of surgical techniques, including either a cochleostomy or round window insertion, and the use of either a free-hand or tool-assisted approach. The objective of this survey was to evaluate how the HiFocus Mid-Scala electrode and insertion tools was used across a population of cochlear implant recipients of differing ages, audiologic profiles, and anatomical characteristics. The intent was to understand the type and frequency of surgical techniques applicable with the electrode, and to provide guidelines for clinical practice. Two questionnaires were completed by surgeons at implant centres located in the United States, Europe, and Asia. Before any surgeries were conducted, surgeons completed a questionnaire that assessed their overall cochlear implant surgical practice and preferences. Following each HiFocus Mid-Scala electrode insertion, surgeons completed a questionnaire that summarized their experience during that surgical procedure. Questionnaires were completed by 32 surgeons from 16 centres for a total of 143 surgeries (112 adults, 31 children). Most surgeons (62 %) preferred to insert the electrode via the round window or an extended round window compared with a cochleostomy (16 %), whereas the remaining 22 % indicated that they made an insertion choice based on presenting anatomy. Sixty-nine percent preferred a free-hand approach over using insertion tools. In 32 procedures, surgeons elected to deviate from an intended round window insertion to either an extended round window or cochleostomy approach.

Problems of cleaning the large diameter sections of deep wells

Energy Technology Data Exchange (ETDEWEB)

Patsch, F; Gilicz, B

1966-01-01

In drilling deep wells, great importance is being given to the problem of cutting removal from the hole bottom of sections drilled by large diameter bits. The length of borehole sections drilled by 12-1/4-in. and larger bits has been more than doubled in Hungary in the course of the past 4 years. When the drilling fluid jet is struck against the borehole bottom, pressure waves are brought about which take on a crossed flow pattern and result in a retardation of cleaning of the well bottom, particularly in the case of larger bottom surfaces. In large diameter boreholes, the cleaning efficiency is being achieved by full utilization of the pump power and increased pump delivery. Friction losses in drill pipes are being reduced by using 6-in. XH pipes.

Posology of insulins: A review of standard textbooks and product inserts.

Science.gov (United States)

Bhutani, Garima; Kalra, Sanjay

2015-01-01

The study is aimed to assess whether the information contained in standard pharmacology, endocrinology, and diabetology textbooks regarding timings of administration, frequency and dose of various insulins is adequate and also to see whether the information contained in these texts is concordant with product inserts. Four standard textbooks of pharmacology, two of diabetology and three of endocrinology were assessed for the published information regarding dose, timing, and frequency of insulin administration. The product inserts of commonly available insulins in India were also studied for the same. Various omissions and disparities could be seen in the coverage of insulins in standard textbooks. Posology information about premixed insulins and basal insulins have been omitted by the majority of the textbooks. Details about dose, frequency and timings of ultra-short acting insulins have also not been covered by all textbooks. Some discrepancies regarding prescribing information was also noted in product inserts, especially in case of newer insulins. Thus, this article stresses upon the need of a uniform source of information for providing adequate and standardized knowledge regarding timing, frequency, and dose of insulins.

CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles.

Science.gov (United States)

Lemos, Brenda R; Kaplan, Adam C; Bae, Ji Eun; Ferrazzoli, Alexander E; Kuo, James; Anand, Ranjith P; Waterman, David P; Haber, James E

2018-02-27

Harnessing CRISPR-Cas9 technology provides an unprecedented ability to modify genomic loci via DNA double-strand break (DSB) induction and repair. We analyzed nonhomologous end-joining (NHEJ) repair induced by Cas9 in budding yeast and found that the orientation of binding of Cas9 and its guide RNA (gRNA) profoundly influences the pattern of insertion/deletions (indels) at the site of cleavage. A common indel created by Cas9 is a 1-bp (+1) insertion that appears to result from Cas9 creating a 1-nt 5' overhang that is filled in by a DNA polymerase and ligated. The origin of +1 insertions was investigated by using two gRNAs with PAM sequences located on opposite DNA strands but designed to cleave the same sequence. These templated +1 insertions are dependent on the X-family DNA polymerase, Pol4. Deleting Pol4 also eliminated +2 and +3 insertions, which are biased toward homonucleotide insertions. Using inverted PAM sequences, we also found significant differences in overall NHEJ efficiency and repair profiles, suggesting that the binding of the Cas9:gRNA complex influences subsequent NHEJ processing. As with events induced by the site-specific HO endonuclease, CRISPR-Cas9-mediated NHEJ repair depends on the Ku heterodimer and DNA ligase 4. Cas9 events are highly dependent on the Mre11-Rad50-Xrs2 complex, independent of Mre11's nuclease activity. Inspection of the outcomes of a large number of Cas9 cleavage events in mammalian cells reveals a similar templated origin of +1 insertions in human cells, but also a significant frequency of similarly templated +2 insertions.

LOFT voltage insertion calibaration program

International Nuclear Information System (INIS)

Tillitt, D.N.; Miyasaki, F.S.

1975-08-01

The Loss-of-Fluid Test (LOFT) Facility is an experimental facility built around a ''scaled'' version of a large pressurized water reactor (LPWR). Part of this facility is the Data Acquisition and Visual Display System (DAVDS) as defined by the LOFT System Design Document SDD 1.4.2C. The DAVDS has a 702 data channel recording capability of which 548 are recorded digitally. The DAVDS also contains a Voltage Insertion Calibration Subsystem used to inject precise and known voltage steps into the recording systems. The computer program that controls the Voltage Insertion Calibration Subsystem is presented. 7 references. (auth)

Benchmarking Deep Learning Models on Large Healthcare Datasets.

Science.gov (United States)

Purushotham, Sanjay; Meng, Chuizheng; Che, Zhengping; Liu, Yan

2018-06-04

Deep learning models (aka Deep Neural Networks) have revolutionized many fields including computer vision, natural language processing, speech recognition, and is being increasingly used in clinical healthcare applications. However, few works exist which have benchmarked the performance of the deep learning models with respect to the state-of-the-art machine learning models and prognostic scoring systems on publicly available healthcare datasets. In this paper, we present the benchmarking results for several clinical prediction tasks such as mortality prediction, length of stay prediction, and ICD-9 code group prediction using Deep Learning models, ensemble of machine learning models (Super Learner algorithm), SAPS II and SOFA scores. We used the Medical Information Mart for Intensive Care III (MIMIC-III) (v1.4) publicly available dataset, which includes all patients admitted to an ICU at the Beth Israel Deaconess Medical Center from 2001 to 2012, for the benchmarking tasks. Our results show that deep learning models consistently outperform all the other approaches especially when the 'raw' clinical time series data is used as input features to the models. Copyright © 2018 Elsevier Inc. All rights reserved.

Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat

Czech Academy of Sciences Publication Activity Database

Šafář, Jan; Šimková, Hana; Kubaláková, Marie; Čihalíková, Jarmila; Suchánková, Pavla; Bartoš, Jan; Doležel, Jaroslav

2010-01-01

Roč. 129, 1-3 (2010), s. 211-223 ISSN 1424-8581 R&D Projects: GA ČR GA521/07/1573; GA MŠk(CZ) LC06004 Grant - others:European Community’s Seventh Framework Programme(XE) FP7/2007–2013 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC library * Chromosome * DNA markers Subject RIV: GE - Plant Breeding Impact factor: 1.783, year: 2010

BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper (Capsicum annuum L.).

Science.gov (United States)

Kim, Hyoun-Joung; Nahm, Seok-Hyeon; Lee, Heung-Ryul; Yoon, Gi-Bo; Kim, Ki-Taek; Kang, Byoung-Cheorl; Choi, Doil; Kweon, Oh Yeol; Cho, Myeong-Cheoul; Kwon, Jin-Kyung; Han, Jung-Heon; Kim, Jeong-Ho; Park, Minkyu; Ahn, Jong Hwa; Choi, Soon Ho; Her, Nam Han; Sung, Joo-Hee; Kim, Byung-Dong

2008-12-01

Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F(2) individuals from a cross between Capsicum annuum 'CM334' and C. annuum 'Chilsungcho'. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F(2:3) originated from a cross between resistant Mexican landrace C. annuum 'CM334' and susceptible Korean landrace C. annuum 'Chilsungcho' using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum 'CM334' was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.

Coverage of Large-Scale Food Fortification of Edible Oil, Wheat Flour, and Maize Flour Varies Greatly by Vehicle and Country but Is Consistently Lower among the Most Vulnerable: Results from Coverage Surveys in 8 Countries.

Science.gov (United States)

Aaron, Grant J; Friesen, Valerie M; Jungjohann, Svenja; Garrett, Greg S; Neufeld, Lynnette M; Myatt, Mark

2017-05-01

Background: Large-scale food fortification (LSFF) of commonly consumed food vehicles is widely implemented in low- and middle-income countries. Many programs have monitoring information gaps and most countries fail to assess program coverage. Objective: The aim of this work was to present LSFF coverage survey findings (overall and in vulnerable populations) from 18 programs (7 wheat flour, 4 maize flour, and 7 edible oil programs) conducted in 8 countries between 2013 and 2015. Methods: A Fortification Assessment Coverage Toolkit (FACT) was developed to standardize the assessments. Three indicators were used to assess the relations between coverage and vulnerability: 1 ) poverty, 2 ) poor dietary diversity, and 3 ) rural residence. Three measures of coverage were assessed: 1 ) consumption of the vehicle, 2 ) consumption of a fortifiable vehicle, and 3 ) consumption of a fortified vehicle. Individual program performance was assessed based on the following: 1 ) achieving overall coverage ≥50%, 2) achieving coverage of ≥75% in ≥1 vulnerable group, and 3 ) achieving equity in coverage for ≥1 vulnerable group. Results: Coverage varied widely by food vehicle and country. Only 2 of the 18 LSFF programs assessed met all 3 program performance criteria. The 2 main program bottlenecks were a poor choice of vehicle and failure to fortify a fortifiable vehicle (i.e., absence of fortification). Conclusions: The results highlight the importance of sound program design and routine monitoring and evaluation. There is strong evidence of the impact and cost-effectiveness of LSFF; however, impact can only be achieved when the necessary activities and processes during program design and implementation are followed. The FACT approach fills an important gap in the availability of standardized tools. The LSFF programs assessed here need to be re-evaluated to determine whether to further invest in the programs, whether other vehicles are appropriate, and whether other approaches

Insertion Testing of Polyethylene Glycol Microneedle Array into Cultured Human Skin with Biaxial Tension

Science.gov (United States)

Takano, Naoki; Tachikawa, Hiroto; Miyano, Takaya; Nishiyabu, Kazuaki

Aiming at the practical use of polyethylene glycol (PEG) microneedles for transdermal drug delivery system (DDS), a testing apparatus for their insertion into cultured human skin has been developed. To simulate the variety of conditions of human skin, biaxial tension can be applied to the cultured human skin. An adopted testing scheme to apply and control the biaxial tension is similar to the deep-draw forming technique. An attention was also paid to the short-time setup of small, thin and wet cultured skin. One dimensional array with four needles was inserted and influence of tension was discussed. It was found that tension, deflection of skin during insertion and original curvature of skin are the important parameters for microneedles array design.

BacHBerry:: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

DEFF Research Database (Denmark)

Dudnik, Alexey; Almeida, A. Filipa; Andrade, Ricardo

2017-01-01

BACterial Hosts for production of Bioactive phenolics from bERRY fruits (BacHBerry) was a 3-year project funded by the Seventh Framework Programme (FP7) of the European Union that ran between November 2013 and October 2016. The overall aim of the project was to establish a sustainable and economi...

HTS Insert Magnet Design Study

CERN Document Server

Devaux, M; Fleiter, J; Fazilleau, P; Lécrevisse, T; Pes, C; Rey, J-M; Rifflet, J-M; Sorbi, M; Stenvall, A; Tixador, P; Volpini, G

2011-01-01

Future accelerator magnets will need to reach higher field in the range of 20 T. This field level is very difficult to reach using only Low Temperature Superconductor materials whereas High Temperature Superconductors (HTS) provide interesting opportunities. High current densities and stress levels are needed to design such magnets. YBCO superconductor indeed carries large current densities under high magnetic field and provides good mechanical properties especially when produced using the IBAD approach. The HFM EUCARD program studies the design and the realization of an HTS insert of 6 T inside a Nb$_{3}$Sn dipole of 13T at 4.2 K. In the2HTS insert, engineering current densities higher than 250 MA/m under 19 T are required to fulfill the specifications. The stress level is also very severe. YBCO IBAD tapes theoretically meet these challenges from presented measurements. The insert protection is also a critical because HTS materials show low quench propagation velocities and the coupling with the Nb$_{3}$Sn m...

Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

KAUST Repository

Hunt, Paul; Martinelli, Axel; Modrzynska, Katarzyna; Borges, Sofia; Creasey, Alison; Rodrigues, Louise; Beraldi, Dario; Loewe, Laurence; Fawcett, Richard; Kumar, Sujai; Thomson, Marian; Trivedi, Urmi; Otto, Thomas D; Pain, Arnab; Blaxter, Mark; Cravo, Pedro

2010-01-01

was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (IlluminaSolexa) defined the point mutations, insertions, deletions and copy-number variations arising

Coverage of Large-Scale Food Fortification of Edible Oil, Wheat Flour, and Maize Flour Varies Greatly by Vehicle and Country but Is Consistently Lower among the Most Vulnerable: Results from Coverage Surveys in 8 Countries123

Science.gov (United States)

Aaron, Grant J; Friesen, Valerie M; Jungjohann, Svenja; Garrett, Greg S; Myatt, Mark

2017-01-01

Background: Large-scale food fortification (LSFF) of commonly consumed food vehicles is widely implemented in low- and middle-income countries. Many programs have monitoring information gaps and most countries fail to assess program coverage. Objective: The aim of this work was to present LSFF coverage survey findings (overall and in vulnerable populations) from 18 programs (7 wheat flour, 4 maize flour, and 7 edible oil programs) conducted in 8 countries between 2013 and 2015. Methods: A Fortification Assessment Coverage Toolkit (FACT) was developed to standardize the assessments. Three indicators were used to assess the relations between coverage and vulnerability: 1) poverty, 2) poor dietary diversity, and 3) rural residence. Three measures of coverage were assessed: 1) consumption of the vehicle, 2) consumption of a fortifiable vehicle, and 3) consumption of a fortified vehicle. Individual program performance was assessed based on the following: 1) achieving overall coverage ≥50%, 2) achieving coverage of ≥75% in ≥1 vulnerable group, and 3) achieving equity in coverage for ≥1 vulnerable group. Results: Coverage varied widely by food vehicle and country. Only 2 of the 18 LSFF programs assessed met all 3 program performance criteria. The 2 main program bottlenecks were a poor choice of vehicle and failure to fortify a fortifiable vehicle (i.e., absence of fortification). Conclusions: The results highlight the importance of sound program design and routine monitoring and evaluation. There is strong evidence of the impact and cost-effectiveness of LSFF; however, impact can only be achieved when the necessary activities and processes during program design and implementation are followed. The FACT approach fills an important gap in the availability of standardized tools. The LSFF programs assessed here need to be re-evaluated to determine whether to further invest in the programs, whether other vehicles are appropriate, and whether other approaches are needed

Templated sequence insertion polymorphisms in the human genome

Science.gov (United States)

Onozawa, Masahiro; Aplan, Peter

2016-11-01

Templated Sequence Insertion Polymorphism (TSIP) is a recently described form of polymorphism recognized in the human genome, in which a sequence that is templated from a distant genomic region is inserted into the genome, seemingly at random. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show features of insertions that are mediated via the LINE-1 ORF2 protein, including 1) target-site duplication (TSD), 2) polyadenylation 10-30 nucleotides downstream of a “cryptic” polyadenylation signal, and 3) preference for insertion at a 5’-TTTT/A-3’ sequence. In contrast, class 2 TSIPs show features consistent with repair of a DNA double-strand break via insertion of a DNA “patch” that is derived from a distant genomic region. Survey of a large number of normal human volunteers demonstrates that most individuals have 25-30 TSIPs, and that these TSIPs track with specific geographic regions. Similar to other forms of human polymorphism, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases.

Observation of events with a large rapidity gap in deep inelastic scattering at HERA

International Nuclear Information System (INIS)

Derrick, M.; Krakauer, D.; Magill, S.

1993-07-01

In deep inelastic, neutral current scattering of electrons and protons at √s=296 GeV, we observe in the ZEUS detector events with a large rapidity gap in the hadronic final state. They occur in the region of small Bjorken x and are observed up to Q 2 of 100 GeV 2 . They account for about 5% of the events with Q 2 ≥10 GeV 2 . Their general properties are inconsistent with the dominant mechanism of deep inelastic scattering, where color is transferred between the scattered quark and the proton remnant, and suggest that the underlying production mechanism is the diffractive dissociation of the virtual photon. (orig.)

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.

Science.gov (United States)

Ragupathy, Raja; Rathinavelu, Rajkumar; Cloutier, Sylvie

2011-05-09

Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be

Posology of insulins: A review of standard textbooks and product inserts

Directory of Open Access Journals (Sweden)

Garima Bhutani

2015-01-01

Full Text Available Objectives: The study is aimed to assess whether the information contained in standard pharmacology, endocrinology, and diabetology textbooks regarding timings of administration, frequency and dose of various insulins is adequate and also to see whether the information contained in these texts is concordant with product inserts. Materials and Methods: Four standard textbooks of pharmacology, two of diabetology and three of endocrinology were assessed for the published information regarding dose, timing, and frequency of insulin administration. The product inserts of commonly available insulins in India were also studied for the same. Results: Various omissions and disparities could be seen in the coverage of insulins in standard textbooks. Posology information about premixed insulins and basal insulins have been omitted by the majority of the textbooks. Details about dose, frequency and timings of ultra-short acting insulins have also not been covered by all textbooks. Some discrepancies regarding prescribing information was also noted in product inserts, especially in case of newer insulins. Conclusions: Thus, this article stresses upon the need of a uniform source of information for providing adequate and standardized knowledge regarding timing, frequency, and dose of insulins.

Driving performance on the descending limb of blood alcohol concentration (BAC) in undergraduate students: a pilot study.

Science.gov (United States)

Tremblay, Mathieu; Gallant, François; Lavallière, Martin; Chiasson, Martine; Silvey, Dustin; Behm, David; Albert, Wayne J; Johnson, Michel J

2015-01-01

Young drivers are overrepresented in collisions resulting in fatalities. It is not uncommon for young drivers to socially binge drink and decide to drive a vehicle a few hours after consumption. To better understand the risks that may be associated with this behaviour, the present study has examined the effects of a social drinking bout followed by a simulated drive in undergraduate students on the descending limb of their BAC (blood alcohol concentration) curve. Two groups of eight undergraduate students (n = 16) took part in this study. Participants in the alcohol group were assessed before drinking, then at moderate and low BAC as well as 24 hours post-acute consumption. This group consumed an average of 5.3 ± 1.4 (mean ± SD) drinks in an hour in a social context and were then submitted to a driving and a predicted crash risk assessment. The control group was assessed at the same time points without alcohol intake or social context.; at 8 a.m., noon, 3 p.m. and 8 a.m. the next morning. These multiple time points were used to measure any potential learning effects from the assessment tools (i.e. driving simulator and useful field of view test (UFOV)). Diminished driving performance at moderate BAC was observed with no increases in predicted crash risk. Moderate correlations between driving variables were observed. No association exists between driving variables and UFOV variables. The control group improved measures of selective attention after the third assessment. No learning effect was observed from multiple sessions with the driving simulator. Our results show that a moderate BAC, although legal, increases the risky behaviour. Effects of alcohol expectancy could have been displayed by the experimental group. UFOV measures and predicted crash risk categories were not sensitive enough to predict crash risk for young drivers, even when intoxicated.

Test manufacturing of copper canisters with cast inserts. Assessment report

Energy Technology Data Exchange (ETDEWEB)

Andersson, C.G

1998-08-01

The current design of canisters for the deep repository for spent nuclear fuel consists of an outer corrosion-protective copper casing in the form of a tubular section with lid and bottom and an inner pressure-resistant insert. The insert is designed to be manufactured by casting and inside are channels in which the fuel assemblies are to be placed. Over the last years, a number of full-scale manufacturing tests of all canister components have been carried out. The purpose has been to determine and develop the best manufacturing technique and to establish long-term contacts with the best suppliers of material and technology. Part of the work has involved the developing and implementing of a quality assurance system in accordance with ISO 9001, covering the whole chain from suppliers of material up to and including the delivery of assembled canisters. This report consists of a description of the design of the canister together with current drawings and complementary technical specifications stipulating, among other things, requirements placed on different materials. The different manufacturing methods that have been used are also described and commented on in both text and illustrations. For the manufacturing of copper tubes, the roll-forming of rolled plate to tube halves and longitudinal welding is a method that has been tested on a relatively large number of tubes by now, and that probably can be developed into a functioning production method. However, the very promising outcome of performed tests on seamless tube manufacturing, has resulted in a change in direction in tube manufacturing, focusing on continued testing of extrusion as well as pierce and draw processing in the immediate future. In connection with ongoing operations, new manufacturing tests of tubes with less material thickness will be carried out. Test manufacturing of cast inserts has resulted in the choice of nodular iron as material in the continued work. This improvement in design has resulted

Test manufacturing of copper canisters with cast inserts. Assessment report

International Nuclear Information System (INIS)

Andersson, C.G.

1998-08-01

The current design of canisters for the deep repository for spent nuclear fuel consists of an outer corrosion-protective copper casing in the form of a tubular section with lid and bottom and an inner pressure-resistant insert. The insert is designed to be manufactured by casting and inside are channels in which the fuel assemblies are to be placed. Over the last years, a number of full-scale manufacturing tests of all canister components have been carried out. The purpose has been to determine and develop the best manufacturing technique and to establish long-term contacts with the best suppliers of material and technology. Part of the work has involved the developing and implementing of a quality assurance system in accordance with ISO 9001, covering the whole chain from suppliers of material up to and including the delivery of assembled canisters. This report consists of a description of the design of the canister together with current drawings and complementary technical specifications stipulating, among other things, requirements placed on different materials. The different manufacturing methods that have been used are also described and commented on in both text and illustrations. For the manufacturing of copper tubes, the roll-forming of rolled plate to tube halves and longitudinal welding is a method that has been tested on a relatively large number of tubes by now, and that probably can be developed into a functioning production method. However, the very promising outcome of performed tests on seamless tube manufacturing, has resulted in a change in direction in tube manufacturing, focusing on continued testing of extrusion as well as pierce and draw processing in the immediate future. In connection with ongoing operations, new manufacturing tests of tubes with less material thickness will be carried out. Test manufacturing of cast inserts has resulted in the choice of nodular iron as material in the continued work. This improvement in design has resulted

Etude du risque d'inondation en aval du delta du fleuve rouge en utilisant la teledetection et les sig: Le cas du district de Bac Hung Hai

Science.gov (United States)

Bui, Duc Viet

The Bac Hung Hai zone is the greatest basin in the Red River Delta in Vietnam and also one of the most densely populated regions of the planet. It is mainly a rural region and its economy is dominated by agriculture. In the context of frequent and larger floods in the Bac Hung Hai zone, causing deep socio-economical consequences, the focus of this study is to establish cartography of the high risk areas for flooding in the Bac Hung Hai region using remote sensing and GIS to assist land management. The preparation of a map describing land management in this region is more complicated because parcels for farming are very small and not homogeneous. A consistent and precise map of land use is essential for studies of flooding. The secondary objective is to improve the land use map. To this effect, a classification has been applied to the combination of the spectral bands and textures (TM and ETM+) of Landsat and a radar image (ERS). The addition of this information to the spectral bands increases the accuracy of classification by 1% to 4%, according to the dates selected. Additionally, in the study zone where there are few days without clouds, a problem related to the optical satellite image is the cloud cover. Then, the use of radar images will provide ground information for areas hidden by clouds where spectral images are not sufficient. To reach these goals, we have determined the main biophysical considerations that influence flooding. Then, these considerations have been combined in a multi-criteria analysis to evaluate the risks of flooding in the entire basin area. The results show that high to very high risks affect 47% of the area studied and that the south-east region, center, and north-east present the greatest risk. Keywords. Flood risks, remote sensing, GIS, land use, multicriteria analysis, Red river delta, Vietnam.

BAC and Beer: Operationalizing Drunk Driving Laws in a Research Methods Course Exercise.

Science.gov (United States)

Taylor, Ralph B.; McConnell, Patrick

2001-01-01

Focuses on an exercise utilized in a research methods class and based on social problems that invites student interest. Explains the exercise has students determine their blood alcohol level (BAC) by asking them to estimate the number of beers it would take to have them just reach driving under the influence (DUI) status. (CMK)

The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.)

Czech Academy of Sciences Publication Activity Database

Kasprzak, A.; Šafář, Jan; Janda, Jaroslav; Doležel, Jaroslav; Wolko, B.; Naganowska, B.

2006-01-01

Roč. 11, - (2006), s. 396-407 ISSN 1425-8153 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC * genomic DNA library * Lupinus angustifolius L. Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.238, year: 2006

Within-Subject Comparison of Maxillary Implant-Supported Overdentures with and without Palatal Coverage.

Science.gov (United States)

Zembic, Anja; Tahmaseb, Ali; Wismeijer, Daniel

2015-06-01

The purpose of this study was to compare patient-reported outcomes for maxillary implant-supported overdentures with and without palatal coverage. Twenty-one maxillary edentulous patients (six women, 15 men) were included. In total, 42 implants were inserted in the anterior maxilla. All patients received implant-supported overdentures on two retentive anchors with palatal coverage for 2 months. Thereafter, patient satisfaction was assessed by means of questionnaires capturing the oral health impact profile (OHIP) on functional limitation, physical pain, psychological discomfort, physical, psychological and social disability, and handicap. Additionally, cleaning ability, general satisfaction, speech, comfort, esthetics, stability, and chewing ability were rated. Subsequently, palatal coverage was reduced, and the patients wore the overdentures for another 2 months. Patient satisfaction was obtained in the same way as above, and the evaluated parameters were compared for the two overdenture designs. There were no significant differences between implant-supported overdentures with and without palatal coverage for any of the OHIP domains. The evaluation of additional parameters revealed significantly higher patient satisfaction for esthetics (mean difference 8.8 mm ± 24.6) and taste (mean difference 28.4 mm ± 29.9) without palatal coverage, p overdentures supported by two implants were equally satisfactory with and without palatal coverage. © 2013 Wiley Periodicals, Inc.

Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library

Directory of Open Access Journals (Sweden)

Cribiu Edmond-Paul

2000-07-01

Full Text Available Abstract In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57. This study allowed us, (i, to anchor all linkage groups on sheep chromosomes, (ii, to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii, to contradict the previous orientation of the ovine × linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.

Forward and reverse genetics: The LORE1 retrotransposon insertion mutants

DEFF Research Database (Denmark)

Fukai, Eigo; Malolepszy, Anna; Sandal, Niels Nørgaard

2014-01-01

The endogenous Lotus retrotransposon 1 (LORE1) transposes in the germ line of Lotus japonicus plants that carry an active element. This feature of LORE1 has been exploited for generation of a large non-transgenic insertion mutant population, where insertions have been annotated using next-generat...

Expression of Human CAR Splicing Variants in BAC-Transgenic Mice

OpenAIRE

Zhang, Yu-Kun Jennifer; Lu, Hong; Klaassen, Curtis D.

2012-01-01

The nuclear receptor constitutive androstane receptor (CAR) is a key regulator for drug metabolism in liver. Human CAR (hCAR) transcripts are subjected to alternative splicing. Some hCAR splicing variants (SVs) have been shown to encode functional proteins by reporter assays. However, in vivo research on the activity of these hCAR SVs has been impeded by the absence of a valid model. This study engineered an hCAR-BAC-transgenic (hCAR-TG) mouse model by integrating the 8.5-kbp hCAR gene as wel...

Flexible deep brain neural probes based on a parylene tube structure

Science.gov (United States)

Zhao, Zhiguo; Kim, Eric; Luo, Hao; Zhang, Jinsheng; Xu, Yong

2018-01-01

Most microfabricated neural probes have limited shank length, which prevents them from reaching many deep brain structures. This paper reports deep brain neural probes with ultra-long penetrating shanks based on a simple but novel parylene tube structure. The mechanical strength of the parylene tube shank is temporarily enhanced during implantation by inserting a metal wire. The metal wire can be removed after implantation, making the implanted probe very flexible and thus minimizing the stress caused by micromotions of brain tissues. Optogenetic stimulation and chemical delivery capabilities can be potentially integrated by taking advantage of the tube structure. Single-shank prototypes with a shank length of 18.2 mm have been developed. The microfabrication process comprises of deep reactive ion etching (DRIE) of silicon, parylene conformal coating/refilling, and XeF2 isotropic silicon etching. In addition to bench-top insertion characterization, the functionality of developed probes has been preliminarily demonstrated by implanting into the amygdala of a rat and recording neural signals.

The renormalization of several composite operator insertions, Wilson expansions of composite operators, and the applications to short-distance behaviour

International Nuclear Information System (INIS)

Collecott, P.S.

1978-01-01

The renormalization of composite operator insertions is examined within a normal product framework, and various identities between composite operator insertions are proved. In particular a proof of the Wilson expansion of composite operators in the presence of other composite operators is given. The analysis necessitates a re-examination of several physical processes, and it is shown in particular why the results for deep inelastic scattering still hold. (Auth.)

Analysis of risk factors and the establishment of a risk model for peripherally inserted central catheter thrombosis

OpenAIRE

Fang Hu; Ruo-Nan Hao; Jie Zhang; Zhi-Cheng Ma

2016-01-01

Objective: To investigate the main risk factors of peripherally inserted central catheter (PICC) related upper extremity deep venous thrombosis and establish the risk predictive model of PICC-related upper extremity deep venous thrombosis. Methods: Patients with PICC who were hospitalized between January 2014 and July 2015 were studied retrospectively; they were divided into a thrombosis group (n = 52), with patients who had a venous thrombosis complication after PICC, and a no-thrombosis ...

Development of a Set of Chromosome-Specific Cytogenetic DNA Markers in Sunflower Using BAC-FISH

Science.gov (United States)

In diploid sunflower (2n=34), conventional karyotypes and various genetic linkage maps have been established. However, the relationship between genetic linkage groups and individual chromosomes of sunflower remains unknown. Recently, a set of linkage group-specific BAC and BIBAC clones were identifi...

Uncertainty of Blood Alcohol Concentration (BAC Results as Related to Instrumental Conditions: Optimization and Robustness of BAC Analysis Headspace Parameters

Directory of Open Access Journals (Sweden)

Haleigh A. Boswell

2015-12-01

Full Text Available Analysis of blood alcohol concentration is a routine analysis performed in many forensic laboratories. This analysis commonly utilizes static headspace sampling, followed by gas chromatography combined with flame ionization detection (GC-FID. Studies have shown several “optimal” methods for instrumental operating conditions, which are intended to yield accurate and precise data. Given that different instruments, sampling methods, application specific columns and parameters are often utilized, it is much less common to find information on the robustness of these reported conditions. A major problem can arise when these “optimal” conditions may not also be robust, thus producing data with higher than desired uncertainty or potentially inaccurate results. The goal of this research was to incorporate the principles of quality by design (QBD in the adjustment and determination of BAC (blood alcohol concentration instrumental headspace parameters, thereby ensuring that minor instrumental variations, which occur as a matter of normal work, do not appreciably affect the final results of this analysis. This study discusses both the QBD principles as well as the results of the experiments, which allow for determination of more favorable instrumental headspace conditions. Additionally, method detection limits will also be reported in order to determine a reporting threshold and the degree of uncertainty at the common threshold value of 0.08 g/dL. Furthermore, the comparison of two internal standards, n-propanol and t-butanol, will be investigated. The study showed that an altered parameter of 85 °C headspace oven temperature and 15 psi headspace vial pressurization produces the lowest percent relative standard deviation of 1.3% when t-butanol is implemented as an internal standard, at least for one very common platform. The study also showed that an altered parameter of 100 °C headspace oven temperature and 15-psi headspace vial pressurization

Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

Directory of Open Access Journals (Sweden)

Shultz Jeffry

2008-07-01

Full Text Available Abstract Background Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS. Here the aim was to use BAC end sequences (BES derived from three minimum tile paths (MTP to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs were single nucleotide polymorphisms (SNPs; 89% and single nucleotide indels (SNIs 10%. Larger indels were rare but present (1%. Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. Conclusion The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de

Cardiac and pulmonary dose reduction for tangentially irradiated breast cancer, utilizing deep inspiration breath-hold with audio-visual guidance, without compromising target coverage

International Nuclear Information System (INIS)

Vikstroem, Johan; Hjelstuen, Mari H.B.; Mjaaland, Ingvil; Dybvik, Kjell Ivar

2011-01-01

Background and purpose. Cardiac disease and pulmonary complications are documented risk factors in tangential breast irradiation. Respiratory gating radiotherapy provides a possibility to substantially reduce cardiopulmonary doses. This CT planning study quantifies the reduction of radiation doses to the heart and lung, using deep inspiration breath-hold (DIBH). Patients and methods. Seventeen patients with early breast cancer, referred for adjuvant radiotherapy, were included. For each patient two CT scans were acquired; the first during free breathing (FB) and the second during DIBH. The scans were monitored by the Varian RPM respiratory gating system. Audio coaching and visual feedback (audio-visual guidance) were used. The treatment planning of the two CT studies was performed with conformal tangential fields, focusing on good coverage (V95>98%) of the planning target volume (PTV). Dose-volume histograms were calculated and compared. Doses to the heart, left anterior descending (LAD) coronary artery, ipsilateral lung and the contralateral breast were assessed. Results. Compared to FB, the DIBH-plans obtained lower cardiac and pulmonary doses, with equal coverage of PTV. The average mean heart dose was reduced from 3.7 to 1.7 Gy and the number of patients with >5% heart volume receiving 25 Gy or more was reduced from four to one of the 17 patients. With DIBH the heart was completely out of the beam portals for ten patients, with FB this could not be achieved for any of the 17 patients. The average mean dose to the LAD coronary artery was reduced from 18.1 to 6.4 Gy. The average ipsilateral lung volume receiving more than 20 Gy was reduced from 12.2 to 10.0%. Conclusion. Respiratory gating with DIBH, utilizing audio-visual guidance, reduces cardiac and pulmonary doses for tangentially treated left sided breast cancer patients without compromising the target coverage

Cardiac and pulmonary dose reduction for tangentially irradiated breast cancer, utilizing deep inspiration breath-hold with audio-visual guidance, without compromising target coverage

Energy Technology Data Exchange (ETDEWEB)

Vikstroem, Johan; Hjelstuen, Mari H.B.; Mjaaland, Ingvil; Dybvik, Kjell Ivar (Dept. of Radiotherapy, Stavanger Univ. Hospital, Stavanger (Norway)), e-mail: vijo@sus.no

2011-01-15

Background and purpose. Cardiac disease and pulmonary complications are documented risk factors in tangential breast irradiation. Respiratory gating radiotherapy provides a possibility to substantially reduce cardiopulmonary doses. This CT planning study quantifies the reduction of radiation doses to the heart and lung, using deep inspiration breath-hold (DIBH). Patients and methods. Seventeen patients with early breast cancer, referred for adjuvant radiotherapy, were included. For each patient two CT scans were acquired; the first during free breathing (FB) and the second during DIBH. The scans were monitored by the Varian RPM respiratory gating system. Audio coaching and visual feedback (audio-visual guidance) were used. The treatment planning of the two CT studies was performed with conformal tangential fields, focusing on good coverage (V95>98%) of the planning target volume (PTV). Dose-volume histograms were calculated and compared. Doses to the heart, left anterior descending (LAD) coronary artery, ipsilateral lung and the contralateral breast were assessed. Results. Compared to FB, the DIBH-plans obtained lower cardiac and pulmonary doses, with equal coverage of PTV. The average mean heart dose was reduced from 3.7 to 1.7 Gy and the number of patients with >5% heart volume receiving 25 Gy or more was reduced from four to one of the 17 patients. With DIBH the heart was completely out of the beam portals for ten patients, with FB this could not be achieved for any of the 17 patients. The average mean dose to the LAD coronary artery was reduced from 18.1 to 6.4 Gy. The average ipsilateral lung volume receiving more than 20 Gy was reduced from 12.2 to 10.0%. Conclusion. Respiratory gating with DIBH, utilizing audio-visual guidance, reduces cardiac and pulmonary doses for tangentially treated left sided breast cancer patients without compromising the target coverage

Sequencing of 15622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Czech Academy of Sciences Publication Activity Database

Munoz-Amatriain, M.; Lonardi, S.; Luo, M.C.; Madishetty, K.; Svensson, J.T.; Moscou, M. J.; Wanamaker, S.; Kudrna, D.; Zheng, J.; Šimková, Hana; Doležel, Jaroslav; Grimwood, J.; Mammadov, J.; Close, T.J.

2015-01-01

Roč. 84, č. 1 (2015), s. 216-227 ISSN 0960-7412 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Barley * Hordeum vulgare L * BAC sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.468, year: 2015

Insertion compounds of transition-metal and uranium oxides

International Nuclear Information System (INIS)

Chippindale, A.M.; Dickens, P.G.; Powell, A.V.

1991-01-01

Several transition-metal and actinide oxides, in which the metal occurs in a high oxidation state, have open covalent structures and are capable of incorporating alkali and other electropositive metals under mild conditions to form insertion compounds A x MO n . These are solids which have several features in common: Over a range of compositions, A x MO n exists as one or more stable or metastable phases in which the structure of the parent oxide MO n is largely retained and the insertion element A is accommodated interstitially. Insertion is accompanied by a redox process A=A i . + e - M in which M is reduced and the electronic properties of the parent oxide change to those typical of a mixed-valence compound. The insertion process xA + MO n = A x MO n can be reversed, at least to some extent, by chemical or electrochemical reaction, with retention of structure (topotactic reaction). This review concentrates on methods of synthesis, characterisation, crystal structure and thermochemistry of these insertion compounds. It updates and extends previous work. (author)

[Interest of a new instrument to assess cognition in schizophrenia: The Brief Assessment of Cognition in Schizophrenia (BACS)].

Science.gov (United States)

Bralet, M C; Navarre, M; Eskenazi, A M; Lucas-Ross, M; Falissard, B

2008-12-01

SCHIZOPHRENIA: It is therefore of great interest to create an available and easily used battery of validated tests. This would enable one to measure the different cognitive deficits and to repeat the tests, and assess evolution through longitudinal follow up of the patients. The BACS is a new instrument developed by Keefe et al. in the Department of Psychiatry and Behavioural Sciences at the University of Duke Medical Centre. It evaluates the cognitive dimensions specifically altered in schizophrenia and correlated with the evolution of the disease. This test is simple to use, requiring only paper, pencils and a stopwatch. It can be administered by different carers. The duration of the test session is approximately 35min. This battery of tests was validated on a sample of 150 patients compared with a sample of 50 controls, matched for age, parent education and ethnic groups. This aim of this study is to create a French adaptation of the BACS (translation and back translation approved by the Department of Psychiatry and Behavioural Sciences at the University of Duke Medical Centre) and then to test its easiness of administration and its sensitivity, performing correlation analysis between the French Version of the BACS (version A) and a standard battery. Its adaptation and validation in French would at first be useful for the French-speaking areas and then would add some new data for the pertinence of using the BACS. 35 French stabilized schizophrenic patients were recruited from the inpatient and outpatient facilities at the Clermont-de-L'Oise Mental Health Hospital (Picardie area, France) in Dr Boitard's Psychiatric Department (FJ 5.) Patients were required to meet DSM-IV criteria for schizophrenia or schizoaffective illness. The patients were tested on two separate days by two independent clinicians with less than two weeks between the two assessments. During the first test session, subjects received the French A version of the BACS and during the second session, they were

Feasibility of a novel positive feedback effect of 131I-promoted Bac-Egr1-hNIS expression in malignant glioma via baculovirus

International Nuclear Information System (INIS)

Guo Rui; Tian Lipeng; Han Bing; Xu Haoping; Zhang Miao; Li Biao

2011-01-01

Purpose: As intracellular iodine is released rapidly, increased expression of sodium/iodide symporter (NIS) is required for effective radioiodine treatment of tumor. As Egr1 promoter is activated by 131 I and may promote human NIS (hNIS) expression, hNIS also induces 131 I uptake and activates Egr1, so the existence of a positive feedback effect of 131 I-promoted Egr1-hNIS expression is possible. Our purpose was to investigate the possible existence of this positive feedback effect through a series of in vitro pioneer studies. Method: Recombinant baculovirus (Bac-Egr1-hNIS) encoding the hNIS gene under the control of a radiation-inducible Egrl promoter was constructed. To test 131 I-promoted hNIS expression, human malignant glioma U87 cells were transfected with Bac-Egr1-hNIS, stimulated with or without 131 I; the expression of hNIS protein was detected by immunofluorescence and flow cytometry test. In addition, the uptake and efflux of 131 I were determined after the incubation of Bac-Egr1-hNIS-transfected U87 cells with or without 131 I. Results: Immunocytochemical staining and flow cytometry test showed a higher hNIS protein expression in Bac-Egr1-hNIS-transfected U87 cells with 131 I stimulation than in cells without stimulation. Bac-Egr1-hNIS-transfected U87 cells accumulated up to about 4.05 times of 131 I after 131 I stimulation. The amount of 131 I uptake in both groups showed a baculovirus dose-dependent manner. However, rapid efflux of radioactivity was observed in both groups, with 50% lost during the first 2 min after the 131 I-containing medium had been replaced by a nonradioactive medium. Conclusion: Our results indicated that an improved transgene expression of 131 I-stimulated hNIS in U87 cells using a baculovirus vector containing the Egr1 promoter is possible, and the increased expression of hNIS is responsible for a higher 131 I uptake. It might provide a reference for the existence of a positive feedback effect in 131 I-promoted Bac-Egr1-h

Bilateral inferior vena cava filter insertion in a patient with duplication of the infrarenal vena cava.

LENUS (Irish Health Repository)

Leong, S

2010-06-19

BACKGROUND: Inferior vena cava (IVC) filter insertion is a commonly performed procedure for indications such as recurrent pulmonary emboli or contraindication to anticoagulation. Symptomatic duplication of the IVC is exceedingly rare with only a handful of cases being described in the literature. AIM: We report an unusual case of a patient with symptomatic duplication of the IVC. RESULT: A 53-year-old woman presented at our hospital for resection of a cerebral metastasis from a non-small cell lung cancer following a recent diagnosis of bilateral lower limb deep venous thrombosis. This required perioperative reversal of anticoagulation and IVC filter insertion. Conventional venography performed during filter insertion documented the existence of a duplicated IVC. CONCLUSION: We present a case of a symptomatic duplication of the IVC requiring filter insertion. We review the developmental anatomy of the IVC along with the diagnostic findings and management strategies available.

Seamless lesion insertion in digital mammography: methodology and reader study

Science.gov (United States)

Pezeshk, Aria; Petrick, Nicholas; Sahiner, Berkman

2016-03-01

Collection of large repositories of clinical images containing verified cancer locations is costly and time consuming due to difficulties associated with both the accumulation of data and establishment of the ground truth. This problem poses a significant challenge to the development of machine learning algorithms that require large amounts of data to properly train and avoid overfitting. In this paper we expand the methods in our previous publications by making several modifications that significantly increase the speed of our insertion algorithms, thereby allowing them to be used for inserting lesions that are much larger in size. These algorithms have been incorporated into an image composition tool that we have made publicly available. This tool allows users to modify or supplement existing datasets by seamlessly inserting a real breast mass or micro-calcification cluster extracted from a source digital mammogram into a different location on another mammogram. We demonstrate examples of the performance of this tool on clinical cases taken from the University of South Florida Digital Database for Screening Mammography (DDSM). Finally, we report the results of a reader study evaluating the realism of inserted lesions compared to clinical lesions. Analysis of the radiologist scores in the study using receiver operating characteristic (ROC) methodology indicates that inserted lesions cannot be reliably distinguished from clinical lesions.

The BDGP gene disruption project: Single transposon insertions associated with 40 percent of Drosophila genes

Energy Technology Data Exchange (ETDEWEB)

Bellen, Hugo J.; Levis, Robert W.; Liao, Guochun; He, Yuchun; Carlson, Joseph W.; Tsang, Garson; Evans-Holm, Martha; Hiesinger, P. Robin; Schulze, Karen L.; Rubin, Gerald M.; Hoskins, Roger A.; Spradling, Allan C.

2004-01-13

The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in more than 30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6,300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7,140 lines. It now includes individual lines predicted to disrupt 5,362 of the 13,666 currently annotated Drosophila genes (39 percent). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene mis-expression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.

A paternally transmitted complex chromosomal rearrangement (CCR) involving chromosomes 2, 6, and 18 includes eight breakpoints and five insertional translocations (ITs) through three generations.

Science.gov (United States)

Gruchy, Nicolas; Barreau, Morgane; Kessler, Ketty; Gourdier, Dominique; Leporrier, Nathalie

2010-01-01

Complex chromosomal rearrangements (CCRs) are uncommon and mainly occur de novo. We report here on a familial CCR involving chromosomes 2, 6, and 18. The propositus is a boy first referred because of growth delays, hypotonia, and facial anomalies, suggestive of deletion 18q syndrome. However, a cytogenetic family study disclosed a balanced CCR in three generations, which was detailed by FISH using BAC clones, and consisted of eight breakpoints with five insertional translocations (ITs). The propositus had a cryptic 18q deletion and a 6p duplication. Paternal transmission of this CCR was observed through three generations without meiotic recombination. Our investigation allowed us to provide porosities counseling and management of prenatal diagnosis for propositus cousin who carries this particular CCR.

Additive Manufacturing for Highly Efficient Window Inserts CRADA Report

Energy Technology Data Exchange (ETDEWEB)

Roschli, Alex C. [ORNL; Chesser, Phillip C. [ORNL; Love, Lonnie J. [ORNL

2018-04-01

ORNL partnered with the Mackinac Technology Company to demonstrate how additive manufacturing can be used to create highly energy efficient window inserts for retrofit in pre-existing buildings. Many early iterations of the window inserts were fabricated using carbon fiber reinforced thermoplastics and polycarbonate films as a stand in for the low-e coated films produced by the Mackinac Technology Company. After demonstration of the proof of concept, i.e. custom window inserts with tensioned film, the materials used for the manufacture of the frames was more closely examined. Hollow particle-filled syntactic foam and low-density polymer composites formed by expandable microspheres were explored as the materials used to additively manufacture the frames of the inserts. It was concluded that low-cost retrofit window inserts in custom sizes could be easily fabricated using large scale additive manufacturing. Furthermore, the syntactic and expanded foams developed and tested satisfy the mechanical performance requirements for the application.

Cross-species BAC-FISH painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements

NARCIS (Netherlands)

Tang, X.; Szinay, D.; Ramanna, M.S.; Vossen, van der E.A.G.; Datema, E.; Klein Lankhorst, R.M.; Boer, de J.M.; Peters, S.A.; Bachem, C.W.B.; Stiekema, W.J.; Visser, R.G.F.; Jong, de J.H.; Bai, Y.

2008-01-01

Ongoing genomics projects of tomato (Solanum lycopersicum ) and potato (Solanum tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, BACs can be positioned on pachytene comple-ments by fluorescent in situ hybridization (FISH) on homoeologous

A virus vector based on Canine Herpesvirus for vaccine applications in canids.

Science.gov (United States)

Strive, T; Hardy, C M; Wright, J; Reubel, G H

2007-01-31

Canine Herpesvirus (CHV) is being developed as a virus vector for the vaccination of European red foxes. However, initial studies using recombinant CHV vaccines in foxes revealed viral attenuation and lack of antibody response to inserted foreign antigens. These findings were attributed both to inactivation of the thymidine kinase (TK) gene and excess foreign genetic material in the recombinant viral genome. In this study, we report an improved CHV-bacterial artificial chromosome (BAC) vector system designed to overcome attenuation in foxes. A non-essential region was identified in the CHV genome as an alternative insertion site for foreign genes. Replacement of a guanine/cytosine (GC)-rich intergenic region between UL21 and UL22 of CHV with a marker gene did not change growth behaviour in vitro, showing that this region is not essential for virus growth in cell culture. We subsequently produced a CHV-BAC vector with an intact TK gene in which the bacterial genes and the antigen expression cassette were inserted into this GC-rich locus. Unlike earlier constructs, the new CHV-BAC allowed self-excision of the bacterial genes via homologous recombination after transfection of BACs into cell culture. The BAC-CHV system was used to produce a recombinant virus that constitutively expressed porcine zona pellucida subunit C protein between the UL21 and UL22 genes of CHV. Complete self-excision of the bacterial genes from CHV was achieved within one round of replication whilst retaining antigen gene expression.

The deep lymphatic anatomy of the hand.

Science.gov (United States)

Ma, Chuan-Xiang; Pan, Wei-Ren; Liu, Zhi-An; Zeng, Fan-Qiang; Qiu, Zhi-Qiang

2018-04-03

The deep lymphatic anatomy of the hand still remains the least described in medical literature. Eight hands were harvested from four nonembalmed human cadavers amputated above the wrist. A small amount of 6% hydrogen peroxide was employed to detect the lymphatic vessels around the superficial and deep palmar vascular arches, in webs from the index to little fingers, the thenar and hypothenar areas. A 30-gauge needle was inserted into the vessels and injected with a barium sulphate compound. Each specimen was dissected, photographed and radiographed to demonstrate deep lymphatic distribution of the hand. Five groups of deep collecting lymph vessels were found in the hand: superficial palmar arch lymph vessel (SPALV); deep palmar arch lymph vessel (DPALV); thenar lymph vessel (TLV); hypothenar lymph vessel (HTLV); deep finger web lymph vessel (DFWLV). Each group of vessels drained in different directions first, then all turned and ran towards the wrist in different layers. The deep lymphatic drainage of the hand has been presented. The results will provide an anatomical basis for clinical management, educational reference and scientific research. Copyright © 2018 Elsevier GmbH. All rights reserved.

Periodontal Plastic Microsurgery in the Treatment of Deep Gingival Recession after Orthodontic Movement

Directory of Open Access Journals (Sweden)

Sérgio Kahn

2013-01-01

Full Text Available Gingival recession is a condition that affects a large portion of the young and adult population and negatively affects the aesthetic aspects of the smile. Many factors are related to its development, including orthodontic movement beyond the osseous limits. Many treatment options have been proposed to cover the exposed root surface. The aim of this article was to describe three cases where a subepithelial connective tissue graft was performed, using a microsurgical technique, in the treatment of deep gingival recession after orthodontic treatment. This technique resulted in successful root coverage and keratinized tissue gain, improving the gingival esthetic pattern.

DeepSimulator: a deep simulator for Nanopore sequencing

KAUST Repository

Li, Yu

2017-12-23

Motivation: Oxford Nanopore sequencing is a rapidly developed sequencing technology in recent years. To keep pace with the explosion of the downstream data analytical tools, a versatile Nanopore sequencing simulator is needed to complement the experimental data as well as to benchmark those newly developed tools. However, all the currently available simulators are based on simple statistics of the produced reads, which have difficulty in capturing the complex nature of the Nanopore sequencing procedure, the main task of which is the generation of raw electrical current signals. Results: Here we propose a deep learning based simulator, DeepSimulator, to mimic the entire pipeline of Nanopore sequencing. Starting from a given reference genome or assembled contigs, we simulate the electrical current signals by a context-dependent deep learning model, followed by a base-calling procedure to yield simulated reads. This workflow mimics the sequencing procedure more naturally. The thorough experiments performed across four species show that the signals generated by our context-dependent model are more similar to the experimentally obtained signals than the ones generated by the official context-independent pore model. In terms of the simulated reads, we provide a parameter interface to users so that they can obtain the reads with different accuracies ranging from 83% to 97%. The reads generated by the default parameter have almost the same properties as the real data. Two case studies demonstrate the application of DeepSimulator to benefit the development of tools in de novo assembly and in low coverage SNP detection. Availability: The software can be accessed freely at: https://github.com/lykaust15/DeepSimulator.

Large-Scale Image Analytics Using Deep Learning

Science.gov (United States)

Ganguly, S.; Nemani, R. R.; Basu, S.; Mukhopadhyay, S.; Michaelis, A.; Votava, P.

2014-12-01

High resolution land cover classification maps are needed to increase the accuracy of current Land ecosystem and climate model outputs. Limited studies are in place that demonstrates the state-of-the-art in deriving very high resolution (VHR) land cover products. In addition, most methods heavily rely on commercial softwares that are difficult to scale given the region of study (e.g. continents to globe). Complexities in present approaches relate to (a) scalability of the algorithm, (b) large image data processing (compute and memory intensive), (c) computational cost, (d) massively parallel architecture, and (e) machine learning automation. In addition, VHR satellite datasets are of the order of terabytes and features extracted from these datasets are of the order of petabytes. In our present study, we have acquired the National Agricultural Imaging Program (NAIP) dataset for the Continental United States at a spatial resolution of 1-m. This data comes as image tiles (a total of quarter million image scenes with ~60 million pixels) and has a total size of ~100 terabytes for a single acquisition. Features extracted from the entire dataset would amount to ~8-10 petabytes. In our proposed approach, we have implemented a novel semi-automated machine learning algorithm rooted on the principles of "deep learning" to delineate the percentage of tree cover. In order to perform image analytics in such a granular system, it is mandatory to devise an intelligent archiving and query system for image retrieval, file structuring, metadata processing and filtering of all available image scenes. Using the Open NASA Earth Exchange (NEX) initiative, which is a partnership with Amazon Web Services (AWS), we have developed an end-to-end architecture for designing the database and the deep belief network (following the distbelief computing model) to solve a grand challenge of scaling this process across quarter million NAIP tiles that cover the entire Continental United States. The

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L. genome

Directory of Open Access Journals (Sweden)

Cloutier Sylvie

2011-05-01

Full Text Available Abstract Background Flax (Linum usitatissimum L. is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb. The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%, followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable

An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

Directory of Open Access Journals (Sweden)

Hsiao Yu-Yun

2011-01-01

Full Text Available Abstract Background Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC end sequences (BESs can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding. Results We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively, at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6% were predicted to represent protein-encoding regions, whereas 1,272 (23.0% contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively, whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6% of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species. Conclusion Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive

Method of inserting fuel rod

International Nuclear Information System (INIS)

Kamimoto, Shuji; Imoo, Makoto; Tsuchida, Kenji.

1991-01-01

The present invention concerns a method of inserting a fuel rod upon automatic assembling, automatic dismantling and reassembling of a fuel assembly in a light water moderated reactor, as well as a device and components used therefor. That is, a fuel rod is inserted reliably to an aimed point of insertion by surrounding the periphery of the fuel rod to be inserted with guide rods, and thereby suppressing the movement of the fuel rod during insertion. Alternatively, a fuel rod is inserted reliably to a point of insertion by inserting guide rods at the periphery of the point of insertion for the fuel rod to be inserted thereby surrounding the point of insertion with the guide rods or fuel rods. By utilizing fuel rods already present in the fuel assembly as the guide rods described above, the fuel rod can be inserted reliably to the point of insertion with no additional devices. Dummy fuel rods are previously inserted in a fuel assembly which are then utilized as the above-mentioned guide rods to accurately insert the fuel rod to the point of insertion. (I.S.)

Collinear factorization for deep inelastic scattering structure functions at large Bjorken xB

International Nuclear Information System (INIS)

Accardi, Alberto; Qiu, Jian-Wei

2008-01-01

http://dx.doi.org/10.1088/1126-6708/2008/07/090 We examine the uncertainty of perturbative QCD factorization for hadron structure functions in deep inelastic scattering at a large value of the Bjorken variable xB. We analyze the target mass correction to the structure functions by using the collinear factorization approach in the momentum space. We express the long distance physics of structure functions and the leading target mass corrections in terms of parton distribution functions with the standard operator definition. We compare our result with existing work on the target mass correction. We also discuss the impact of a final-state jet function on the extraction of parton distributions at large fractional momentum x.

Rapid generation of markerless recombinant MVA vaccines by en passant recombineering of a self-excising bacterial artificial chromosome.

Science.gov (United States)

Cottingham, Matthew G; Gilbert, Sarah C

2010-09-01

The non-replicating poxviral vector modified vaccinia virus Ankara (MVA) is currently a leading candidate for development of novel recombinant vaccines against globally important diseases. The 1980s technology for making recombinant MVA (and other poxviruses) is powerful and robust, but relies on rare recombination events in poxviral-infected cells. In the 21st century, it has become possible to apply bacterial artificial chromosome (BAC) technology to poxviruses, as first demonstrated by B. Moss' lab in 2002 for vaccinia virus. A similar BAC clone of MVA was subsequently derived, but while recombination-mediated genetic engineering for rapid production was used of deletion mutants, an alternative method was required for efficient insertion of transgenes. Furthermore "markerless" viruses, which carry no trace of the selectable marker used for their isolation, are increasingly required for clinical trials, and the viruses derived via the new method contained the BAC sequence in their genomic DNA. Two methods are adapted to MVA-BAC to provide more rapid generation of markerless recombinants in weeks rather than months. "En passant" recombineering is applied to the insertion of a transgene expression cassette and the removal of the selectable marker in bacteria; and a self-excising variant of MVA-BAC is constructed, in which the BAC cassette region is rapidly and efficiently lost from the viral genome following rescue of the BAC into infectious virus. These methods greatly facilitate and accelerate production of recombinant MVA, including markerless constructs. Copyright 2010 Elsevier B.V. All rights reserved.

Insertion Device Upgrade Plans at the NSLS

CERN Document Server

Tanabe, Toshiya; Harder, David; Lehecka, Michael; Rakowsky, George; Skaritka, John

2005-01-01

This paper describes plans to upgrade insertion devices at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, U.S.A. The aging wiggler (W80) at X25 is being replaced by a 1 m long in-vacuum mini-gap undulator (MGU-18) optimized for a dedicated macromolecular crystallography program. A new, 1/3 m long, in-vacuum undulator (MGU-13.5), will be installed between a pair of RF cavities at X9, and will serve a new beamline dedicated for small angle x-ray scattering (SAXS). Both MGU’s will have provision for cryocooling the NdFeB hybrid arrays to 150K to raise the field and K-value and to obtain better spectral coverage. Design issues of the devices and other considerations, especially magnetic measurement methods in low temperature will be discussed.

Impact on demersal fish of a large-scale and deep sand extraction site with ecosystem-based landscaped sandbars

Science.gov (United States)

de Jong, Maarten F.; Baptist, Martin J.; van Hal, Ralf; de Boois, Ingeborg J.; Lindeboom, Han J.; Hoekstra, Piet

2014-06-01

For the seaward harbour extension of the Port of Rotterdam in the Netherlands, approximately 220 million m3 sand was extracted between 2009 and 2013. In order to decrease the surface area of direct impact, the authorities permitted deep sand extraction, down to 20 m below the seabed. Biological and physical impacts of large-scale and deep sand extraction are still being investigated and largely unknown. For this reason, we investigated the colonization of demersal fish in a deep sand extraction site. Two sandbars were artificially created by selective dredging, copying naturally occurring meso-scale bedforms to increase habitat heterogeneity and increasing post-dredging benthic and demersal fish species richness and biomass. Significant differences in demersal fish species assemblages in the sand extraction site were associated with variables such as water depth, median grain size, fraction of very fine sand, biomass of white furrow shell (Abra alba) and time after the cessation of sand extraction. Large quantities of undigested crushed white furrow shell fragments were found in all stomachs and intestines of plaice (Pleuronectes platessa), indicating that it is an important prey item. One and two years after cessation, a significant 20-fold increase in demersal fish biomass was observed in deep parts of the extraction site. In the troughs of a landscaped sandbar however, a significant drop in biomass down to reference levels and a significant change in species assemblage was observed two years after cessation. The fish assemblage at the crests of the sandbars differed significantly from the troughs with tub gurnard (Chelidonichthys lucerna) being a Dufrêne-Legendre indicator species of the crests. This is a first indication of the applicability of landscaping techniques to induce heterogeneity of the seabed although it remains difficult to draw a strong conclusion due the lack of replication in the experiment. A new ecological equilibrium is not reached after 2

A new normalizing algorithm for BAC CGH arrays with quality control metrics.

Science.gov (United States)

Miecznikowski, Jeffrey C; Gaile, Daniel P; Liu, Song; Shepherd, Lori; Nowak, Norma

2011-01-01

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose "SmoothArray", a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package "aCGHplus," this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

Directory of Open Access Journals (Sweden)

Jeffrey C. Miecznikowski

2011-01-01

Full Text Available The main focus in pin-tip (or print-tip microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose “SmoothArray”, a new method to preprocess comparative genomic hybridization (CGH bacterial artificial chromosome (BAC arrays and we show the effects on a cancer dataset. As part of our R software package “aCGHplus,” this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

Lattice insertions for POPAE

International Nuclear Information System (INIS)

Cho, Y.; Crosbie, E.A.; Diebold, R.; Johnson, D.E.; Ohnuma, S.; Ruggiero, A.G.; Teng, L.C.

1977-01-01

Four types of insertions are described for the six 200-m straight sections of POPAE. All have dispersion matched to zero. (1) Injection-ejection insertion--This has proper high-β values and phase advances for horizontal injection and vertical ejection. (2) Phase-adjust insertion--The phase advance in this insertion is adjustable over a range of approximately 100 0 . (3) General-purpose insertion--The β* is adjustable from 2.5. to 200 m and the crossing angle is adjustable from 0 to 11 mrad. (4) High-luminosity insertion--This gives an even lower β + of meter

A PiggyBac mediated approach for lactoferricin gene transfer in bovine mammary epithelial stem cells for management of bovine mastitis.

Science.gov (United States)

Sharma, Neelesh; Huynh, Do Luong; Kim, Sung Woo; Ghosh, Mrinmoy; Sodhi, Simrinder Singh; Singh, Amit Kumar; Kim, Nam Eun; Lee, Sung Jin; Hussain, Kafil; Oh, Sung Jong; Jeong, Dong Kee

2017-11-28

The antibacterial and anti-inflammatory properties of lactoferricin have been ascribed to its ability to sequester essential iron. The objective of the study was to clone bovine lactoferricin ( LFcinB ) gene into PiggyBac Transposon vector, expression study in the bovine mammary epithelial stem cells (bMESCs) and also to determine the antimicrobial property of recombinant LFcinB against bovine mastitis-causing organisms. The PiggyBac-LFcinB was transfected into bMESCs by electroporation and a three fold of LFcinB secretion was observed in the transfected bMESCs medium by ELISA assay. Furthermore, the assessment of antimicrobial activity against mastitis causing pathogens Staphylococcus aureus and Escherichia coli demonstrated convincing evidence to prove strong antibacterial activity of LFcinB with 14.0±1.0 mm and 18.0±1.5 mm zone of inhibition against both organisms, respectively. The present study provides the convincing evidence to suggest the potential of PiggyBac transposon system to transfer antibacterial peptide into bMESCs or cow mammary gland and also pave the way to use bovine mammary gland as the bioreactors. Simultaneously, it also suggest toward commercial utilization of LFcinB bioreactor system in pharmaceutical industry.

Deep-UV patterning of commercial grade PMMA for low-cost, large-scale microfluidics

International Nuclear Information System (INIS)

Haiducu, M; Rahbar, M; Foulds, I G; Johnstone, R W; Sameoto, D; Parameswaran, M

2008-01-01

Although PMMA can be exposed using a variety of exposure sources, deep-UV at 254 nm is of interest because it is relatively inexpensive. Additionally, deep-UV sources can be readily scaled to large area exposures. Moreover, this paper will show that depths of over 100µm can be created in commercial grade PMMA using an uncollimated source. These depths are sufficient for creating microfluidic channels. This paper will provide measurements of the dissolution depth of commercial grade PMMA as a function of the exposure dose and etch time, using an IPA:H 2 O developer. Additionally, experiments were run to characterize the dependence of the dissolution rate on temperature and agitation. The patterned substrates were thermally bonded to blank PMMA pieces to enclose the channels and ports were drilled into the reservoirs. The resulting fluidic systems were then tested for leakage. The work herein presents the patterning, development and system behaviour of a complete microfluidics system based on commercial grade PMMA

Contributions of Bacău to the economic literature and culture – The life and work of Professor Vasile Pătruţ

OpenAIRE

Mihai Deju

2012-01-01

The economic culture and accounting theory in Bacău area has its beginnings in the setting up of the first practical school of agriculture, by Ion Ionescu de la Brad, who included in the curriculum an accounting course, as well. Over the years, the economic education of Bacău area education has evolved from “The School of Accounting and Co-operative Education” (1919) to the modern economic higher education, in our days. During an important period of the evolution of education and culture in B...

Insertion Modeling and Its Applications

OpenAIRE

Alexander Letichevsky; Oleksandr Letychevskyi; Vladimir Peschanenko

2016-01-01

The paper relates to the theoretical and practical aspects of insertion modeling. Insertion modeling is a theory of agents and environments interaction where an environment is considered as agent with a special insertion function. The main notions of insertion modeling are presented. Insertion Modeling System is described as a tool for development of different kinds of insertion machines. The research and industrial applications of Insertion Modeling System are presented.

Accelerating Deep Learning with Shrinkage and Recall

OpenAIRE

Zheng, Shuai; Vishnu, Abhinav; Ding, Chris

2016-01-01

Deep Learning is a very powerful machine learning model. Deep Learning trains a large number of parameters for multiple layers and is very slow when data is in large scale and the architecture size is large. Inspired from the shrinking technique used in accelerating computation of Support Vector Machines (SVM) algorithm and screening technique used in LASSO, we propose a shrinking Deep Learning with recall (sDLr) approach to speed up deep learning computation. We experiment shrinking Deep Lea...

Concept and analytical basis for revistas - A fast, flexible computer/graphic system for generating periodic satellite coverage patterns

Science.gov (United States)

King, J. C.

1976-01-01

The generation of satellite coverage patterns is facilitated by three basic strategies: use of a simplified physical model, permitting rapid closed-form calculation; separation of earth rotation and nodal precession from initial geometric analyses; and use of symmetries to construct traces of indefinite length by repetitive transposition of basic one-quadrant elements. The complete coverage patterns generated consist of a basic nadir trace plus a number of associated off-nadir traces, one for each sensor swath edge to be delineated. Each trace is generated by transposing one or two of the basic quadrant elements into a circle on a nonrotating earth model sphere, after which the circle is expanded into the actual 'helical' pattern by adding rotational displacements to the longitude coordinates. The procedure adapts to the important periodic coverage cases by direct insertion of the characteristic integers N and R (days and orbital revolutions, respectively, per coverage period).

COMPARATIVE STUDY OF EARLY POSTPARTUM IUCD INSERTION TO INTERVAL IUCD INSERTION

Directory of Open Access Journals (Sweden)

Shibani Devi

2016-07-01

Full Text Available INTRODUCTION According to National Family Health Survey-3, Indian women have 13% unmet need for contraception and according to District Level Household & Facility Survey-3, it is 21.3% in the postpartum period. Postpartum intrauterine contraceptive device insertion - both immediately post-placental delivery and somewhat later, but within 48 hours after delivery are options which merit consideration as the woman is likely to have a high motivation for accepting contraception and the healthcare centre provides a convenient setting for insertion of IUCD. AIM Comparison of efficacy and complications of IUCD insertions in post-placental with interval period: 6-month followup. METHOD This perspective study was conducted among 100 women: - 50 women had IUCD inserted within 10 minutes of placental delivery and 50 had insertion more than 6 weeks after delivery. They were followed till 6 months post insertion and were compared regarding early and late complications, continuation rates and expulsion rates. RESULT At the end of six months, we found higher occurrence of lower abdominal pain, heavy menstrual bleeding in case of interval insertion as compared to post-placental insertion which was statistically significant (p value-0.04 & 0.007 respectively. However, the expulsion rates of post-placental IUCD were somewhat elevated (14% compared to interval insertions (2%. Continuation rates at the end of 6 months in both the groups were 82% and 86% respectively which is comparable. CONCLUSION Post-placental IUCD is thus found to be an ideal method to meet the unmet need of postpartum women as it is easily accessible and convenient for both women and their health care providers, is associated with less discomfort and fewer side effects and allow women to obtain safe, long acting, highly effective contraception while still in the health care system.

Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus

DEFF Research Database (Denmark)

Urbanski, Dorian Fabian; Malolepszy, Anna; Stougaard, Jens

2012-01-01

Insertion mutants facilitate functional analysis of genes, but for most plant species it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics. The main challenge is developing efficient high-throughput procedures for both mutagenesis and insert......Insertion mutants facilitate functional analysis of genes, but for most plant species it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics. The main challenge is developing efficient high-throughput procedures for both mutagenesis...... plants. The identified insertions showed that the endogenous LORE1 retrotransposon is well suited for insertion mutagenesis due to its homogenous gene targeting and exonic insertion preference. Since LORE1 transposition occurs in the germline, harvesting seeds from a single founder line and cultivating...... progeny generates a complete mutant population. This ease of LORE1 mutagenesis combined with the efficient FSTpoolit protocol, which exploits 2D pooling, Illumina sequencing, and automated data analysis, allows highly cost-efficient development of a comprehensive reverse genetic resource....

WRF nested large-eddy simulations of deep convection during SEAC4RS

Science.gov (United States)

Heath, Nicholas K.; Fuelberg, Henry E.; Tanelli, Simone; Turk, F. Joseph; Lawson, R. Paul; Woods, Sarah; Freeman, Sean

2017-04-01

Large-eddy simulations (LES) and observations are often combined to increase our understanding and improve the simulation of deep convection. This study evaluates a nested LES method that uses the Weather Research and Forecasting (WRF) model and, specifically, tests whether the nested LES approach is useful for studying deep convection during a real-world case. The method was applied on 2 September 2013, a day of continental convection that occurred during the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) campaign. Mesoscale WRF output (1.35 km grid length) was used to drive a nested LES with 450 m grid spacing, which then drove a 150 m domain. Results reveal that the 450 m nested LES reasonably simulates observed reflectivity distributions and aircraft-observed in-cloud vertical velocities during the study period. However, when examining convective updrafts, reducing the grid spacing to 150 m worsened results. We find that the simulated updrafts in the 150 m run become too diluted by entrainment, thereby generating updrafts that are weaker than observed. Lastly, the 450 m simulation is combined with observations to study the processes forcing strong midlevel cloud/updraft edge downdrafts that were observed on 2 September. Results suggest that these strong downdrafts are forced by evaporative cooling due to mixing and by perturbation pressure forces acting to restore mass continuity around neighboring updrafts. We conclude that the WRF nested LES approach, with further development and evaluation, could potentially provide an effective method for studying deep convection in real-world cases.

DeepQA: improving the estimation of single protein model quality with deep belief networks.

Science.gov (United States)

Cao, Renzhi; Bhattacharya, Debswapna; Hou, Jie; Cheng, Jianlin

2016-12-05

Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. We introduce a novel single-model quality assessment method DeepQA based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy, physio-chemical characteristics, and structural information. The deep belief network is trained on several large datasets consisting of models from the Critical Assessment of Protein Structure Prediction (CASP) experiments, several publicly available datasets, and models generated by our in-house ab initio method. Our experiments demonstrate that deep belief network has better performance compared to Support Vector Machines and Neural Networks on the protein model quality assessment problem, and our method DeepQA achieves the state-of-the-art performance on CASP11 dataset. It also outperformed two well-established methods in selecting good outlier models from a large set of models of mostly low quality generated by ab initio modeling methods. DeepQA is a useful deep learning tool for protein single model quality assessment and protein structure prediction. The source code, executable, document and training/test datasets of DeepQA for Linux is freely available to non-commercial users at http://cactus.rnet.missouri.edu/DeepQA/ .

Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs

Science.gov (United States)

M.N. lslam-Faridi; C.D. Nelson; S.P. DiFazio; L.E. Gunter; G.A. Tuskan

2009-01-01

The 185-285 rDNA and 55 rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 185-285 rDNA sites and one 55 rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis-type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones...

The genome of the pear (Pyrus bretschneideri Rehd.)

DEFF Research Database (Denmark)

Wu, Jun; Wang, Zhiwen; Shi, Zebin

2013-01-01

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps ...

Lithium Insertion In Silicon Nanowires: An ab Initio Study

KAUST Repository

Zhang, Qianfan

2010-09-08

The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process. © 2010 American Chemical Society.

FEATURES OF THE LARGE INTESTINE MICROFLORA OF CHILDREN – DONOR LIVER TRANSPLANT RECIPIENTS

Directory of Open Access Journals (Sweden)

N. I. Gabrielyan

2013-01-01

Full Text Available Aim. The study microecology of the large intestine of children with cirrhosis before transplantation of the share liver. Materials and methods. Studied the flora of the colon 157 children of 1 to 17 years admitted to hospital for liver transplantation fragment from a related donor. Identification was carried out using microbial panels BD Crystal and databases BBL Crystal MIND. Methicillin-resistant staphylococci were determined by their sensiti- vity to oxacillin and cefoxitin. Beta-lactamase activity was tested using discs with ceftazidime and ceftazidime/ clavulanic acid. Results. Microecological revealed deep irregularities in the large intestine transplantation in children up lobe of the liver on a spectrum and composition of the microflora. Among the resident microflora decreased levels of bifidobacteria, lactobacilli and coliform bacteria, especially in children under one year. A sig- nificant portion of the children surveyed (over 60–70% had an increase of frequency of finding stateally bacteria, especially Klebsiella and enterobacteria in third children – non-fermenting bacteria – Pseudomonas and Acine- tobacter spp. Revealed the spread of strains of gram-negative bacteria with extended-spectrum betalaktamaz.Conclusion. Expressed microecological violations in the large intestine in children with higher levels of bac- teria are conditionally risk factor reeks of infectious complications in the postoperative period and require are complex tools to assist in eliminatsii.s given antibiotic resistance of bacteria. 

Percutaneous insertion of inferior vean cava filter:clinical results of 8 patients

International Nuclear Information System (INIS)

Bae, Kyung Soo; Shin, Hyun Woong; Park, No Hyuck; Ryeom, Hun Kyu; Kim, Yong Joo

1997-01-01

To evaluate the efficacy and clinical results of percutaneous insertion of inferior vena cava(IVC) filter. Over a two year period, eight IVC filters were placed in eight patients with pulmonary thromboembolism resulting from deep vein thrombosis of the legs. The indications for placement were contraindication to anticoagulation(3), and recurrent pulmonary embolism during anticoagulant therapy(5). Both femoral(7) and jugular(1) routes were used for percutaneous transvenous insertion. To delineate the caval anatomy and to ensure placement just caudal to the renal vein, a cavogram was obtained before filter placement. Bird's Nest (7) and Greenfield (1) filters were inserted. Follow-up information was obtained by means of duplex sonography, CT scan, abdominal radiograph, and perfusion scan of the lungs, followed by clinical evaluation. In all cases, procedures were technically successful. Placement complications occurred in three patients. In one, the filter was inadvertently placed above the iliac bifurcation; in the other two, prolapse of the Bird's Nest filter wire occurred. Occlusion of IVC occurred in two patients, and recurrent pulmonary embolism was suspected in one, who suffered from chest pain and short-ness of breath. In the other patients, there was no clinical evidence of recurrence of the pulmonary embolism. Insertion of an inferior vena cava filter is a safe and effective method for the prevention of pulmonary embolism when anticoagulant therapy is either ineffective or contraindicated

The impact of surface composition on Tafel kinetics leading to enhanced electrochemical insertion of hydrogen in palladium

Science.gov (United States)

Dmitriyeva, Olga; Hamm, Steven C.; Knies, David L.; Cantwell, Richard; McConnell, Matt

2018-05-01

Our previous work experimentally demonstrated the enhancement of electrochemical hydrogen insertion into palladium by modifying the chemical composition of the cathode surface with Pb, Pt and Bi, referred to as surface promoters. The experiment demonstrated that an optimal combination of the surface promoters led to an increase in hydrogen fugacity of more than three orders of magnitude, while maintaining the same current density. This manuscript discusses the application of Density Functional Theory (DFT) to elucidate the thermodynamics and kinetics of observed enhancement of electrochemical hydrogen insertion into palladium. We present theoretical simulations that: (1) establish the elevation of hydrogen's chemical potential on Pb and Bi surfaces to enhance hydrogen insertion, (2) confirm the increase of a Tafel activation barrier that results in a decrease of the reaction rate at the given hydrogen overpotential, and (3) explain why the surface promoter's coverage needs to be non-uniform, namely to allow hydrogen insertion into palladium bulk while simultaneously locking hydrogen below the surface (the corking effect). The discussed DFT-based method can be used for efficient scanning of different material configurations to design a highly effective hydrogen storage system.

Deep Feature Learning and Cascaded Classifier for Large Scale Data

DEFF Research Database (Denmark)

Prasoon, Adhish

from data rather than having a predefined feature set. We explore deep learning approach of convolutional neural network (CNN) for segmenting three dimensional medical images. We propose a novel system integrating three 2D CNNs, which have a one-to-one association with the xy, yz and zx planes of 3D......This thesis focuses on voxel/pixel classification based approaches for image segmentation. The main application is segmentation of articular cartilage in knee MRIs. The first major contribution of the thesis deals with large scale machine learning problems. Many medical imaging problems need huge...... amount of training data to cover sufficient biological variability. Learning methods scaling badly with number of training data points cannot be used in such scenarios. This may restrict the usage of many powerful classifiers having excellent generalization ability. We propose a cascaded classifier which...

Efficient Strategy to Generate a Vectored Duck Enteritis Virus Delivering Envelope of Duck Tembusu Virus

Directory of Open Access Journals (Sweden)

Zhong Zou

2014-06-01

Full Text Available Duck Tembusu virus (DTMUV is a recently emerging pathogenic flavivirus that has resulted in a huge economic loss in the duck industry. However, no vaccine is currently available to control this pathogen. Consequently, a practical strategy to construct a vaccine against this pathogen should be determined. In this study, duck enteritis virus (DEV was examined as a candidate vaccine vector to deliver the envelope (E of DTMUV. A modified mini-F vector was inserted into the SORF3 and US2 gene junctions of the attenuated DEV vaccine strain C-KCE genome to generate an infectious bacterial artificial chromosome (BAC of C-KCE (vBAC-C-KCE. The envelope (E gene of DTMUV was inserted into the C-KCE genome through the mating-assisted genetically integrated cloning (MAGIC strategy, resulting in the recombinant vector, pBAC-C-KCE-E. A bivalent vaccine C-KCE-E was generated by eliminating the BAC backbone. Immunofluorescence and western blot analysis results indicated that the E proteins were vigorously expressed in C-KCE-E-infected chicken embryo fibroblasts (CEFs. Duck experiments demonstrated that the insertion of the E gene did not alter the protective efficacy of C-KCE. Moreover, C-KCE-E-immunized ducks induced neutralization antibodies against DTMUV. These results demonstrated, for the first time, that recombinant C-KCE-E can serve as a potential bivalent vaccine against DEV and DTMUV.

A bacterial artificial chromosome-based physical map of Manihot esculenta ssp.flabellifolia

Institute of Scientific and Technical Information of China (English)

Yuhua FU; Zhiqiang XIA; Shujuan WANG; Xin CHEN; Cheng LU; Mingcheng LUO; Hongbin ZHANG; Wenquan WANG

2016-01-01

Cassava (Manihot esculenta) is known as the third most important food crop in the tropics and also used for industrial feedstock for biofuels.Two new bacterial artificial chromosome (BAC) libraries were constructed for W14 (M.Esculenta ssp.flabellifolia),a wild ancestor of domesticated cassava.The libraries were constructed with EcoRI and HindⅢ insertion vectors,respectively.The EcoRI library has 29952 clones with an average insert size of 115 kb,while the HindⅢ library consists of 29952 clones with an average insert of 129 kb.The combined libraries contain a total of 59904 clones with an average insert size of 125 kb,representing approximately 10×haploid genome equivalents.A total of 29952 clones were fingerprinted and resulted in a cassava physical map composed of 2485 contigs with an average physical length of 336 kb and 2909 singletons,representing approximately 762 Mb of the cassava genome.5000 clones located at the ends of BAC contigs were selected and sequenced.A total of 6077 SNPs and 231 indels were identified,that covered 459 gene sequences,of which 6 genes were associated with starch and sucrose metabolism.This BAC-based physical map provides valuable tools to understand the genetics and evolution of cassava.

Computing Convex Coverage Sets for Faster Multi-Objective Coordination

NARCIS (Netherlands)

Roijers, D.M.; Whiteson, S.; Oliehoek, F.A.

2015-01-01

In this article, we propose new algorithms for multi-objective coordination graphs (MO-CoGs). Key to the efficiency of these algorithms is that they compute a convex coverage set (CCS) instead of a Pareto coverage set (PCS). Not only is a CCS a sufficient solution set for a large class of problems,

Risk of venous thromboembolism associated with peripherally inserted central catheters: a systematic review and meta-analysis.

Science.gov (United States)

Chopra, Vineet; Anand, Sarah; Hickner, Andy; Buist, Michael; Rogers, Mary Am; Saint, Sanjay; Flanders, Scott A

2013-07-27

Peripherally inserted central catheters (PICCs) are associated with an increased risk of venous thromboembolism. However, the size of this risk relative to that associated with other central venous catheters (CVCs) is unknown. We did a systematic review and meta-analysis to compare the risk of venous thromboembolism associated with PICCs versus that associated with other CVCs. We searched several databases, including Medline, Embase, Biosis, Cochrane Central Register of Controlled Trials, Conference Papers Index, and Scopus. Additional studies were identified through hand searches of bibliographies and internet searches, and we contacted study authors to obtain unpublished data. All human studies published in full text, abstract, or poster form were eligible for inclusion. All studies were of adult patients aged at least 18 years who underwent insertion of a PICC. Studies were assessed with the Newcastle-Ottawa risk of bias scale. In studies without a comparison group, the pooled frequency of venous thromboembolism was calculated for patients receiving PICCs. In studies comparing PICCs with other CVCs, summary odds ratios (ORs) were calculated with a random effects meta-analysis. Of the 533 citations identified, 64 studies (12 with a comparison group and 52 without) including 29 503 patients met the eligibility criteria. In the non-comparison studies, the weighted frequency of PICC-related deep vein thrombosis was highest in patients who were critically ill (13·91%, 95% CI 7·68-20·14) and those with cancer (6·67%, 4·69-8·64). Our meta-analysis of 11 studies comparing the risk of deep vein thrombosis related to PICCs with that related to CVCs showed that PICCs were associated with an increased risk of deep vein thrombosis (OR 2·55, 1·54-4·23, p<0·0001) but not pulmonary embolism (no events). With the baseline PICC-related deep vein thrombosis rate of 2·7% and pooled OR of 2·55, the number needed to harm relative to CVCs was 26 (95% CI 13-71). PICCs are

Coverage of the migrant population in large-scale assessment surveys. Experiences from PIAAC in Germany

Directory of Open Access Journals (Sweden)

Débora B. Maehler

2017-03-01

Full Text Available Abstract Background European countries, and especially Germany, are currently very much affected by human migration flows, with the result that the task of integration has become a challenge. Only very little empirical evidence on topics such as labor market participation and processes of social integration of migrant subpopulations is available to date from large-scale population surveys. The present paper provides an overview of the representation of the migrant population in the German Programme for the International Assessment of Adult Competencies (PIAAC sample and evaluates reasons for the under-coverage of this population. Methods We examine outcome rates and reasons for nonresponse among the migrant population based on sampling frame data, and we also examine para data from the interviewers’ contact protocols to evaluate time patterns for the successful contacting of migrants. Results and Conclusions This is the first time that results of this kind have been presented for a large-scale assessment in educational research. These results are also discussed in the context of future PIAAC cycles. Overall, they confirm the expectations in the literature that factors such as language problems result in lower contact and response rates among migrants.

Development of Health Education Learning Module in Bac.TSE-LDPE Programme in TTI: Needs Analysis Study

Science.gov (United States)

Ujang, Alijah; Alias, Norlidah; Siraj, Saedah

2015-01-01

This study is to explore the need to develop learning modules of health education for trainee teachers in the Bachelor Of Teaching (Hons)(Special Education-Learning Disabilities For Primary Education) Programme (Bac.TSE-LDPE) in the Teacher Training Institute (TTI). The questionnaire uses the Likert scale with the close ended questions analysed by…

LookSeq: a browser-based viewer for deep sequencing data.

Science.gov (United States)

Manske, Heinrich Magnus; Kwiatkowski, Dominic P

2009-11-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods.

Design, Fabrication and Initial Testing of a Large Bore Single Aperture 1 m Long Superconducting Dipole Made with Phenolic Inserts

CERN Document Server

Boschmann, H; Kirby, G A; Lucas, J; Ostojic, R; Russenschuck, Stephan; Siemko, A; Vanenkov, I; Weterings, W

1997-01-01

In the framework of the LHC magnet development programme, a large bore single aperture 1-meter long superconducting dipole has been built in collaboration with HOLEC. The magnet features a single layer coil wound using the LHC main dipole outer layer cable, phenolic inserts, and a keyed two part structural iron yoke. This paper presents the magnetic and mechanical design and optimisation of the magnet. We describe the coil winding and curing, and present the construction and assembly procedures. Finally we report on the mechanical behaviour during assembly and cooling, and present the magnet training behaviour.

Genome-wide retroviral insertional tagging of genes involved in cancer in Cdkn2a-deficient mice

DEFF Research Database (Denmark)

Lund, Anders H; Turner, Geoffrey; Trubetskoy, Alla

2002-01-01

We have used large-scale insertional mutagenesis to identify functional landmarks relevant to cancer in the recently completed mouse genome sequence. We infected Cdkn2a(-/-) mice with Moloney murine leukemia virus (MoMuLV) to screen for loci that can participate in tumorigenesis in collaboration...... retroviral integration sites and mapped them against the mouse genome sequence databases from Celera and Ensembl. In addition to 17 insertions targeting gene loci known to be cancer-related, we identified a total of 37 new common insertion sites (CISs), of which 8 encode components of signaling pathways...... that are involved in cancer. The effectiveness of large-scale insertional mutagenesis in a sensitized genetic background is demonstrated by the preference for activation of MAP kinase signaling, collaborating with Cdkn2a loss in generating the lymphoid and myeloid tumors. Collectively, our results show that large...

Coverage-dependent adsorption thermodynamics of oxygen on ZnO(0001)

Energy Technology Data Exchange (ETDEWEB)

Li, Ming; Seebauer, Edmund G., E-mail: eseebaue@illinois.edu

2017-03-01

Highlights: • Adsorption enthalpy and entropy of oxygen on Zn-term ZnO(0001) were measured by photoreflectance. • These parameters are large in magnitude and vary nonmonotonically with coverage. • Many kinds of sites, chemical species and reconstructions contribute to this behavior. • Entropic and enthalpic contributions to the free energy are comparable near room temperature. - Abstract: The equilibrium behavior of oxygen adsorbed on metal oxide surfaces such as ZnO(0001) often affects their behavior in applications such as gas sensing. The present work attempts to bridge this distinct gap to applications from an alternate perspective by employing the optical technique of photoreflectance (PR) to measure the enthalpy ΔH{sub ads} and entropy ΔS{sub ads} of oxygen adsorption as a function of coverage on Zn-terminated ZnO(0001). The large and strongly coverage-dependent parameters, stemming from a multiplicity of sites, chemical species and reconstructions, lead to a nonmonotonic coverage variation in both ΔH{sub ads} and ΔS{sub ads}. The entropic contribution to the free energy is comparable to the enthalpic contribution even near room temperature, so that temperature effects on oxygen adsorption may be uncommonly large.

ASTER cloud coverage reassessment using MODIS cloud mask products

Science.gov (United States)

Tonooka, Hideyuki; Omagari, Kunjuro; Yamamoto, Hirokazu; Tachikawa, Tetsushi; Fujita, Masaru; Paitaer, Zaoreguli

2010-10-01

In the Advanced Spaceborne Thermal Emission and Reflection radiometer (ASTER) Project, two kinds of algorithms are used for cloud assessment in Level-1 processing. The first algorithm based on the LANDSAT-5 TM Automatic Cloud Cover Assessment (ACCA) algorithm is used for a part of daytime scenes observed with only VNIR bands and all nighttime scenes, and the second algorithm based on the LANDSAT-7 ETM+ ACCA algorithm is used for most of daytime scenes observed with all spectral bands. However, the first algorithm does not work well for lack of some spectral bands sensitive to cloud detection, and the two algorithms have been less accurate over snow/ice covered areas since April 2008 when the SWIR subsystem developed troubles. In addition, they perform less well for some combinations of surface type and sun elevation angle. We, therefore, have developed the ASTER cloud coverage reassessment system using MODIS cloud mask (MOD35) products, and have reassessed cloud coverage for all ASTER archived scenes (>1.7 million scenes). All of the new cloud coverage data are included in Image Management System (IMS) databases of the ASTER Ground Data System (GDS) and NASA's Land Process Data Active Archive Center (LP DAAC) and used for ASTER product search by users, and cloud mask images are distributed to users through Internet. Daily upcoming scenes (about 400 scenes per day) are reassessed and inserted into the IMS databases in 5 to 7 days after each scene observation date. Some validation studies for the new cloud coverage data and some mission-related analyses using those data are also demonstrated in the present paper.

Chest tube insertion

Science.gov (United States)

Chest drainage tube insertion; Insertion of tube into chest; Tube thoracostomy; Pericardial drain ... Be careful there are no kinks in your tube. The drainage system should always sit upright and be placed ...

BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins

Directory of Open Access Journals (Sweden)

MuthuKrishnan Selvaraj

2016-01-01

Full Text Available The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Support vector machine (SVM models were developed for predicting HbL proteins based upon amino acid composition (AC, dipeptide composition (DC, hybrid method (AC + DC, and position specific scoring matrix (PSSM. In addition, we introduce for the first time a new prediction method based on max to min amino acid residue (MM profiles. The average accuracy, standard deviation (SD, false positive rate (FPR, confusion matrix, and receiver operating characteristic (ROC were analyzed. We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques. Prediction accuracy was further investigated through confusion matrix and ROC curve analysis. All experimental results indicate that the proposed BacHbpred can be a perspective predictor for determination of HbL related proteins. BacHbpred, a web tool, has been developed for HbL prediction.

Enhanced Expression of Anti-CD19 Chimeric Antigen Receptor in piggyBac Transposon-Engineered T Cells

Directory of Open Access Journals (Sweden)

Daisuke Morita

2018-03-01

Full Text Available Adoptive T cell therapy using chimeric antigen receptor (CAR-modified T cells is a promising cancer immunotherapy. We previously developed a non-viral method of gene transfer into T cells using a piggyBac transposon system to improve the cost-effectiveness of CAR-T cell therapy. Here, we have further improved our technology by a novel culture strategy to increase the transfection efficiency and to reduce the time of T cell manufacturing. Using a CH2CH3-free CD19-specific CAR transposon vector and combining irradiated activated T cells (ATCs as feeder cells and virus-specific T cell receptor (TCR stimulation, we achieved 51.4% ± 14% CAR+ T cells and 2.8-fold expansion after 14 culture days. Expanded CD19.CAR-T cells maintained a significant fraction of CD45RA+CCR7+ T cells and demonstrated potent antitumor activity against CD19+ leukemic cells both in vitro and in vivo. Therefore, piggyBac-based gene transfer may provide an alternative to viral gene transfer for CAR-T cell therapy.

Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.

Directory of Open Access Journals (Sweden)

Chris T Yohn

2005-04-01

Full Text Available Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1] that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes. We unambiguously map 287 retroviral integration sites and determine that approximately 95.8% of the insertions occur at non-orthologous regions between closely related species. Phylogenetic analysis of the endogenous retrovirus reveals that the gorilla and chimpanzee elements share a monophyletic origin with a subset of the Old World monkey retroviral elements, but that the average sequence divergence exceeds neutral expectation for a strictly nuclear inherited DNA molecule. Within the chimpanzee, there is a significant integration bias against genes, with only 14 of these insertions mapping within intronic regions. Six out of ten of these genes, for which there are expression data, show significant differences in transcript expression between human and chimpanzee. Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3-4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes.

When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality.

Science.gov (United States)

Lonardi, Stefano; Mirebrahim, Hamid; Wanamaker, Steve; Alpert, Matthew; Ciardo, Gianfranco; Duma, Denisa; Close, Timothy J

2015-09-15

As the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing. We explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on 'divide and conquer': we 'slice' a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data. Python scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/MIyZHs stelo@cs.ucr.edu or timothy.close@ucr.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Experimental insertions

International Nuclear Information System (INIS)

Sandweiss, J.; Kycia, T.F.

1975-01-01

A discussion is given of the eight identical experimental insertions for the planned ISABELLE storage rings. Four sets of quadrupole doublets are used to match the β functions in the insertions to the values in the cells, and the total free space available at the crossing point is 40 meters. An asymmetric beam energy operation is planned, which will be useful in a number of experiments

Manganese oxide octahedral molecular sieves as insertion electrodes for rechargeable Mg batteries

KAUST Repository

Rasul, Shahid

2013-11-01

Magnesium has been inserted electrochemically into manganese oxide octahedral molecular sieves (OMS-5 MnO2) at room temperature. Discharge/charge profiles show that a large amount of Mg, i.e., 0.37 Mg/Mn can be inserted electrochemically using 1 M Mg(ClO4)2/AN electrolyte when OMS-5 is prepared in presence of acetylene black. X-ray diffraction analysis and discharge/charge profiles verify that a solid state solution reaction takes place upon Mg insertion into the host lattice with concurrent reduction of Mn4+ to Mn2+. However, upon each reduction of Mn by Mg insertion and resultant dissolution into electrolyte, decrease in the active compound occurs consequently. A low intrinsic electronic conductivity of OMS-5 was suggested to play a vital role in Mg insertion into the host. © 2013 Elsevier Ltd.

Manganese oxide octahedral molecular sieves as insertion electrodes for rechargeable Mg batteries

KAUST Repository

Rasul, Shahid; Suzuki, Shinya; Yamaguchi, Shu; Miyayama, Masaru

2013-01-01

Magnesium has been inserted electrochemically into manganese oxide octahedral molecular sieves (OMS-5 MnO2) at room temperature. Discharge/charge profiles show that a large amount of Mg, i.e., 0.37 Mg/Mn can be inserted electrochemically using 1 M Mg(ClO4)2/AN electrolyte when OMS-5 is prepared in presence of acetylene black. X-ray diffraction analysis and discharge/charge profiles verify that a solid state solution reaction takes place upon Mg insertion into the host lattice with concurrent reduction of Mn4+ to Mn2+. However, upon each reduction of Mn by Mg insertion and resultant dissolution into electrolyte, decrease in the active compound occurs consequently. A low intrinsic electronic conductivity of OMS-5 was suggested to play a vital role in Mg insertion into the host. © 2013 Elsevier Ltd.

Coverage of the Stanford Prison Experiment in Introductory Psychology Courses

Science.gov (United States)

Bartels, Jared M.; Milovich, Marilyn M.; Moussier, Sabrina

2016-01-01

The present study examined the coverage of Stanford prison experiment (SPE), including criticisms of the study, in introductory psychology courses through an online survey of introductory psychology instructors (N = 117). Results largely paralleled those of the recently published textbook analyses with ethical issues garnering the most coverage,…

Using Flipped Classroom Approach to Explore Deep Learning in Large Classrooms

Directory of Open Access Journals (Sweden)

Brenda Danker

2015-01-01

Full Text Available This project used two Flipped Classroom approaches to stimulate deep learning in large classrooms during the teaching of a film module as part of a Diploma in Performing Arts course at Sunway University, Malaysia. The flipped classes utilized either a blended learning approach where students first watched online lectures as homework, and then completed their assignments and practical work in class; or utilized a guided inquiry approach at the beginning of class using this same process. During the class the lecturers were present to help the students, and in addition, the students were advantaged by being able to help one another. The in-class learning activities also included inquiry-based learning, active learning, and peer-learning. This project used an action research approach to improve the in-class instructional design progressively to achieve its impact of deep learning among the students. The in-class learning activities that was included in the later flipped classes merged aspects of blended learning with an inquiry-based learning cycle which focused on the exploration of concepts. Data was gathered from questionnaires filled out by the students and from short interviews with the students, as well as from the teacher’s reflective journals. The findings verified that the flipped classrooms were able to remodel large lecture classes into active-learning classes. The results also support the possibility of individualised learning for the students as being high as a result of the teacher’s ability to provide one-on-one tutoring through technology-infused lessons. It is imperative that the in-class learning activities are purposefully designed as the inclusion of the exploratory learning through guided inquiry-based activities in the flipped classes was a successful way to engage students on a deeper level and increased the students’ curiosity and engaged them to develop higher-order thinking skills. This project also concluded that

Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates.

Science.gov (United States)

Acker, Leah C; Pino, Erica N; Boyden, Edward S; Desimone, Robert

2017-10-03

This protocol describes a large-volume illuminator, which was developed for optogenetic manipulations in the non-human primate brain. The illuminator is a modified plastic optical fiber with etched tip, such that the light emitting surface area is > 100x that of a conventional fiber. In addition to describing the construction of the large-volume illuminator, this protocol details the quality-control calibration used to ensure even light distribution. Further, this protocol describes techniques for inserting and removing the large volume illuminator. Both superficial and deep structures may be illuminated. This large volume illuminator does not need to be physically coupled to an electrode, and because the illuminator is made of plastic, not glass, it will simply bend in circumstances when traditional optical fibers would shatter. Because this illuminator delivers light over behaviorally-relevant tissue volumes (≈ 10 mm 3 ) with no greater penetration damage than a conventional optical fiber, it facilitates behavioral studies using optogenetics in non-human primates.

Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

Science.gov (United States)

Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

2012-05-01

The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

Directory of Open Access Journals (Sweden)

Gonser Rusty A

2011-06-01

Full Text Available Abstract Background The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis, which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.

Creation of a BAC resource to study the structure and evolution of the banana (Musa balbisiana) genome

Czech Academy of Sciences Publication Activity Database

Šafář, Jan; Noa-Carrazana, J. C.; Vrána, Jan; Bartoš, Jan; Alkhimova, Olena; Lheureux, F.; Šimková, Hana; Caruana, M. L.; Doležel, Jaroslav; Piffanelli, P.

2004-01-01

Roč. 47, - (2004), 1182ů1191 E-ISSN 1480-3321 R&D Projects: GA AV ČR IAA6038201 Grant - others:research contract IAEA(FR) 12230/RBF Institutional research plan: CEZ:AV0Z5038910 Keywords : bacterial artificial chromosome library * banana * BAC-FISH Subject RIV: EB - Genetics ; Molecular Biology

Time-to-detection of bacteria and yeast with the BACTEC FX versus BacT/Alert Virtuo blood culture systems.

Science.gov (United States)

Somily, Ali Mohammed; Habib, Hanan Ahmed; Torchyan, Armen Albert; Sayyed, Samina B; Absar, Muhammed; Al-Aqeel, Rima; Binkhamis, A Khalifa

2018-01-01

Bloodstream infections are associated with high rates of morbidity and mortality. Rapid detection of bloodstream infections is important in achieving better patient outcomes. Compare the time-to-detection (TTD) of the new BacT/Alert Virtuo and the BACTEC FX automated blood culture systems. Prospective simulated comparison of two instruments using seeded samples. Medical microbiology laboratory. Blood culture bottles were seeded in triplicate with each of the standard ATCC strains of aerobes, anaerobes and yeast. TTD was calculated as the length of time from the beginning of culture incubation to the detection of bacterial growth. TTD for the various tested organisms on the two microbial detection systems. The 99 bottles of seeded blood cultures incubated in each of the blood culture systems included 21 anaerobic, 39 aerobic and 39 pediatric bottles. The BacT/Alert Virtuo system exhibited significantly shorter TTD for 72.7 % of the tested organisms compared to BACTEC FX system with a median difference in mean TTD of 2.1 hours (interquartile range: 1.5-3.5 hours). The BACTEC FX system was faster in 15.2% (5/33) of microorganisms, with a median difference in mean TTD of 25.9 hours (IQR: 9.1-29.2 hours). TTD was significantly shorter for most of the microorganisms tested on the new BacT/Alert Virtuo system compared to the BACTEC FX system. Use of simulated cultures to assess TTD may not precisely represent clinical blood cultures. None.

Recommendation system for immunization coverage and monitoring.

Science.gov (United States)

Bhatti, Uzair Aslam; Huang, Mengxing; Wang, Hao; Zhang, Yu; Mehmood, Anum; Di, Wu

2018-01-02

Immunization averts an expected 2 to 3 million deaths every year from diphtheria, tetanus, pertussis (whooping cough), and measles; however, an additional 1.5 million deaths could be avoided if vaccination coverage was improved worldwide. 1 1 Data source for immunization records of 1.5 M: http://www.who.int/mediacentre/factsheets/fs378/en/ New vaccination technologies provide earlier diagnoses, personalized treatments and a wide range of other benefits for both patients and health care professionals. Childhood diseases that were commonplace less than a generation ago have become rare because of vaccines. However, 100% vaccination coverage is still the target to avoid further mortality. Governments have launched special campaigns to create an awareness of vaccination. In this paper, we have focused on data mining algorithms for big data using a collaborative approach for vaccination datasets to resolve problems with planning vaccinations in children, stocking vaccines, and tracking and monitoring non-vaccinated children appropriately. Geographical mapping of vaccination records helps to tackle red zone areas, where vaccination rates are poor, while green zone areas, where vaccination rates are good, can be monitored to enable health care staff to plan the administration of vaccines. Our recommendation algorithm assists in these processes by using deep data mining and by accessing records of other hospitals to highlight locations with lower rates of vaccination. The overall performance of the model is good. The model has been implemented in hospitals to control vaccination across the coverage area.

Effect of fiber inserts on gingival margin microleakage of Class II bulk-fill composite resin restorations.

Science.gov (United States)

Shafiei, Fereshteh; Doozandeh, Maryam; Karimi, Vahid

2018-01-01

This study evaluated the effect of fiber inserts combined with composite resins on enamel and dentin margin microleakage. The fiber inserts were used with high- (x-tra fil) and low-viscosity (x-tra base) bulk-fill composite resins and as well as conventional composite resins (Grandio and Grandio Flow). In 96 sound, recently extracted molars, 2 standardized Class II cavities were prepared. The teeth were randomly divided into 8 groups of 12 teeth each, based on composite resin type and presence or absence of fiber inserts: groups 1 and 2, x-tra fil with and without fiber inserts, respectively; groups 3 and 4, x-tra base with and without fiber inserts; groups 5 and 6, Grandio with and without fiber inserts; and groups 7 and 8, Grandio Flow liner (gingival floor)/Grandio (remainder of cavity) with and without fiber inserts. In all the groups, a 2-step etch-and-rinse adhesive was used. The specimens were processed in a dye penetration technique to determine microleakage percentages. Data were analyzed with analysis of variance, Tukey, and t tests. There was significantly less leakage at the enamel margins than the dentin margins. Fiber reinforcement significantly decreased enamel microleakage in all the groups, with no significant differences among the groups. Concerning dentin microleakage, there were no significant differences among the 4 groups without fiber inserts, while a significant difference was detected in groups 2 (x-tra fil plus fiber) and 8 (Grandio Flow plus fiber/Grandio). Fibers significantly improved dentin sealing in groups 2 and 8. These findings suggest that a fiber insert reinforcing bulk-fill and conventional composite resins might improve enamel sealing in shallow Class II cavi-ties. The effect of fiber reinforcement on the dentin margins of deep cavities depended on the viscosity of the composite resins; fiber reinforcement was effective for flowable bulk-fill and conventional composite resin restorations.

Comparison of energy flows in deep inelastic scattering events with and without a large rapidity gap

International Nuclear Information System (INIS)

Derrick, M.; Krakauer, D.; Magill, S.

1994-07-01

Energy flows in deep inelastic electron-proton scattering are investigated at a centre-of-mass energy of 296 GeV for the range Q 2 ≥10 GeV 2 using the ZEUS detector. A comparison is made between events with and without a large rapidity gap between the hadronic system and the proton direction. The energy flows, corrected for detector acceptance and resolution, are shown for these two classes of events in both the HERA laboratory frame and the Breit frame. From the differences in the shapes of these energy flows we conclude that QCD radiation is suppressed in the large-rapidity-gap events compared to the events without a large rapidity gap. (orig.)

Effect of heavy-metal insertions at Fe/MgO interfaces on electric-field-induced modification of magnetocrystalline anisotropy

Energy Technology Data Exchange (ETDEWEB)

Nakamura, K.; Nomura, T. [Department of Physics Engineering, Mie University, Tsu, Mie 514-8507 (Japan); Pradipto, A.-M. [Department of Physics Engineering, Mie University, Tsu, Mie 514-8507 (Japan); Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Nawa, K.; Akiyama, T.; Ito, T. [Department of Physics Engineering, Mie University, Tsu, Mie 514-8507 (Japan)

2017-05-01

Magnetocrystalline anisotropy (MCA) at Fe/MgO interfaces with insertions of 3d (Co, Ni), 4d (Ru, Rh, Pd), and 5d (Os, Ir, Pt) elements in external electric fields was investigated from first-principles calculations. The MCA energy and the electric-field-induced MCA modification dramatically depend on the inserted elements. Large MCA modification may be achieved by heavy-metal insertions, in which the strength of spin-orbit coupling of inserted elements and the position of the Fermi level relative to d band level play key roles. - Highlights: • MCA at Fe/MgO interface dramatically depends on insertions of 3d, 4d, and 5d elements. • Large electric-field-induced MCA modification is achieved by heavy-metal insertions. • Position of Fermi level relative to d band level plays key role in determining MCA.

Facile construction of a random protein domain insertion library using an engineered transposon.

Science.gov (United States)

Shah, Vandan; Pierre, Brennal; Kim, Jin Ryoun

2013-01-15

Insertional fusion between multiple protein domains represents a novel means of creating integrated functionalities. Currently, there is no robust guideline for selection of insertion sites ensuring the desired functional outcome of insertional fusion. Therefore, construction and testing of random domain insertion libraries, in which a host protein domain is randomly inserted into a guest protein domain, significantly benefit extensive exploration of sequence spaces for insertion sites. Short peptide residues are usually introduced between protein domains to alleviate structural conflicts, and the interdomain linker residues may affect the functional outcome of protein insertion complexes. Unfortunately, optimal control of interdomain linker residues is not always available in conventional methods used to construct random domain insertion libraries. Moreover, most conventional methods employ blunt-end rather than sticky-end ligation between host and guest DNA fragments, thus lowering library construction efficiency. Here, we report the facile construction of random domain insertion libraries using an engineered transposon. We show that random domain insertion with optimal control of interdomain linker residues was possible with our engineered transposon-based method. In addition, our method employs sticky-end rather than blunt-end ligation between host and guest DNA fragments, thus allowing for facile construction of relatively large sized libraries. Copyright © 2012 Elsevier Inc. All rights reserved.

Chromaticity correction in the TRISTAN phase I main ring with two types of insertion

International Nuclear Information System (INIS)

Wu, Yingzhi; Egawa, Kazumi.

1984-07-01

The TRISTAN main ring now under construction has four insertions. Besides the normal modes in which the four insertions have the same optics, the TRISTAN main ring will be operated in somewhat more complicated configurations with insertions having different optics. This report will consider chromaticity corrections using six families of sextupoles for the TRISTAN main ring with two different insertion types; opposite insertions have the same optics. The strength of correcting sextupoles is determined mainly using the W-correction method. The program PATRICIA is used to track the trajectories of test particles over 800 turns. The results show that the correction scheme adopted allows adequately large amplitudes of betatron and synchrotron oscillations. (author)

Deep Adaptive Log-Demons: Diffeomorphic Image Registration with Very Large Deformations

Directory of Open Access Journals (Sweden)

Liya Zhao

2015-01-01

Full Text Available This paper proposes a new framework for capturing large and complex deformation in image registration. Traditionally, this challenging problem relies firstly on a preregistration, usually an affine matrix containing rotation, scale, and translation and afterwards on a nonrigid transformation. According to preregistration, the directly calculated affine matrix, which is obtained by limited pixel information, may misregistrate when large biases exist, thus misleading following registration subversively. To address this problem, for two-dimensional (2D images, the two-layer deep adaptive registration framework proposed in this paper firstly accurately classifies the rotation parameter through multilayer convolutional neural networks (CNNs and then identifies scale and translation parameters separately. For three-dimensional (3D images, affine matrix is located through feature correspondences by a triplanar 2D CNNs. Then deformation removal is done iteratively through preregistration and demons registration. By comparison with the state-of-the-art registration framework, our method gains more accurate registration results on both synthetic and real datasets. Besides, principal component analysis (PCA is combined with correlation like Pearson and Spearman to form new similarity standards in 2D and 3D registration. Experiment results also show faster convergence speed.

Deep inelastic scattering near the Coulomb barrier

International Nuclear Information System (INIS)

Gehring, J.; Back, B.; Chan, K.

1995-01-01

Deep inelastic scattering was recently observed in heavy ion reactions at incident energies near and below the Coulomb barrier. Traditional models of this process are based on frictional forces and are designed to predict the features of deep inelastic processes at energies above the barrier. They cannot be applied at energies below the barrier where the nuclear overlap is small and friction is negligible. The presence of deep inelastic scattering at these energies requires a different explanation. The first observation of deep inelastic scattering near the barrier was in the systems 124,112 Sn + 58,64 Ni by Wolfs et al. We previously extended these measurements to the system 136 Xe + 64 Ni and currently measured the system 124 Xe + 58 Ni. We obtained better statistics, better mass and energy resolution, and more complete angular coverage in the Xe + Ni measurements. The cross sections and angular distributions are similar in all of the Sn + Ni and Xe + Ni systems. The data are currently being analyzed and compared with new theoretical calculations. They will be part of the thesis of J. Gehring

A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

DEFF Research Database (Denmark)

Benkel, Bernhard F.; Smith, Amanda; Christensen, Knud

2012-01-01

In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000th of the mink genome, suggests that simple sequence repeats (SSRs...

Simultaneous identification of long similar substrings in large sets of sequences

Directory of Open Access Journals (Sweden)

Wittig Burghardt

2007-05-01

Full Text Available Abstract Background Sequence comparison faces new challenges today, with many complete genomes and large libraries of transcripts known. Gene annotation pipelines match these sequences in order to identify genes and their alternative splice forms. However, the software currently available cannot simultaneously compare sets of sequences as large as necessary especially if errors must be considered. Results We therefore present a new algorithm for the identification of almost perfectly matching substrings in very large sets of sequences. Its implementation, called ClustDB, is considerably faster and can handle 16 times more data than VMATCH, the most memory efficient exact program known today. ClustDB simultaneously generates large sets of exactly matching substrings of a given minimum length as seeds for a novel method of match extension with errors. It generates alignments of maximum length with a considered maximum number of errors within each overlapping window of a given size. Such alignments are not optimal in the usual sense but faster to calculate and often more appropriate than traditional alignments for genomic sequence comparisons, EST and full-length cDNA matching, and genomic sequence assembly. The method is used to check the overlaps and to reveal possible assembly errors for 1377 Medicago truncatula BAC-size sequences published at http://www.medicago.org/genome/assembly_table.php?chr=1. Conclusion The program ClustDB proves that window alignment is an efficient way to find long sequence sections of homogenous alignment quality, as expected in case of random errors, and to detect systematic errors resulting from sequence contaminations. Such inserts are systematically overlooked in long alignments controlled by only tuning penalties for mismatches and gaps. ClustDB is freely available for academic use.

A Measurement of Nuclear Structure Functions in the Large $X$ Large $Q^{2}$ Kinematic Region in Neutrino Deep Inelastic Scattering

Energy Technology Data Exchange (ETDEWEB)

Vakili, Masoud [Cincinnati U.

1997-01-01

Data from the CCFR E770 Neutrino Deep Inelastic Scatter- ing (DIS) experiment at Fermilab contain large Bjorken x, high $Q^2$ events. A comparison of the data with a model, based on no nuclear effects at large $x$, shows an excess of events in the data. Addition of Fermi gas motion of the nucleons in the nucleus to the model does not explain the model's deficit. Adding higher momentum tail due to the formation of "quasi-deuterons" makes the agreement better. Certain models based on "multi- quark clusters" and "few-nucleon correlations" predict an exponentially falling behavior for $F_2$ as $F_2 \\sim e^{s(x -x_0)}$ at large $x$. We measure a $s$ = 8.3 $\\pm$ 0.8 for the best fit to our data. This corresponds to a value of $F_2$($x = 1, Q^2 > 50) \\approx 2$ x $10^{-3}$ in neutrino DIS. These values agree with results from theoretical models and the $SLAC$ $E133$ experiment but seem to be different from the result of the BCDMS experiment

Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies.

Science.gov (United States)

Wang, Gang; Yang, Luhan; Grishin, Dennis; Rios, Xavier; Ye, Lillian Y; Hu, Yong; Li, Kai; Zhang, Donghui; Church, George M; Pu, William T

2017-01-01

Genome editing of human induced pluripotent stem cells (hiPSCs) offers unprecedented opportunities for in vitro disease modeling and personalized cell replacement therapy. The introduction of Cas9-directed genome editing has expanded adoption of this approach. However, marker-free genome editing using standard protocols remains inefficient, yielding desired targeted alleles at a rate of ∼1-5%. We developed a protocol based on a doxycycline-inducible Cas9 transgene carried on a piggyBac transposon to enable robust and highly efficient Cas9-directed genome editing, so that a parental line can be expeditiously engineered to harbor many separate mutations. Treatment with doxycycline and transfection with guide RNA (gRNA), donor DNA and piggyBac transposase resulted in efficient, targeted genome editing and concurrent scarless transgene excision. Using this approach, in 7 weeks it is possible to efficiently obtain genome-edited clones with minimal off-target mutagenesis and with indel mutation frequencies of 40-50% and homology-directed repair (HDR) frequencies of 10-20%.

Experience of Google's latest deep learning library, TensorFlow, in a large-scale WLCG cluster

Energy Technology Data Exchange (ETDEWEB)

Kawamura, Gen; Smith, Joshua Wyatt; Quadt, Arnulf [II. Physikalisches Institut, Georg-August-Universitaet Goettingen (Germany)

2016-07-01

The researchers at the Google Brain team released their second generation's Deep Learning library, TensorFlow, as an open-source package under the Apache 2.0 license in November, 2015. Google has already deployed the first generation's library using DistBlief in various systems such as Google Search, advertising systems, speech recognition systems, Google Images, Google Maps, Street View, Google Translate and many other latest products. In addition, many researchers in high energy physics have recently started to understand and use Deep Learning algorithms in their own research and analysis. We conceive a first use-case scenario of TensorFlow to create the Deep Learning models from high-dimensional inputs like physics analysis data in a large-scale WLCG computing cluster. TensorFlow carries out computations using a dataflow model and graph structure onto a wide variety of different hardware platforms and systems, such as many CPU architectures, GPUs and smartphone platforms. Having a single library that can distribute the computations to create a model to the various platforms and systems would significantly simplify the use of Deep Learning algorithms in high energy physics. We deploy TensorFlow with the Docker container environments and present the first use in our grid system.

Endovascular Therapy Is Effective for Leriche Syndrome with Deep Vein Thrombosis

Directory of Open Access Journals (Sweden)

Tasuku Higashihara

2015-01-01

Full Text Available A 65-year-old man presented to our hospital due to intermittent claudication and swelling in his left leg. He had Leriche syndrome and deep vein thrombosis. We performed endovascular therapy (EVT for Leriche syndrome, and a temporary filter was inserted in the inferior vena cava. He received anticoagulation therapy for deep vein thrombosis. The stenotic lesion in the terminal aorta was stented with an excellent postprocedural angiographic result and dramatic clinical improvement after EVT. This case suggests that EVT can be a treatment for Leriche syndrome.

Toward forward genetic screens in malaria-causing parasites using the piggyBac transposon

Directory of Open Access Journals (Sweden)

de Koning-Ward Tania F

2011-03-01

Full Text Available Abstract The ability to analyze gene function in malaria-causing Plasmodium parasites has received a boost with a recent paper in BMC Genomics that describes a genome-wide mutagenesis system in the rodent malaria species Plasmodium berghei using the transposon piggyBac. This advance holds promise for identifying and validating new targets for intervention against malaria. But further improvements are still needed for the full power of genome-wide molecular genetic screens to be utilized in this organism. See research article: http://www.biomedcentral.com/1471-2164/12/155

Characterization of pig farms in Hung Yen, Hai Duong and Bac Ninh provinces

OpenAIRE

Nguyen Van Duy; Vu Dinh; Dang Vu, Binh; Vo Trong, Thanh; Nguyen Cong, oanh; Phan Van, Chung

2007-01-01

In order to characterization of pig farms in the Red River Delta, a study was conducted on 90 pig farms in Hung Yen, Hai Duong and Bac Ninh provinces from June to December 2006. Results show that most of the pig farms had been built for five years with a small size (0.5 hectare per farm). The invested capital was about 300-400 millions VND per farm. Four main sow groups used in the farms included crossbred exotic sows (51.1%), crossbred sow between local and exotic breeds (14.4%), purebred La...

A review of reagents for fluorescence microscopy of cellular compartments and structures, part I: BacMam labeling and reagents for vesicular structures.

Science.gov (United States)

Dolman, Nick J; Kilgore, Jason A; Davidson, Michael W

2013-07-01

Fluorescent labeling of vesicular structures in cultured cells, particularly for live cells, can be challenging for a number of reasons. The first challenge is to identify a reagent that will be specific enough where some structures have a number of potential reagents and others very few options. The emergence of BacMam constructs has allowed more easy-to-use choices. Presented here is a discussion of BacMam constructs as well as a review of commercially-available reagents for labeling vesicular structures in cells, including endosomes, peroxisomes, lysosomes, and autophagosomes, complete with a featured reagent for each structure, recommended protocol, troubleshooting guide, and example image. © 2013 by John Wiley & Sons, Inc.

Acute changes associated with electrode insertion measured with optical coherence microscopy

Science.gov (United States)

Hammer, Daniel X.; Lozzi, Andrea; Boretsky, Adam; Agrawal, Anant; Welle, Cristin G.

2016-03-01

Despite advances in functional neural imaging, penetrating microelectrodes provide the most direct interface for the extraction of neural signals from the nervous system and are a critical component of many high degree-of-freedom braincomputer interface devices. Electrode insertion is a traumatic event that elicits a complex neuroinflammatory response. In this investigation we applied optical coherence microscopy (OCM), particularly optical coherence angiography (OCA), to characterize the immediate tissue response during microelectrode insertion. Microelectrodes of varying dimension and footprint (one-, two-, and four-shank) were inserted into mouse motor cortex beneath a window after craniotomy surgery. The microelectrodes were inserted in 3-4 steps at 15-20°, with approximately 250 μm linear insertion distance for each step. Before insertion and between each step, OCM datasets were collected, including for quantitative capillary velocimetry. A cohort of control animals without microelectrode insertion was also imaged over a similar time period (2-3 hours). Mechanical tissue deformation was observed in all the experimental animals. The quantitative angiography results varied across animals, and were not correlated with device dimensions. In some cases, localized flow drop-out was observed in a small region surrounding the electrode, while in other instances a global disruption in flow occurred, perhaps as a result of large vessel compression caused by mechanical pressure. OCM is a tool that can be used in various neurophotonics applications, including quantification of the neuroinflammatory response to penetrating electrode insertion.

Analyses of Tissue Culture Adaptation of Human Herpesvirus-6A by Whole Genome Deep Sequencing Redefines the Reference Sequence and Identifies Virus Entry Complex Changes.

Science.gov (United States)

Tweedy, Joshua G; Escriva, Eric; Topf, Maya; Gompels, Ursula A

2017-12-31

Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus entry complex, which affected cellular tropism, virulence, and vaccine development. Here, we analyse these effects on the reference genome for related betaherpesviruses, Roseolovirus, human herpesvirus 6A (HHV-6A) strain U1102. This virus is also naturally "cloned" by germline subtelomeric chromosomal-integration in approximately 1% of human populations, and accurate references are key to understanding pathological relationships between exogenous and endogenous virus. Using whole genome next-generation deep-sequencing Illumina-based methods, we compared the original isolate to tissue-culture passaged and the BACmid-cloned virus. This re-defined the reference genome showing 32 corrections and 5 polymorphisms. Furthermore, minor variant analyses of passaged and BACmid virus identified emerging populations of a further 32 single nucleotide polymorphisms (SNPs) in 10 loci, half non-synonymous indicating cell-culture selection. Analyses of the BAC-virus genome showed deletion of the BAC cassette via loxP recombination removing green fluorescent protein (GFP)-based selection. As shown for HCMV culture effects, select HHV-6A SNPs mapped to genes encoding mediators of virus cellular entry, including virus envelope glycoprotein genes gB and the gH/gL complex. Comparative models suggest stabilisation of the post-fusion conformation. These SNPs are essential to consider in vaccine-design, antimicrobial-resistance, and pathogenesis.

Extensive young silicic volcanism produces large deep submarine lava flows in the NE Lau Basin

Science.gov (United States)

Embley, Robert W.; Rubin, Kenneth H.

2018-04-01

New field observations reveal that extensive (up to 402 km2) aphyric, glassy dacite lavas were erupted at multiple sites in the recent past in the NE Lau basin, located about 200 km southwest of Samoa. This discovery of volumetrically significant and widespread submarine dacite lava flows extends the domain for siliceous effusive volcanism into the deep seafloor. Although several lava flow fields were discovered on the flank of a large silicic seamount, Niuatahi, two of the largest lava fields and several smaller ones ("northern lava flow fields") were found well north of the seamount. The most distal portion of the northernmost of these fields is 60 km north of the center of Niuatahi caldera. We estimate that lava flow lengths from probable eruptive vents to the distal ends of flows range from a few km to more than 10 km. Camera tows on the shallower, near-vent areas show complex lava morphology that includes anastomosing tube-like pillow flows and ropey surfaces, endogenous domes and/or ridges, some with "crease-like" extrusion ridges, and inflated lobes with extrusion structures. A 2 × 1.5 km, 30-m deep depression could be an eruption center for one of the lava flow fields. The Lau lava flow fields appear to have erupted at presumptive high effusion rates and possibly reduced viscosity induced by presumptive high magmatic water content and/or a high eruption temperature, consistent with both erupted composition ( 66% SiO2) and glassy low crystallinity groundmass textures. The large areal extent (236 km2) and relatively small range of compositional variation ( σ = 0.60 for wt% Si02%) within the northern lava flow fields imply the existence of large, eruptible batches of differentiated melt in the upper mantle or lower crust of the NE Lau basin. At this site, the volcanism could be controlled by deep crustal fractures caused by the long-term extension in this rear-arc region. Submarine dacite flows exhibiting similar morphology have been described in ancient

The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS.

Directory of Open Access Journals (Sweden)

Mohammed Almuhayawi

Full Text Available Detection and identification of anaerobic bacteria in blood cultures (BC is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux, BACTEC-Plus and -Lytic (Becton Dickinson BioSciences BC bottles in detection and time to detection (TTD of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94% than BacT/ALERT FN Plus (80/100, 80% (p<0.01 in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001. The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h, BACTEC Plus (27 h and finally BacT/ALERT FN Plus (38 h bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76% BacT/ALERT FN, 51/67 (76% BacT/ALERT FN Plus, 53/67 (79% BACTEC Plus and 50/67 (75% BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.

MRI findings in Kirner deformity: normal insertion of the flexor digitorum profundus tendon without soft-tissue enhancement

International Nuclear Information System (INIS)

Lee, Jaejoon; Ahn, Joong Kyong; Koh, Eun-Mi; Cha, Hoon-Suk; Choi, Sang-Hee

2010-01-01

Kirner deformity is characterized by volar and radial incurvature of the distal phalanx of the 5th finger. A proposed causative mechanism includes abnormal distal insertion of the flexor digitorum profundus tendon along the volar surface of the distal phalanx of the 5th finger. A chronic inflammatory process or altered vascularisation of the soft tissues has also been suggested as the underlying causative mechanism based on MRI findings. We present a teenage boy with Kirner deformity, along with supplementary imaging of his father who also has the deformity, to illustrate MRI findings that dispute the above hypotheses. MRI in both son and father show normal insertion of the deep flexor tendon and no signs of inflammation. (orig.)

MBBR evaluation for oil refinery wastewater treatment, with post-ozonation and BAC, for wastewater reuse.

Science.gov (United States)

Schneider, E E; Cerqueira, A C F P; Dezotti, M

2011-01-01

This work evaluated the performance of a Moving Bed Biofilm Reactor (MBBR) in the treatment of an oil refinery wastewater. Also, it investigated the possibility of reuse of the MBBR effluent, after ozonation in series with a biological activated carbon (BAC) column. The best performance of the MBBR was achieved with a hydraulic retention time (HRT) of 6 hours, employing a bed to bioreactor volume ratio (V(B)/V(R)) of 0.6. COD and N-NH₄(+) MBBR effluent concentrations ranged from 40 to 75 mg L⁻¹ (removal efficiency of 69-89%) and 2 to 6 mg L⁻¹ (removal efficiency of 45-86%), respectively. Ozonation carried out for 15 min with an ozone concentration of 5 mg L⁻¹ was able to improve the treated wastewater biodegradability. The treatment performance of the BAC columns was practically the same for ozonated and non ozonated MBBR effluents. The dissolved organic carbon (DOC) content of the columns of the activated carbon columns (CAG) was in the range of 2.1-3.8 mg L⁻¹, and the corresponding DOC removal efficiencies were comprised between 52 and 75%. The effluent obtained at the end of the proposed treatment presented a quality, which meet the requirements for water reuse in the oil refinery.

MUTATION ON Bacillus subtilis BAC4 USING ACRIDINE ORANGE AS AN EFFORT FOR INCREASING ANTIBIOTIC PRODUCTION

Directory of Open Access Journals (Sweden)

Supartono Supartono

2010-06-01

Full Text Available The efforts to get a new antibiotic require to be done continuously, because infection diseases still become the main health problems in Indonesia. A new local strain of Bacillus subtilis BAC4 has been known producing an antibiotic that inhibites Serratia marcescens ATCC 27117 growth. Nevertheless, the optimum conditions have not been studied seriously. The objective of this research was to conduct mutation on B. subtilis BAC4 in order to obtain a mutant cell that overproduct in producing antibiotic. The mutation process was performed by using acridine orange of 1 g.L-1 randomly at various volumes. The production of antibiotic was conducted using batch fermentation and antibiotic assay was performed with agar absorption method using S.  marcescens ATCC 27117 as bacteria assay. Research result provided a B. subtilis M10 mutant with overproduction of antibiotic. Characterization of B. subtilis M10 mutant showed that the mutant cell has size of (0.5-1.0 µm x (1.85-2.5 µm; spore has the form of ellipse with thick wavy wall, positive reaction for catalase, and forming acid from glucose and xylose.   Keywords: mutant, Bacillus, acridin, and antibiotics

Insertion device and method for accurate and repeatable target insertion

Science.gov (United States)

Gubeli, III, Joseph F.; Shinn, Michelle D.; Bevins, Michael E.; Dillon-Townes, Lawrence; Neil, George R.

2017-07-04

The present invention discloses a device and a method for inserting and positioning a target within a free electron laser, particle accelerator, or other such device that generates or utilizes a beam of energy or particles. The system includes a three-point registration mechanism that insures angular and translational accuracy and repeatability of positioning upon multiple insertions within the same structure.

INTERACTION BETWEEN DIFFERENT MOLECULAR FORMS OF IMMUNOGLOBULIN A AND RECOMBINANT DERIVATIVES POLYPEPTIDES OF BAC RECEPTOR PROTEINS FROM GROUP B STREPTOCOCCI

Directory of Open Access Journals (Sweden)

A. S. Korzhueva

2008-01-01

Full Text Available Abstract. The article concerns interactions between immunoglobulin A and recombinant P6, P7, P8 polypeptides, designed on the basis of externally localized Bac protein of the Group B streptococci, possessing IgA-binding activity.There is a current demand for immunochemical reagents that are strictly specific for IgA, in order to develop antigenic standards for detection of IgA levels in biological fluids, as well as for affinity purification of IgA and its fragments.To analyze an opportunity of the abovementioned application ways for these proteins, a special study was performed to assay an interaction capability of recombinant P6, P7, P8 polypeptides binding to Fc regions of different IgA forms (serum IgA, secretory IgA, subclasses of serum IgA – IgA1, IgA2. Selectivity of ligand binding was specially confirmed.It was found out that, among three presented polypeptides, the structure of recombinant P6 derivative proved to be optimal for IgA-binding ability of Bac protein.Structural features of IgA-binding fragments of Bac protein, i.e., binding site position on the IgA molecule (proximity to epitopes for three monoclonal antibodies, variability of the site structure, as well as resistance of binding site for P6, P7, P8 in IgA molecule against partial disulfide bonds reduction. (Med. Immunol., vol. 10, N 4-5, pp 327-336.

Medicare Coverage Database

Data.gov (United States)

U.S. Department of Health & Human Services — The Medicare Coverage Database (MCD) contains all National Coverage Determinations (NCDs) and Local Coverage Determinations (LCDs), local articles, and proposed NCD...

Analysis on deep metallogenic trace and simulation experiment in xiangshan large-scale volcanic hydrothermal type uranium deposit

International Nuclear Information System (INIS)

Liu Zhengyi; Liu Zhangyue; Wen Zhijian; Du Letian

2010-01-01

Based on series experiments on field geologic analysis, and associated with deep metallogenic trace experiment model transformed from establishment of field deep metallogenic trace model, this paper come to the conclusion that distribution coefficients of U and Th first domestic from the magmatic experiment, and then discuss the geochemical behaviors of U, Th, K during magmatic evolution stage. The experiment shows that close relationship between U and Na during the hydrothermal alteration stage; and relationship between U and K during metallogenic stage, which prove that U and K are incompatible and regularity of variation between K and Na. The conclusion of uranium dissolving ability increased accompany with pressure increasing in basement metamorphic rocks and host rocks, is obtained from this experiment, which indicate a good deep metallogenic prospect. Furthermore, Pb, Sr, Nd, He isotopes show that the volcanic rocks and basement rocks are ore source beds; due to the combined functions of volcanic hydrothermal and mantle ichor, uranium undergo multi-migration and enrichment and finally concentrated to large rich deposit. (authors)

Incidence of upper limb venous thrombosis associated with peripherally inserted central catheters (PICC).

Science.gov (United States)

Abdullah, B J J; Mohammad, N; Sangkar, J V; Abd Aziz, Y F; Gan, G G; Goh, K Y; Benedict, I

2005-07-01

The objective of this study was to prospectively determine the incidence of venous thrombosis (VT) in the upper limbs in patients with peripherally inserted central catheters (PICC). We prospectively investigated the incidence of VT in the upper limbs of 26 patients who had PICC inserted. The inclusion criteria were all patients who had a PICC inserted, whilst the exclusion criterion was the inability to perform a venogram (allergies, previous contrast medium reaction and inability of gaining venous access). Both valved and non-valved catheters were evaluated. Prior to removal of the PICC, an upper limb venogram was performed. The number of segments involved with VT were determined. The duration of central venous catheterization was classified as; less than 6 days, between 6 days and 14 days and more than 14 days. VT was confirmed in 38.5% (10/26) of the patients. The majority 85.7% (12/14) were complete occlusive thrombi and the majority of VT only involved one segment. There was no statistical correlation between the site of insertion of the PICC and the location of VT. Neither was there any observed correlation between the occurrence of VT with the patient's history of hypertension, hypercholesterolaemia, coronary artery disease, diabetes mellitus, cardiac insufficiency, smoking or cancer. There was also no statistical correlation with the size of the catheter. In conclusion, PICCs are associated with a significant risk of upper extremity deep vein thrombosis (UEVT).

DeepSpark: A Spark-Based Distributed Deep Learning Framework for Commodity Clusters

OpenAIRE

Kim, Hanjoo; Park, Jaehong; Jang, Jaehee; Yoon, Sungroh

2016-01-01

The increasing complexity of deep neural networks (DNNs) has made it challenging to exploit existing large-scale data processing pipelines for handling massive data and parameters involved in DNN training. Distributed computing platforms and GPGPU-based acceleration provide a mainstream solution to this computational challenge. In this paper, we propose DeepSpark, a distributed and parallel deep learning framework that exploits Apache Spark on commodity clusters. To support parallel operation...

Disruption of a Transcriptional Repressor by an Insertion Sequence Element Integration Leads to Activation of a Novel Silent Cellobiose Transporter in Lactococcus lactis MG1363.

Science.gov (United States)

Solopova, Ana; Kok, Jan; Kuipers, Oscar P

2017-12-01

Lactococcus lactis subsp. cremoris strains typically carry many dairy niche-specific adaptations. During adaptation to the milk environment these former plant strains have acquired various pseudogenes and insertion sequence elements indicative of ongoing genome decay and frequent transposition events in their genomes. Here we describe the reactivation of a silenced plant sugar utilization cluster in an L. lactis MG1363 derivative lacking the two main cellobiose transporters, PtcBA-CelB and PtcBAC, upon applying selection pressure to utilize cellobiose. A disruption of the transcriptional repressor gene llmg_1239 by an insertion sequence (IS) element allows expression of the otherwise silent novel cellobiose transporter Llmg_1244 and leads to growth of mutant strains on cellobiose. Llmg_1239 was labeled CclR, for c ellobiose cl uster r epressor. IMPORTANCE Insertion sequences (ISs) play an important role in the evolution of lactococci and other bacteria. They facilitate DNA rearrangements and are responsible for creation of new genetic variants with selective advantages under certain environmental conditions. L. lactis MG1363 possesses 71 copies in a total of 11 different types of IS elements. This study describes yet another example of an IS-mediated adaptive evolution. An integration of IS 981 or IS 905 into a gene coding for a transcriptional repressor led to activation of the repressed gene cluster coding for a plant sugar utilization pathway. The expression of the gene cluster allowed assembly of a novel cellobiose-specific transporter and led to cell growth on cellobiose. Copyright © 2017 American Society for Microbiology.

Identification of genomic insertion and flanking sequence of G2-EPSPS and GAT transgenes in soybean using whole genome sequencing method

Directory of Open Access Journals (Sweden)

Bingfu Guo

2016-07-01

Full Text Available Molecular characterization of sequences flanking exogenous fragment insertions is essential for safety assessment and labeling of genetically modified organisms (GMO. In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS method. About 21 Gb sequence data (~21× coverage for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundary of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of the genomic insertion site of the G2-EPSPS and GAT transgenes will facilitate the use of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS is a cost-effective and rapid method of identifying sites of T-DNA insertions and flanking sequences in soybean.

Facility target insert shielding assessment

Energy Technology Data Exchange (ETDEWEB)

Mocko, Michal [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-10-06

Main objective of this report is to assess the basic shielding requirements for the vertical target insert and retrieval port. We used the baseline design for the vertical target insert in our calculations. The insert sits in the 12”-diameter cylindrical shaft extending from the service alley in the top floor of the facility all the way down to the target location. The target retrieval mechanism is a long rod with the target assembly attached and running the entire length of the vertical shaft. The insert also houses the helium cooling supply and return lines each with 2” diameter. In the present study we focused on calculating the neutron and photon dose rate fields on top of the target insert/retrieval mechanism in the service alley. Additionally, we studied a few prototypical configurations of the shielding layers in the vertical insert as well as on the top.

Influence of Palatal Coverage and Implant Distribution on Denture Strain in Maxillary Implant Overdentures.

Science.gov (United States)

Takahashi, Toshihito; Gonda, Tomoya; Tomita, Akiko; Mizuno, Yoko; Maeda, Yoshinobu

2016-01-01

As maxillary implant overdentures are being increasingly used in clinical practice, prosthodontic complications related to these dentures are also reported more often. The purpose of this study was to examine the influence of palatal coverage and implant distribution on the shear strain of maxillary implant overdentures. A maxillary edentulous model with implants inserted in the anterior, premolar, and molar areas was fabricated. Two kinds of experimental overdentures, with and without palatal coverage, were also fabricated, and two strain gauges were attached at the midline of the labial and palatal sides. A vertical occlusal load of 98 N was applied through a mandibular complete denture, and the shear strain in each denture was compared by analysis of variance (P = .05). In all situations, the shear strain in palateless dentures was significantly higher than in dentures with palate on both sides (P overdentures exhibited much higher strain than overdentures with palate regardless of the implant distribution; this may cause more prosthodontic and implant complications. The most favorable configuration to prevent complications in maxillary implant overdentures was palatal coverage that was supported by more than four widely distributed implants.

Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS6110 Insertions and Tandem Repeat Analysis

Directory of Open Access Journals (Sweden)

Eriko Maeda-Mitani

2016-01-01

Full Text Available QUB11a is used as a locus for variable number of tandem repeats (VNTR analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp investigated contained IS6110 insertions and varied in the number of repeats (18 patterns and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.

Deep-Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives

Directory of Open Access Journals (Sweden)

Mitchell M. Holland

2018-02-01

Full Text Available Distinguishing between maternal relatives through mitochondrial (mt DNA sequence analysis has been a longstanding desire of the forensic community. Using a deep-coverage, massively parallel sequencing (DCMPS approach, we studied the pattern of mtDNA heteroplasmy across the mtgenomes of 39 mother-child pairs of European decent; haplogroups H, J, K, R, T, U, and X. Both shared and differentiating heteroplasmy were observed on a frequent basis in these closely related maternal relatives, with the minor variant often presented as 2–10% of the sequencing reads. A total of 17 pairs exhibited differentiating heteroplasmy (44%, with the majority of sites (76%, 16 of 21 occurring in the coding region, further illustrating the value of conducting sequence analysis on the entire mtgenome. A number of the sites of differentiating heteroplasmy resulted in non-synonymous changes in protein sequence (5 of 21, and to changes in transfer or ribosomal RNA sequences (5 of 21, highlighting the potentially deleterious nature of these heteroplasmic states. Shared heteroplasmy was observed in 12 of the 39 mother-child pairs (31%, with no duplicate sites of either differentiating or shared heteroplasmy observed; a single nucleotide position (16093 was duplicated between the data sets. Finally, rates of heteroplasmy in blood and buccal cells were compared, as it is known that rates can vary across tissue types, with similar observations in the current study. Our data support the view that differentiating heteroplasmy across the mtgenome can be used to frequently distinguish maternal relatives, and could be of interest to both the medical genetics and forensic communities.

Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations

Directory of Open Access Journals (Sweden)

Aurélien Chateigner

2015-07-01

Full Text Available Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%. K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs. Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential.

Coral Reef Coverage Percentage on Binor Paiton-Probolinggo Seashore

Directory of Open Access Journals (Sweden)

Dwi Budi Wiyanto

2016-01-01

Full Text Available The coral reef damage in Probolinggo region was expected to be caused by several factors. The first one comes from its society that exploits fishery by using cyanide toxin and bomb. The second one goes to the extraction of coral reef, which is used as decoration or construction materials. The other factor is likely caused by the existence of large industry on the seashore, such as Electric Steam Power Plant (PLTU Paiton and others alike. Related to the development of coral reef ecosystem, availability of an accurate data is crucially needed to support the manner of future policy, so the research of coral reef coverage percentage needs to be conducted continuously. The aim of this research is to collect biological data of coral reef and to identify coral reef coverage percentage in the effort of constructing coral reef condition basic data on Binor, Paiton, and Probolinggo regency seashore. The method used in this research is Line Intercept Transect (LIT method. LIT method is a method that used to decide benthic community on coral reef based on percentage growth, and to take note of benthic quantity along transect line. Percentage of living coral coverage in 3 meters depth on this Binor Paiton seashore that may be categorized in a good condition is 57,65%. While the rest are dead coral that is only 1,45%, other life form in 23,2%, and non-life form in 17,7%. A good condition of coral reef is caused by coral reef transplantation on the seashore, so this coral reef is dominated by Acropora Branching. On the other hand, Mortality Index (IM of coral reef resulted in 24,5%. The result from observation and calculation of coral reef is dominated by Hard Coral in Acropora Branching (ACB with coral reef coverage percentage of 39%, Coral Massive (CM with coral reef coverage percentage of 2,85%, Coral Foliose (CF with coral reef coverage percentage of 1,6%, and Coral Mushroom (CRM with coral reef coverage percentage of 8,5%. Observation in 10 meters depth

Coral Reef Coverage Percentage on Binor Paiton-Probolinggo Seashore

Directory of Open Access Journals (Sweden)

Dwi Budi Wiyanto

2016-02-01

Full Text Available The coral reef damage in Probolinggo region was expected to be caused by several factors. The first one comes from its society that exploits fishery by using cyanide toxin and bomb. The second one goes to the extraction of coral reef, which is used as decoration or construction materials. The other factor is likely caused by the existence of large industry on the seashore, such as Electric Steam Power Plant (PLTU Paiton and others alike. Related to the development of coral reef ecosystem, availability of an accurate data is crucially needed to support the manner of future policy, so the research of coral reef coverage percentage needs to be conducted continuously. The aim of this research is to collect biological data of coral reef and to identify coral reef coverage percentage in the effort of constructing coral reef condition basic data on Binor, Paiton, and Probolinggo regency seashore. The method used in this research is Line Intercept Transect (LIT method. LIT method is a method that used to decide benthic community on coral reef based on percentage growth, and to take note of benthic quantity along transect line. Percentage of living coral coverage in 3 meters depth on this Binor Paiton seashore that may be categorized in a good condition is 57,65%. While the rest are dead coral that is only 1,45%, other life form in 23,2%, and non-life form in 17,7%. A good condition of coral reef is caused by coral reef transplantation on the seashore, so this coral reef is dominated by Acropora Branching. On the other hand, Mortality Index (IM of coral reef resulted in 24,5%. The result from observation and calculation of coral reef is dominated by Hard Coral in Acropora Branching (ACB with coral reef coverage percentage of 39%, Coral Massive (CM with coral reef coverage percentage of 2,85%, Coral Foliose (CF with coral reef coverage percentage of 1,6%, and Coral Mushroom (CRM with coral reef coverage percentage of 8,5%. Observation in 10 meters depth

A multiple objective magnet sorting algorithm for the ALS insertion devices

International Nuclear Information System (INIS)

Humphries, D.; Goetz, F.; Kownacki, P.; Marks, S.; Schlueter, R.

1994-07-01

Insertion devices for the Advanced Light Source (ALS) incorporate large numbers of permanent magnets which have a variety of magnetization orientation errors. These orientation errors can produce field errors which affect both the spectral brightness of the insertion devices and the storage ring electron beam dynamics. A perturbation study was carried out to quantify the effects of orientation errors acting in a hybrid magnetic structure. The results of this study were used to develop a multiple stage sorting algorithm which minimizes undesirable integrated field errors and essentially eliminates pole excitation errors. When applied to a measured magnet population for an existing insertion device, an order of magnitude reduction in integrated field errors was achieved while maintaining near zero pole excitation errors

Impact of incomplete metal coverage on the electrical properties of metal-CNT contacts: A large-scale ab initio study

Energy Technology Data Exchange (ETDEWEB)

Fediai, Artem, E-mail: artem.fediai@nano.tu-dresden.de; Ryndyk, Dmitry A. [Institute for Materials Science and Max Bergman Center of Biomaterials, TU Dresden, 01062 Dresden (Germany); Center for Advancing Electronics Dresden, TU Dresden, 01062 Dresden (Germany); Seifert, Gotthard [Theoretical Chemistry, TU Dresden, 01062 Dresden (Germany); Center for Advancing Electronics Dresden, TU Dresden, 01062 Dresden (Germany); Dresden Center for Computational Materials Science, TU Dresden, 01062 Dresden (Germany); Mothes, Sven; Schroter, Michael; Claus, Martin [Chair for Electron Devices and Integrated Circuits, TU Dresden, 01062 Dresden (Germany); Center for Advancing Electronics Dresden, TU Dresden, 01062 Dresden (Germany); Cuniberti, Gianaurelio [Institute for Materials Science and Max Bergman Center of Biomaterials, TU Dresden, 01062 Dresden (Germany); Center for Advancing Electronics Dresden, TU Dresden, 01062 Dresden (Germany); Dresden Center for Computational Materials Science, TU Dresden, 01062 Dresden (Germany)

2016-09-05

Using a dedicated combination of the non-equilibrium Green function formalism and large-scale density functional theory calculations, we investigated how incomplete metal coverage influences two of the most important electrical properties of carbon nanotube (CNT)-based transistors: contact resistance and its scaling with contact length, and maximum current. These quantities have been derived from parameter-free simulations of atomic systems that are as close as possible to experimental geometries. Physical mechanisms that govern these dependences have been identified for various metals, representing different CNT-metal interaction strengths from chemisorption to physisorption. Our results pave the way for an application-oriented design of CNT-metal contacts.

Amino Acid Insertion Frequencies Arising from Photoproducts Generated Using Aliphatic Diazirines

Science.gov (United States)

Ziemianowicz, Daniel S.; Bomgarden, Ryan; Etienne, Chris; Schriemer, David C.

2017-10-01

Mapping proteins with chemical reagents and mass spectrometry can generate a measure of accessible surface area, which in turn can be used to support the modeling and refinement of protein structures. Photolytically generated carbenes are a promising class of reagent for this purpose. Substituent effects appear to influence surface mapping properties, allowing for a useful measure of design control. However, to use carbene labeling data in a quantitative manner for modeling activities, we require a better understanding of their inherent amino acid reactivity, so that incorporation data can be normalized. The current study presents an analysis of the amino acid insertion frequency of aliphatic carbenes generated by the photolysis of three different diazirines: 3,3'-azibutyl-1-ammonium, 3,3'-azibutan-1-ol, and 4,4'-azipentan-1-oate. Leveraging an improved photolysis system for single-shot labeling of sub-microliter frozen samples, we used EThCD to localize insertion products in a large population of labeled peptides. Counting statistics were drawn from data-dependent LC-MS2 experiments and used to estimate the frequencies of insertion as a function of amino acid. We observed labeling of all 20 amino acids over a remarkably narrow range of insertion frequencies. However, the nature of the substituent could influence relative insertion frequencies, within a general preference for larger polar amino acids. We confirm a large (6-fold) increase in labeling yield when carbenes were photogenerated in the solid phase (77 K) relative to the liquid phase (293 K), and we suggest that carbene labeling should always be conducted in the frozen state to avoid information loss in surface mapping experiments. [Figure not available: see fulltext.

US Media Coverage of Tobacco Industry Corporate Social Responsibility Initiatives.

Science.gov (United States)

McDaniel, Patricia A; Lown, E Anne; Malone, Ruth E

2018-02-01

Media coverage of tobacco industry corporate social responsibility (CSR) initiatives represents a competitive field where tobacco control advocates and the tobacco industry vie to shape public and policymaker understandings about tobacco control and the industry. Through a content analysis of 649 US news items, we examined US media coverage of tobacco industry CSR and identified characteristics of media items associated with positive coverage. Most coverage appeared in local newspapers, and CSR initiatives unrelated to tobacco, with non-controversial beneficiaries, were most commonly mentioned. Coverage was largely positive. Tobacco control advocates were infrequently cited as sources and rarely authored opinion pieces; however, when their voices were included, coverage was less likely to have a positive slant. Media items published in the South, home to several tobacco company headquarters, were more likely than those published in the West to have a positive slant. The absence of tobacco control advocates from media coverage represents a missed opportunity to influence opinion regarding the negative public health implications of tobacco industry CSR. Countering the media narrative of virtuous companies doing good deeds could be particularly beneficial in the South, where the burdens of tobacco-caused disease are greatest, and coverage of tobacco companies more positive.

Deep inelastic scattering near the Coulomb barrier

Energy Technology Data Exchange (ETDEWEB)

Gehring, J.; Back, B.; Chan, K. [and others

1995-08-01

Deep inelastic scattering was recently observed in heavy ion reactions at incident energies near and below the Coulomb barrier. Traditional models of this process are based on frictional forces and are designed to predict the features of deep inelastic processes at energies above the barrier. They cannot be applied at energies below the barrier where the nuclear overlap is small and friction is negligible. The presence of deep inelastic scattering at these energies requires a different explanation. The first observation of deep inelastic scattering near the barrier was in the systems {sup 124,112}Sn + {sup 58,64}Ni by Wolfs et al. We previously extended these measurements to the system {sup 136}Xe + {sup 64}Ni and currently measured the system {sup 124}Xe + {sup 58}Ni. We obtained better statistics, better mass and energy resolution, and more complete angular coverage in the Xe + Ni measurements. The cross sections and angular distributions are similar in all of the Sn + Ni and Xe + Ni systems. The data are currently being analyzed and compared with new theoretical calculations. They will be part of the thesis of J. Gehring.

Lesion insertion in the projection domain: Methods and initial results

International Nuclear Information System (INIS)

Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia

2015-01-01

Purpose: To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Methods: Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. Results: For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically

Lesion insertion in the projection domain: Methods and initial results

Energy Technology Data Exchange (ETDEWEB)

Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia, E-mail: mccollough.cynthia@mayo.edu [Department of Radiology, Mayo Clinic, Rochester, Minnesota 55905 (United States)

2015-12-15

Purpose: To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Methods: Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. Results: For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically

Lesion insertion in the projection domain: Methods and initial results.

Science.gov (United States)

Chen, Baiyu; Leng, Shuai; Yu, Lifeng; Yu, Zhicong; Ma, Chi; McCollough, Cynthia

2015-12-01

To perform task-based image quality assessment in CT, it is desirable to have a large number of realistic patient images with known diagnostic truth. One effective way of achieving this objective is to create hybrid images that combine patient images with inserted lesions. Because conventional hybrid images generated in the image domain fails to reflect the impact of scan and reconstruction parameters on lesion appearance, this study explored a projection-domain approach. Lesions were segmented from patient images and forward projected to acquire lesion projections. The forward-projection geometry was designed according to a commercial CT scanner and accommodated both axial and helical modes with various focal spot movement patterns. The energy employed by the commercial CT scanner for beam hardening correction was measured and used for the forward projection. The lesion projections were inserted into patient projections decoded from commercial CT projection data. The combined projections were formatted to match those of commercial CT raw data, loaded onto a commercial CT scanner, and reconstructed to create the hybrid images. Two validations were performed. First, to validate the accuracy of the forward-projection geometry, images were reconstructed from the forward projections of a virtual ACR phantom and compared to physically acquired ACR phantom images in terms of CT number accuracy and high-contrast resolution. Second, to validate the realism of the lesion in hybrid images, liver lesions were segmented from patient images and inserted back into the same patients, each at a new location specified by a radiologist. The inserted lesions were compared to the original lesions and visually assessed for realism by two experienced radiologists in a blinded fashion. For the validation of the forward-projection geometry, the images reconstructed from the forward projections of the virtual ACR phantom were consistent with the images physically acquired for the ACR

The actual current density of gas-evolving electrodes—Notes on the bubble coverage

International Nuclear Information System (INIS)

Vogt, H.

2012-01-01

All investigations of electrochemical reactors with gas-evolving electrodes must take account of the fact that the actual current density controlling cell operation commonly differs substantially from the nominal current density used for practical purposes. Both quantities are interrelated by the fractional bubble coverage. This parameter is shown to be affected by a large number of operational quantities. However, available relationships of the bubble coverage take account only of the nominal current density. A further essential insufficiency is their inconsistency with reality for very large values of the bubble coverage being of relevance for operation conditions leading to anode effects. An improved relationship applicable to the total range is proposed.

Feeding tube insertion - gastrostomy

Science.gov (United States)

... this page: //medlineplus.gov/ency/article/002937.htm Feeding tube insertion - gastrostomy To use the sharing features on this page, please enable JavaScript. A gastrostomy feeding tube insertion is the placement of a feeding ...

SEDS: THE SPITZER EXTENDED DEEP SURVEY. SURVEY DESIGN, PHOTOMETRY, AND DEEP IRAC SOURCE COUNTS

International Nuclear Information System (INIS)

Ashby, M. L. N.; Willner, S. P.; Fazio, G. G.; Huang, J.-S.; Hernquist, L.; Hora, J. L.; Arendt, R.; Barmby, P.; Barro, G.; Faber, S.; Guhathakurta, P.; Bell, E. F.; Bouwens, R.; Cattaneo, A.; Croton, D.; Davé, R.; Dunlop, J. S.; Egami, E.; Finlator, K.; Grogin, N. A.

2013-01-01

The Spitzer Extended Deep Survey (SEDS) is a very deep infrared survey within five well-known extragalactic science fields: the UKIDSS Ultra-Deep Survey, the Extended Chandra Deep Field South, COSMOS, the Hubble Deep Field North, and the Extended Groth Strip. SEDS covers a total area of 1.46 deg 2 to a depth of 26 AB mag (3σ) in both of the warm Infrared Array Camera (IRAC) bands at 3.6 and 4.5 μm. Because of its uniform depth of coverage in so many widely-separated fields, SEDS is subject to roughly 25% smaller errors due to cosmic variance than a single-field survey of the same size. SEDS was designed to detect and characterize galaxies from intermediate to high redshifts (z = 2-7) with a built-in means of assessing the impact of cosmic variance on the individual fields. Because the full SEDS depth was accumulated in at least three separate visits to each field, typically with six-month intervals between visits, SEDS also furnishes an opportunity to assess the infrared variability of faint objects. This paper describes the SEDS survey design, processing, and publicly-available data products. Deep IRAC counts for the more than 300,000 galaxies detected by SEDS are consistent with models based on known galaxy populations. Discrete IRAC sources contribute 5.6 ± 1.0 and 4.4 ± 0.8 nW m –2 sr –1 at 3.6 and 4.5 μm to the diffuse cosmic infrared background (CIB). IRAC sources cannot contribute more than half of the total CIB flux estimated from DIRBE data. Barring an unexpected error in the DIRBE flux estimates, half the CIB flux must therefore come from a diffuse component.

Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.

Science.gov (United States)

Reimer, Lorenz C; Söhngen, Carola; Vetcininova, Anna; Overmann, Jörg

2017-11-10

Microbial data and metadata are scattered throughout the scientific literature, databases and unpublished lab notes and thereby often are difficult to access. Hot spots of (meta)data are internal descriptions of culture collections and initial descriptions of novel taxa in primary literature. Here we describe three exemplary mobilization projects which yielded metadata published through the prokaryotic metadatabase BacDive. The Reichenbach collection of myxobacteria includes information on 12,535 typewritten index cards which were digitized. A total of 37,156 data points were extracted by text mining. In the second mobilization project, Analytical Profile Index (API) tests on paper forms were targeted. Overall 6820 API tests were digitized, which provide physiological data of 4524 microbial strains. Thirdly, the extraction of metadata from 523 new species descriptions of the International Journal of Systematic and Evolutionary Microbiology, yielding 35,651 data points, is described. All data sets were integrated and published in BacDive. Thereby these metadata not only became accessible and searchable but were also linked to strain taxonomy, isolation source, cultivation condition, and molecular biology data. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Successful stent-in-stent insertion of an expandable metallic stent covered with polyuretane placed to obliterate a large bronchial fistula after chemoradiotherapy for inoperable lung cancer

International Nuclear Information System (INIS)

Minami, Hiroya; Tsubota, Noriaki; Miyamoto, Yoshifumi; Yoshimura, Masahiro; Obayashi, Kayoko; Takada, Yoshiki

1999-01-01

Bronchial fistulas in cases of inoperable lung cancer caused by radiochemotherapy are quite refractory and generally cannot be surgically closed. A 45-year-old man with squamous cell carcinoma in the right lung underwent two courses of induction chemotherapy (135 mg CDDP, 5 mg VDS, 13.5 mg MMC) and radiation therapy (2 Gy x 22 times) for invasion of the right main bronchus, the pulmonary artery and superior vena cava. Just before the end of the second course, the empyem second to the bronchial fistula caused by tumor necrosis developed in the right upper bronchus, and fenestration was performed. After the operation, his condition improved remarkably, however the fistula enlarged into the right main bronchus and the purulent discharge flowed into the left lung. An expandable metallic stent (EMS) covered with polyuretane was inserted in the trachea and the left main bronchus to break aspiration pneumonia. As the covered EMS was too unstable to be fixed, a bare EMS was inserted in a stent-in-stent fashion. After the procedure he was followed at the O.P.D. and lived a relatively comfortable life for 9 months until his death due to tumor. We inserted the covered EMS in a stent-in-stent fashion to successfully obliterate a large bronchial fistula. (author)

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

Science.gov (United States)

Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

2016-05-01

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from 86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Expression of the Azotobacter vinelandii Poly-β-Hydroxybutyrate Biosynthetic phbBAC Operon Is Driven by Two Overlapping Promoters and Is Dependent on the Transcriptional Activator PhbR

OpenAIRE

Peralta-Gil, Martín; Segura, Daniel; Guzmán, Josefina; Servín-González, Luis; Espín, Guadalupe

2002-01-01

The Azotobacter vinelandii phbBAC genes encode the enzymes for poly-β-hydroxybutyrate (PHB) synthesis. The phbR gene, which is located upstream of and in the opposite direction of phbBAC, encodes PhbR, a transcriptional activator which is a member of the AraC family of activators. Here we report that a mutation in phbR reduced PHB accumulation and transcription of a phbB-lacZ fusion. We also report that phbB is transcribed from two overlapping promoters, pB1 and pB2. The region corresponding ...

Assessment of Severe Extremity Wound Bioburden at the Time of Definitive Wound Closure or Coverage: Correlation With Subsequent Postclosure Deep Wound Infection (Bioburden Study).

Science.gov (United States)

Bosse, Michael J; Murray, Clinton K; Carlini, Anthony R; Firoozabadi, Reza; Manson, Theodore; Scharfstein, Daniel O; Wenke, Joseph C; Zadnik, Mary; Castillo, Renan C

2017-04-01

Infection remains the most common and significant complication after high-energy fractures. The Bioburden Study is a multicenter, prospective, observational cohort study of wound bacterial bioburden and antibiotic care in severe open lower extremity fractures. The aims of this study are to (1) characterize the contemporary extremity wound "bioburden" at the time of definitive wound closure; (2) determine the concordance between polymerase chain reaction results and hospital microbiology; (3) determine, among those who develop deep infections, the concordance between the pathogens at wound closure and at deep infection; and (4) compare the probability of deep infection between those who did and did not receive an appropriate course of antibiotics based on bioburden at the time of wound closure. To address these aims, sites collected tissue samples from severe lower extremity injuries at the time of wound closure and at first surgery for treatment of a deep infection, nonunion, flap failure, amputation, or other complications (because these surgeries may be due to undetected infection). Otherwise, if no further surgical treatment occurred, participants were followed for 12 months. The study was conducted at 38 US trauma centers and has enrolled 655 participants aged 18-64 years. This is the first large multi-institutional study evaluating the wound bioburden of severe open tibia fractures and correlating this bioburden with the risk of wound complications after definitive soft tissue closure.

Description of the skeleton of the fossil beaked whale Messapicetus gregarius: searching potential proxies for deep-diving abilities

Directory of Open Access Journals (Sweden)

B. Ramassamy

2018-01-01

Full Text Available Ziphiidae (beaked whales are a successful family of medium- to large-sized toothed whales. Their extant members perform regular deep dives beyond the photic zone to forage for cephalopods and fish. Conversely, extinct long-snouted stem ziphiids are interpreted as epipelagic predators. However, some aspects of this hypothesis remain unclear due to the lack of clear morphological proxies for recognizing regular deep divers. We compared the forelimb, neck, and pterygoid sinus system of the fossil ziphiid Messapicetus gregarius with those of other odontocetes to evaluate the potential of these body regions as proxies to assess deep-diving specialization. The reconstructed musculature of the neck and forelimb of M. gregarius was also compared with that of other odontocetes. We also quantified variation in the proportions of the forelimb and the hamular fossa of the pterygoid sinus (HF using 16 linear measurements. The degree of association between diving behaviour in extant odontocetes and these measurements was evaluated with and without phylogenetic correction. Reconstruction of the neck musculature suggests that M. gregarius possessed a neck more flexible than most extant ziphiids due to the lower degree of fusion of the cervical vertebrae and the large insertions for the M. longus colli and Mm. intertransversarii ventrales cervicis. While neck rigidity might be related to deep diving, differences in neck flexibility among extant ziphiids indicate a more complex functional interpretation. The relationship between forelimb morphology and diving behaviour was not significant, both with and without phylogenetic correction, suggesting that it cannot be used to assess deep-diving abilities with the parameters considered here. Measurements of the HF revealed successful to evaluate deep-diving abilities in odontocetes, with an enlargement of this structure in deep divers. Considering other evidence that suggests an epipelagic behaviour, we propose

Evaluation of BacT/Alert 3D Liquid Culture System for Recovery of Mycobacteria from Clinical Specimens Using Sodium Dodecyl (Lauryl) Sulfate-NaOH Decontamination

Science.gov (United States)

Carricajo, A.; Fonsale, N.; Vautrin, A. C.; Aubert, G.

2001-01-01

A total of 52 mycobacterial isolates were recovered from 1,197 clinical specimens decontaminated by a sodium dodecyl (lauryl) sulfate (SDS)-NaOH protocol. Of these, 94% were recovered with the BacT/Alert 3D system (Organon Teknika, Durham, N.C.) and 79% were recovered on Löwenstein-Jensen (LJ) medium. Mean times to detection of organisms of the Mycobacterium tuberculosis complex (n = 47) were 22.8 days with LJ medium and 16.2 days with the system. The BacT/Alert 3D system is a rapid and efficient detection system which can be used with an SDS-NaOH decontamination procedure. PMID:11574623

Coverage of Deep Cutaneous Wounds Using Dermal Template in Combination with Negative-pressure Therapy and Subsequent Skin Graft

Science.gov (United States)

Chang, Alexandre A.; Lobato, Rodolfo C.; Nakamoto, Hugo A.; Tuma, Paulo; Ferreira, Marcus C.

2014-01-01

Background: We consider the use of dermal matrix associated with a skin graft to cover deep wounds in the extremities when tendon and bone are exposed. The objective of this article was to evaluate the efficacy of covering acute deep wounds through the use of a dermal regeneration template (Integra) associated with vacuum therapy and subsequent skin grafting. Methods: Twenty patients were evaluated prospectively. All of them had acute (up to 3 weeks) deep wounds in the limbs. We consider a deep wound to be that with exposure of bone, tendon, or joint. Results: The average area of integration of the dermal regeneration template was 86.5%. There was complete integration of the skin graft over the dermal matrix in 14 patients (70%), partial integration in 5 patients (25%), and total loss in 1 case (5%). The wound has completely closed in 95% of patients. Conclusions: The use of Integra dermal template associated with negative-pressure therapy and skin grafting showed an adequate rate of resolution of deep wounds with low morbidity. PMID:25289363

Spatial attributes of the four-helix bundle group of bacteriocins – The high-resolution structure of BacSp222 in solution

KAUST Repository

Nowakowski, Michał; Jaremko, Łukasz; Wladyka, Benedykt; Dubin, Grzegorz; Ejchart, Andrzej; Mak, Paweł

2017-01-01

collected. The structure was calculated based on NMR-derived constraints and consists of a rigid and tightly packed globular bundle of four alpha-helices separated by three short turns.Although the amino acid sequence of BacSp222 has no significant

Comparison of conventional Injection Mould Inserts to Additively Manufactured Inserts using Life Cycle Assessment

DEFF Research Database (Denmark)

Hofstätter, Thomas; Bey, Niki; Mischkot, Michael

2016-01-01

Polymer Additive Manufacturing can be used to produce soft tooling inserts for injection moulding. Compared to conventional tooling, the energy and time consumption during production are significantly lower. As the life time of such inserts is significantly shorter than the life time of traditional...... of their potential environmental impact and yield throughout the development and pilot phase. Insert geometry is particularly advantageous for pilot production and small production sizes. In this research, Life Cycle Assessment is used to compare the environmental impact of soft tooling by Additive Manufacturing...... (using Digital Light Processing) and three traditional methods for the manufacture of inserts (milling of brass, steel, and aluminium) for injection moulds during the pre-production phase....

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

Science.gov (United States)

Han, Kyudong; Sen, Shurjo K; Wang, Jianxin; Callinan, Pauline A; Lee, Jungnam; Cordaux, Richard; Liang, Ping; Batzer, Mark A

2005-01-01

Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of approximately 18 kb of sequence from the human genome and approximately 15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1-mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions.

Data Insertion in Bitcoin's Blockchain

Directory of Open Access Journals (Sweden)

Andrew Sward

2018-04-01

Full Text Available This paper provides the first comprehensive survey of methods for inserting arbitrary data into Bitcoin’s blockchain. Historical methods of data insertion are described, along with lesser-known techniques that are optimized for efficiency. Insertion methods are compared on the basis of efficiency, cost, convenience of data reconstruction, permanence, and potentially negative impact on the Bitcoin ecosystem.

Intra-disciplinary differences in database coverage and the consequences for bibliometric research

DEFF Research Database (Denmark)

Faber Frandsen, Tove; Nicolaisen, Jeppe

2008-01-01

Bibliographic databases (including databases based on open access) are routinely used for bibliometric research. The value of a specific database depends to a large extent on the coverage of the discipline(s) under study. A number of studies have determined the coverage of databases in specific d...... and psychology). The point extends to include both the uneven coverage of specialties and research traditions. The implications for bibliometric research are discussed, and precautions which need to be taken are outlined. ...

Gastro-oesophageal reflux in large-sized, deep-chested versus small-sized, barrel-chested dogs undergoing spinal surgery in sternal recumbency.

Science.gov (United States)

Anagnostou, Tilemahos L; Kazakos, George M; Savvas, Ioannis; Kostakis, Charalampos; Papadopoulou, Paraskevi

2017-01-01

The aim of this study was to investigate whether an increased frequency of gastro-oesophageal reflux (GOR) is more common in large-sized, deep-chested dogs undergoing spinal surgery in sternal recumbency than in small-sized, barrelchested dogs. Prospective, cohort study. Nineteen small-sized, barrel-chested dogs (group B) and 26 large-sized, deep-chested dogs (group D). All animals were premedicated with intramuscular (IM) acepromazine (0.05 mg kg -1 ) and pethidine (3 mg kg -1 ) IM. Anaesthesia was induced with intravenous sodium thiopental and maintained with halothane in oxygen. Lower oesophageal pH was monitored continuously after induction of anaesthesia. Gastro-oesophageal reflux was considered to have occurred whenever pH values > 7.5 or < 4 were recorded. If GOR was detected during anaesthesia, measures were taken to avoid aspiration of gastric contents into the lungs and to prevent the development of oesophagitis/oesophageal stricture. The frequency of GOR during anaesthesia was significantly higher in group D (6/26 dogs; 23.07%) than in group B (0/19 dogs; 0%) (p = 0.032). Signs indicative of aspiration pneumonia, oesophagitis or oesophageal stricture were not reported in any of the GOR cases. In large-sized, deep-chested dogs undergoing spinal surgery in sternal recumbency, it would seem prudent to consider measures aimed at preventing GOR and its potentially devastating consequences (oesophagitis/oesophageal stricture, aspiration pneumonia). Copyright © 2016 Association of Veterinary Anaesthetists and American College of Veterinary Anesthesia and Analgesia. Published by Elsevier Ltd. All rights reserved.

Coverage and Capacity Analysis of LTE-M and NB-IoT in a Rural Area

DEFF Research Database (Denmark)

Lauridsen, Mads; Kovács, István; Mogensen, Preben Elgaard

2016-01-01

equipped with either of the newly standardized technologies. The study is made for a site specific network deployment of a Danish operator, and the simulation is calibrated using drive test measurements. The results show that LTE-M can provide coverage for 99.9% of outdoor and indoor devices, if the latter......The 3GPP has introduced the LTE-M and NB-IoT User Equipment categories and made amendments to LTE release 13 to support the cellular Internet of Things. The contribution of this paper is to analyze the coverage probability, the number of supported devices, and the device battery life in networks...... is experiencing 10 dB additional loss. However, for deep indoor users NB-IoT is required and provides coverage for about 95% of the users. The cost is support for more than 10 times fewer devices and a 2-6 times higher device power consumption. Thus both LTE-M and NB-IoT provide extended support for the cellular...

A Comparative study of early postpartum IUCD insertion to interval IUCD insertion at Tertiary Care Centre

OpenAIRE

Roopal, Dr.; Bisht, Vandana

2018-01-01

Background: A Comparative study of early postpartum IUCD insertion to interval IUCD insertion at Tertiary Care Centre.Methods: This prospective study was conducted among 100 women at tertiary care centre, Haldwani, Nainital. Patients were divided in to two groups. Group A (n=50)-post placental insertion within 10 minutes of delivery of placenta. Group B (n=50)-Interval insertion after 6 weeks of delivery. Both groups were compared in terms of pain abdomen, bleeding, missing thread, expulsion,...

Assessment of Insert Sizes and Adapter Content in Fastq Data from NexteraXT Libraries

Directory of Open Access Journals (Sweden)

Frances Susan Turner

2014-01-01

Full Text Available The Illumina NexteraXT transposon protocol is a cost effective way to generate paired end libraries. However the resulting insert size is highly sensitive to the concentration of DNA used, and the variation of insert sizes is often large. One consequence of this is some fragments may have an insert shorter than the length of a single read, particularly where the library is designed to produce overlapping paired end reads in order to produce longer continuous sequences. Such small insert sizes mean fewer longer reads, and also result in the presence of adapter at the end of the read. Here is presented a protocol to use publicly available tools to identify read pairs with small insert sizes and so likely to contain adapter, to check the sequence of the adapter, and remove adapter sequence from the reads. This protocol does not require a reference genome or prior knowledge of the sequence to be trimmed. Whilst the presence of fragments with small insert sizes may be a particular problem for NexteraXT libraries, the principle can be applied to any Illumina dataset in which the presence of such small inserts is suspected.

piggyBac transposon somatic mutagenesis with an activated reporter and tracker (PB-SMART for genetic screens in mice.

Directory of Open Access Journals (Sweden)

Sean F Landrette

Full Text Available Somatic forward genetic screens have the power to interrogate thousands of genes in a single animal. Retroviral and transposon mutagenesis systems in mice have been designed and deployed in somatic tissues for surveying hematopoietic and solid tumor formation. In the context of cancer, the ability to visually mark mutant cells would present tremendous advantages for identifying tumor formation, monitoring tumor growth over time, and tracking tumor infiltrations and metastases into wild-type tissues. Furthermore, locating mutant clones is a prerequisite for screening and analyzing most other somatic phenotypes. For this purpose, we developed a system using the piggyBac (PB transposon for somatic mutagenesis with an activated reporter and tracker, called PB-SMART. The PB-SMART mouse genetic screening system can simultaneously induce somatic mutations and mark mutated cells using bioluminescence or fluorescence. The marking of mutant cells enable analyses that are not possible with current somatic mutagenesis systems, such as tracking cell proliferation and tumor growth, detecting tumor cell infiltrations, and reporting tissue mutagenesis levels by a simple ex vivo visual readout. We demonstrate that PB-SMART is highly mutagenic, capable of tumor induction with low copy transposons, which facilitates the mapping and identification of causative insertions. We further integrated a conditional transposase with the PB-SMART system, permitting tissue-specific mutagenesis with a single cross to any available Cre line. Targeting the germline, the system could also be used to conduct F1 screens. With these features, PB-SMART provides an integrated platform for individual investigators to harness the power of somatic mutagenesis and phenotypic screens to decipher the genetic basis of mammalian biology and disease.

BACS: The Brussels Artificial Character Sets for studies in cognitive psychology and neuroscience.

Science.gov (United States)

Vidal, Camille; Content, Alain; Chetail, Fabienne

2017-12-01

Written symbols such as letters have been used extensively in cognitive psychology, whether to understand their contributions to written word recognition or to examine the processes involved in other mental functions. Sometimes, however, researchers want to manipulate letters while removing their associated characteristics. A powerful solution to do so is to use new characters, devised to be highly similar to letters, but without the associated sound or name. Given the growing use of artificial characters in experimental paradigms, the aim of the present study was to make available the Brussels Artificial Character Sets (BACS): two full, strictly controlled, and portable sets of artificial characters for a broad range of experimental situations.

Dosimetric Coverage of the Prostate, Normal Tissue Sparing, and Acute Toxicity with High-Dose-Rate Brachytherapy for Large Prostate Volumes

Directory of Open Access Journals (Sweden)

George Yang

2015-06-01

Full Text Available ABSTRACTPurposeTo evaluate dosimetric coverage of the prostate, normal tissue sparing, and acute toxicity with HDR brachytherapy for large prostate volumes.Materials and MethodsOne hundred and two prostate cancer patients with prostate volumes >50 mL (range: 5-29 mL were treated with high-dose-rate (HDR brachytherapy ± intensity modulated radiation therapy (IMRT to 4,500 cGy in 25 daily fractions between 2009 and 2013. HDR brachytherapy monotherapy doses consisted of two 1,350-1,400 cGy fractions separated by 2-3 weeks, and HDR brachytherapy boost doses consisted of two 950-1,150 cGy fractions separated by 4 weeks. Twelve of 32 (38% unfavorable intermediate risk, high risk, and very high risk patients received androgen deprivation therapy. Acute toxicity was graded according to the Common Terminology Criteria for Adverse Events (CTCAE version 4.ResultsMedian follow-up was 14 months. Dosimetric goals were achieved in over 90% of cases. Three of 102 (3% patients developed Grade 2 acute proctitis. No variables were significantly associated with Grade 2 acute proctitis. Seventeen of 102 (17% patients developed Grade 2 acute urinary retention. American Urological Association (AUA symptom score was the only variable significantly associated with Grade 2 acute urinary retention (p=0.04. There was no ≥ Grade 3 acute toxicity.ConclusionsDosimetric coverage of the prostate and normal tissue sparing were adequate in patients with prostate volumes >50 mL. Higher pre-treatment AUA symptom scores increased the relative risk of Grade 2 acute urinary retention. However, the overall incidence of acute toxicity was acceptable in patients with large prostate volumes.

Dosimetric coverage of the prostate, normal tissue sparing, and acute toxicity with high-dose-rate brachytherapy for large prostate volumes

Energy Technology Data Exchange (ETDEWEB)

Yang, George; Strom, Tobin J.; Shrinath, Kushagra; Mellon, Eric A.; Fernandez, Daniel C.; Biagioli, Matthew C. [Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL (United States); Wilder, Richard B., E-mail: mcbiagioli@yahoo.com [Cancer Treatment Centers of America, Newnan, GA (United States)

2015-05-15

Purpose: to evaluate dosimetric coverage of the prostate, normal tissue sparing, and acute toxicity with HDR brachytherapy for large prostate volumes. Materials and methods: one hundred and two prostate cancer patients with prostate volumes >50 mL (range: 5-29 mL) were treated with high-dose-rate (HDR) brachytherapy ± intensity modulated radiation therapy (IMRT) to 4,500 cGy in 25 daily fractions between 2009 and 2013. HDR brachytherapy monotherapy doses consisted of two 1,350-1,400 cGy fractions separated by 2-3 weeks, and HDR brachytherapy boost doses consisted of two 950-1,150 cGy fractions separated by 4 weeks. Twelve of 32 (38%) unfavorable intermediate risk, high risk, and very high risk patients received androgen deprivation therapy. Acute toxicity was graded according to the Common Terminology Criteria for Adverse Events (CTCAE) version 4. Results: median follow-up was 14 months. Dosimetric goals were achieved in over 90% of cases. Three of 102 (3%) patients developed Grade 2 acute proctitis. No variables were significantly associated with Grade 2 acute proctitis. Seventeen of 102 (17%) patients developed Grade 2 acute urinary retention. American Urological Association (AUA) symptom score was the only variable significantly associated with Grade 2 acute urinary retention (p-0.04). There was no ≥ Grade 3 acute toxicity. Conclusions: dosimetric coverage of the prostate and normal tissue sparing were adequate in patients with prostate volumes >50 mL. Higher pre-treatment AUA symptom scores increased the relative risk of Grade 2 acute urinary retention. However, the overall incidence of acute toxicity was acceptable in patients with large prostate volumes. (author)

Dicty_cDB: SHJ574 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available t in 5'HPRT insertion targeting and chromosome engineering clone MHPN46d24. 44 3.6 1 CR250482 |CR250482.1 Re...verse strand read from insert in 5'HPRT insertion targeting and chromosome engineering...rgeting and chromosome engineering clone MHPN111m08. 44 3.6 1 DU965366 |DU965366.1 312103 Tomato MboI BAC Li... clone MHPN408l04. 44 3.6 1 CR115379 |CR115379.1 Reverse strand read from insert in 5'HPRT insertion ta

DeepQA: Improving the estimation of single protein model quality with deep belief networks

OpenAIRE

Cao, Renzhi; Bhattacharya, Debswapna; Hou, Jie; Cheng, Jianlin

2016-01-01

Background Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. Results We introduce a novel single-model quality assessment method DeepQA based on deep belie...

BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

International Nuclear Information System (INIS)

Samuelson, Emma; Karlsson, Sara; Partheen, Karolina; Nilsson, Staffan; Szpirer, Claude; Behboudi, Afrouz

2012-01-01

Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform. Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic

Automatic insertion of simulated microcalcification clusters in a software breast phantom

Science.gov (United States)

Shankla, Varsha; Pokrajac, David D.; Weinstein, Susan P.; DeLeo, Michael; Tuite, Catherine; Roth, Robyn; Conant, Emily F.; Maidment, Andrew D.; Bakic, Predrag R.

2014-03-01

An automated method has been developed to insert realistic clusters of simulated microcalcifications (MCs) into computer models of breast anatomy. This algorithm has been developed as part of a virtual clinical trial (VCT) software pipeline, which includes the simulation of breast anatomy, mechanical compression, image acquisition, image processing, display and interpretation. An automated insertion method has value in VCTs involving large numbers of images. The insertion method was designed to support various insertion placement strategies, governed by probability distribution functions (pdf). The pdf can be predicated on histological or biological models of tumor growth, or estimated from the locations of actual calcification clusters. To validate the automated insertion method, a 2-AFC observer study was designed to compare two placement strategies, undirected and directed. The undirected strategy could place a MC cluster anywhere within the phantom volume. The directed strategy placed MC clusters within fibroglandular tissue on the assumption that calcifications originate from epithelial breast tissue. Three radiologists were asked to select between two simulated phantom images, one from each placement strategy. Furthermore, questions were posed to probe the rationale behind the observer's selection. The radiologists found the resulting cluster placement to be realistic in 92% of cases, validating the automated insertion method. There was a significant preference for the cluster to be positioned on a background of adipose or mixed adipose/fibroglandular tissues. Based upon these results, this automated lesion placement method will be included in our VCT simulation pipeline.

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

OpenAIRE

Luo, Meizhong; Kim, HyeRan; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A

2006-01-01

Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) ...

Toxicity and genotoxicity of the quaternary ammonium compound benzalkonium chloride (BAC) using Daphnia magna and Ceriodaphnia dubia as model systems

International Nuclear Information System (INIS)

Lavorgna, Margherita; Russo, Chiara; D'Abrosca, Brigida; Parrella, Alfredo; Isidori, Marina

2016-01-01

The toxicity and genotoxicity of the cationic surfactant benzalkonium chloride (BAC) were studied using Daphnia magna and Ceriodaphnia dubia as model systems. Acute and chronic toxicity testing were performed according to the international standard guidelines and the genotoxicity was detected through the comet assay on cells from whole organisms in vivo exposed. Acute effects occurred at concentrations in the order of tens of μg/L in D. magna and hundreds of μg/L in C. dubia. Chronic effects were found at one order of magnitude less than short-term effects maintaining the same difference in sensitivity between D. magna and C. dubia. BAC induced relevant DNA damage, in both cladocerans; the lowest adverse effect levels were 0.4 and 4 ng/L for D. magna and C. dubia, respectively. As these effective concentrations are far lower than BAC occurrence in surface waters (units of μg/L) a concerning environmental risk cannot be excluded. The findings of this study showed that D. magna and C. dubia, could be used as model organisms to detect acute and chronic toxicity as well as genotoxicity at the whole organism level. - Highlights: • Benzalkonium chloride chronic effect in C. dubia was found at dozens of μg/L. • The LOAEC detected by comet assay in D. magna is in the order of hundreds of pg/L. • D. magna and C. dubia are useful model organisms to detect toxicity and genotoxicity. - Benzalkonium chloride showed chronic toxicity and genotoxicity in Daphnia magna and Ceriodaphnia dubia at concentrations of environmental concern. Daphnids are useful model organisms.

Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew.

Science.gov (United States)

Rabah, Samar O; Lee, Chaehee; Hajrah, Nahid H; Makki, Rania M; Alharby, Hesham F; Alhebshi, Alawiah M; Sabir, Jamal S M; Jansen, Robert K; Ruhlman, Tracey A

2017-11-01

In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon ( J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa ( Willd.). In the orchard tree cashew ( L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated. Copyright © 2017 Crop Science Society of America.

In vitro antibacterial and cytotoxicity assessments of an orthodontic bonding agent containing benzalkonium chloride.

Science.gov (United States)

Saito, Kayo; Hayakawa, Tohru; Kawabata, Rihito; Meguro, Daijiro; Kasai, Kazutaka

2009-03-01

To assess the antibacterial activity and cytotoxicity of an orthodontic bonding material containing an antibacterial agent. Superbond C&B (4-methacryloxyethyl trimellitate anhydride/methyl methacrylate-tri-n-butyl borane [4-META/MMA-TBB]) resin was mixed with benzalkonium chloride (BAC) to obtain final BAC concentrations of 0.25%, 0.75%, 1.25%, 1.75%, 2.5%, and 5.0% (wt/ wt). Antibacterial activity against Streptococcus mutans and Streptococcus sobrinus was evaluated by soaking the BAC-resin in distilled water at 37 degrees C for periods of 30, 90, and 180 days. Antibacterial activity of the BAC-resin was measured by the disk diffusion method, and the inhibition zone around each sample was measured and recorded. For evaluation of cytotoxicity, BAC-resin samples were put into cell culture inserts placed above human gingival cells and were incubated at 37 degrees C for 1, 3, and 6 days. Cytotoxicity was assessed with a tetrazolium bromide reduction assay. The antibacterial activity of BAC-incorporated resin samples decreased significantly after immersion in water for 180 days, regardless of BAC concentration. The antibacterial activity of nonimmersed resin containing 0.25% or 1.75% BAC was comparable with that of 5.0% BAC-resin immersed for 180 days. In cytotoxicity tests, most cells died when exposed to resins containing 1.75%, 2.5%, and 5% BAC. No difference was observed between resins containing 0.25% and 0.75% BAC at 1, 3, and 6 days of culture. The addition of BAC to 4-META/MMA-TBB resin confers an antibacterial effect even after immersion in water, and 4-META/MMA-TBB resin containing 0.25% to 0.75% BAC has no significant cytotoxic effect.

Observation of jet production in deep inelastic scattering with a large rapidity gap at HERA

International Nuclear Information System (INIS)

Doeker, T.

1994-01-01

Events with a large rapidity gap in deep inelastic scattering with Q 2 ≥ 10 GeV 2 have been studied in the ZEUS detector. The properties of these events with W > 140 GeV are consistent with a leading twist diffractive production mechanism. In the laboratory frame, with E jet t ≥ 4 GeV, 159% of the events are of the 1-jet type with negligible 2-jet production. The single jet is back-to-back in azimuth with the scattered electron. No energy now is observed between the jet and the proton direction. With a lower jet transverse energy cut 2-jet production is observed both in the laboratory and the γ * P centre-of-mass systems, demonstrating the presence of hard scattering in the virtual photon proton interactions that give rise to large rapidity gap events

Observation of jet production in deep inelastic scattering with a large rapidity gap a HERA

International Nuclear Information System (INIS)

Derrick, M.; Krakauer, D.; Magill, S.

1994-04-01

Events with a large rapidity gap in deep inelastic scattering with Q 2 ≥10 GeV 2 have been studied in the ZEUS detector. The properties of these events with W>140 GeV are consistent with a leading twist diffractive mechanism. In the laboratory frame, with E T jet ≥4 GeV, 15% of the events are of the 1-jet type with negligible 2-jet production. The single jet is back-to-back in azimuth with the scattered electron. No energy flow is observed between the jet and the proton direction. With a lower jet transverse energy cut 2-jet production is observed both in the laboratory and the γ * p centre-of-mass systems demonstrating the presence of hard scattering in the virtual photon interactions that give rise to large rapidity gap events. (orig.)

The kinetics of porous insertion electrodes

Energy Technology Data Exchange (ETDEWEB)

Atlung, S; West, K [British Columbia Univ., Vancouver (Canada)

1989-05-01

The principles of porous electrodes are discussed as well as the discharge of the insertion compound, the working potential, transport in the electrolyte, the time dependence of the electrolyte concentration, and modeling of the porous electrode. The simulation of a TiS2 porous electrode and the composite insertion electrode are considered as well. The influence of electrode thickness and porosity in a typical porous TiS2 electrode is revealed. It is shown that the use of insertion compounds as battery electrodes is limited by the requirement that the inserted ion must be distributed in the interior of the insertion compound particle. 15 refs.

Construction of an infectious clone of canine herpesvirus genome as a bacterial artificial chromosome.

Science.gov (United States)

Arii, Jun; Hushur, Orkash; Kato, Kentaro; Kawaguchi, Yasushi; Tohya, Yukinobu; Akashi, Hiroomi

2006-04-01

Canine herpesvirus (CHV) is an attractive candidate not only for use as a recombinant vaccine to protect dogs from a variety of canine pathogens but also as a viral vector for gene therapy in domestic animals. However, developments in this area have been impeded by the complicated techniques used for eukaryotic homologous recombination. To overcome these problems, we used bacterial artificial chromosomes (BACs) to generate infectious BACs. Our findings may be summarized as follows: (i) the CHV genome (pCHV/BAC), in which a BAC flanked by loxP sites was inserted into the thymidine kinase gene, was maintained in Escherichia coli; (ii) transfection of pCHV/BAC into A-72 cells resulted in the production of infectious virus; (iii) the BAC vector sequence was almost perfectly excisable from the genome of the reconstituted virus CHV/BAC by co-infection with CHV/BAC and a recombinant adenovirus that expressed the Cre recombinase; and (iv) a recombinant virus in which the glycoprotein C gene was deleted was generated by lambda recombination followed by Flp recombination, which resulted in a reduction in viral titer compared with that of the wild-type virus. The infectious clone pCHV/BAC is useful for the modification of the CHV genome using bacterial genetics, and CHV/BAC should have multiple applications in the rapid generation of genetically engineered CHV recombinants and the development of CHV vectors for vaccination and gene therapy in domestic animals.

ALS insertion devices

International Nuclear Information System (INIS)

Hoyer, E.; Chin, J.; Halbach, K.; Hassenzahl, W.V.; Humphries, D.; Kincaid, B.; Lancaster, H.; Plate, D.

1990-11-01

The Advanced Light Source (ALS), the first US third generation synchrotron radiation source, is currently under construction at the Lawrence Berkeley Laboratory. The low-emittance, 1.5 GeV electron storage ring and the insertion devices are specifically designed to produce high brightness beams in the UV to soft X-Ray range. The planned initial complement of insertion devices includes four 4.6 m long undulators, with period lengths of 3.9 cm, 5.0 cm (2) and 8.0 cm, and a 2.9 m long wiggler of 16 cm period length. Undulator design is well advanced and fabrication has begun on the 5.0 cm and 8.0 cm period length undulators. This paper discusses ALS insertion device requirements; general design philosophy; and design of the magnetic structure, support structure/drive systems, control system and vacuum system. 18 refs., 9 figs., 5 tabs

Folding and insertion thermodynamics of the transmembrane WALP peptide

International Nuclear Information System (INIS)

Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

2015-01-01

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA) n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence

Folding and insertion thermodynamics of the transmembrane WALP peptide

Energy Technology Data Exchange (ETDEWEB)

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Bennett, W. F. Drew [Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Pfaendtner, Jim [Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 (United States); Deserno, Markus [Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Karttunen, Mikko [Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, 5600 MB Eindhoven (Netherlands)

2015-12-28

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

FRET-based localization of fluorescent protein insertions within the ryanodine receptor type 1.

Directory of Open Access Journals (Sweden)

Shweta A Raina

Full Text Available Fluorescent protein (FP insertions have often been used to localize primary structure elements in mid-resolution 3D cryo electron microscopic (EM maps of large protein complexes. However, little is known as to the precise spatial relationship between the location of the fused FP and its insertion site within a larger protein. To gain insights into these structural considerations, Förster resonance energy transfer (FRET measurements were used to localize green fluorescent protein (GFP insertions within the ryanodine receptor type 1 (RyR1, a large intracellular Ca(2+ release channel that plays a key role in skeletal muscle excitation contraction coupling. A series of full-length His-tagged GFP-RyR1 fusion constructs were created, expressed in human embryonic kidney (HEK-293T cells and then complexed with Cy3NTA, a His-tag specific FRET acceptor. FRET efficiency values measured from each GFP donor to Cy3NTA bound to each His tag acceptor site were converted into intermolecular distances and the positions of each inserted GFP were then triangulated relative to a previously published X-ray crystal structure of a 559 amino acid RyR1 fragment. We observed that the chromophoric centers of fluorescent proteins inserted into RyR1 can be located as far as 45 Å from their insertion sites and that the fused proteins can also be located in internal cavities within RyR1. These findings should prove useful in interpreting structural results obtained in cryo EM maps using fusions of small fluorescent proteins. More accurate point-to-point distance information may be obtained using complementary orthogonal labeling systems that rely on fluorescent probes that bind directly to amino acid side chains.

Challenges for Insertion of Structural Nanomaterials in Aerospace Applications

Science.gov (United States)

Sochi, Emilie J.

2012-01-01

In the two decades since Iijima's report on carbon nanotubes (CNT), there has been great interest in realizing the benefits of mechanical properties observed at the nanoscale in large-scale structures. The weight savings possible due to dramatic improvements in mechanical properties relative to state-of-the-art material systems can be game changing for applications like aerospace vehicles. While there has been significant progress in commercial production of CNTs, major aerospace applications that take advantage of properties offered by this material have yet to be realized. This paper provides a perspective on the technical challenges and barriers for insertion of CNTs as an emerging material technology in aerospace applications and proposes approaches that may reduce the typical timeframe for technology maturation and insertion into aerospace structures.

Percutaneous Ureteral stent insertion

Energy Technology Data Exchange (ETDEWEB)

Yoon, Yup; Sung, Dong Wook; Choi, Woo Suk; Lee, Dong Ho; Ko, Young Tae; Lee, Sun Wha; Lim, Jae Hoon [Kyung Hee University Hospital, Seoul (Korea, Republic of)

1990-10-15

Percutaneous ureteral stent insertion is a treatment of permanent or temporary urinary diversion to maintain continuity and function of the obstructed and injured ureter. We performed 31 cases of percutaneous double pig tall ureteral stent insertion in 21 patients, included 13 patients with malignant ureteral obstruction and eight patients with injured ureter as well as benign inflammatory stricture. Satisfactory resulted was obtained in all patients but one, who need percutaneous nephrostomy on week later for urinary diversion. No significant complication was encountered. The authors concluded that percutaneous ureteral stent insertion, an interventional procedure alternative to urologic retrograde method, is an effective method for urinary diversion.

'Relax and take a deep breath': print media coverage of asthma and air pollution in the United States.

Science.gov (United States)

Mayer, Brian

2012-09-01

The media are an important social actor in the construction of the public's understanding of the complex relationships between the environment and their health. This paper explores the print media's coverage of the relationship between asthma and air pollution, focusing on the portrayal of causal certainty between exposure to various forms of air pollution and the etiology and exacerbation of the disease. By examining twenty years of newspaper articles from the New York Timeş Los Angeles Times, and the Washington Post, this paper presents findings on trends across time, within papers, and across key themes. Although the print media's coverage of asthma and its environmental correlates has increased over time, this paper finds relatively little coherence in whether asthma is portrayed as directly caused by air pollution or triggered by exposures. In terms of coverage, outdoor sources of air pollution are covered more frequently - but with less certainty in the discussion of specific relationships. This lack of coherence and specificity in the portrayal of asthma as an environmental disease may weaken regulators' ability to act in passing air pollution reforms by lowering the public's interest and concern. Copyright © 2012 Elsevier Ltd. All rights reserved.

Direct conversion of human pluripotent stem cells into cranial motor neurons using a piggyBac vector

Directory of Open Access Journals (Sweden)

Riccardo De Santis

2018-05-01

Full Text Available Human pluripotent stem cells (PSCs are widely used for in vitro disease modeling. One of the challenges in the field is represented by the ability of converting human PSCs into specific disease-relevant cell types. The nervous system is composed of a wide variety of neuronal types with selective vulnerability in neurodegenerative diseases. This is particularly relevant for motor neuron diseases, in which different motor neurons populations show a different susceptibility to degeneration. Here we developed a fast and efficient method to convert human induced Pluripotent Stem Cells into cranial motor neurons of the branchiomotor and visceral motor subtype. These populations represent the motor neuron subgroup that is primarily affected by a severe form of amyotrophic lateral sclerosis with bulbar onset and worst prognosis. This goal was achieved by stable integration of an inducible vector, based on the piggyBac transposon, allowing controlled activation of Ngn2, Isl1 and Phox2a (NIP. The NIP module effectively produced electrophysiologically active cranial motor neurons. Our method can be easily extended to PSCs carrying disease-associated mutations, thus providing a useful tool to shed light on the cellular and molecular bases of selective motor neuron vulnerability in pathological conditions. Keywords: Spinal motor neuron, Cranial motor neuron, Induced pluripotent stem cells, Amyotrophic lateral sclerosis, Phox2a, piggyBac

BACs-on-Beads Technology: A Reliable Test for Rapid Detection of Aneuploidies and Microdeletions in Prenatal Diagnosis

Directory of Open Access Journals (Sweden)

Sandra García-Herrero

2014-01-01

Full Text Available The risk of fetal aneuploidies is usually estimated based on high resolution ultrasound combined with biochemical determination of criterion in maternal blood, with invasive procedures offered to the population at risk. The purpose of this study was to investigate the effectiveness of a new rapid aneuploidy screening test on amniotic fluid (AF or chorionic villus (CV samples based on BACs-on-Beads (BoBs technology and to compare the results with classical karyotyping by Giemsa banding (G-banding of cultured cells in metaphase as the gold standard technique. The prenatal-BoBs kit was used to study aneuploidies involving chromosomes 13, 18, 21, X, and Y as well as nine microdeletion syndromes in 321 AF and 43 CV samples. G-banding of metaphase cultured cells was performed concomitantly for all prenatal samples. A microarray-based comparative genomic hybridization (aCGH was also carried out in a subset of samples. Prenatal-BoBs results were widely confirmed by classical karyotyping. Only six karyotype findings were not identified by Prenatal-BoBs, all of them due to the known limitations of the technique. In summary, the BACs-on-Beads technology was an accurate, robust, and efficient method for the rapid diagnosis of common aneuploidies and microdeletion syndromes in prenatal samples.

Deep-tow magnetic survey above large exhumed mantle domains of the eastern Southwest Indian ridge

Science.gov (United States)

Bronner, A.; Munschy, M.; Carlut, J. H.; Searle, R. C.; Sauter, D.; Cannat, M.

2011-12-01

The recent discovery of a new type of seafloor, the "smooth seafloor", formed with no or very little volcanic activity along the ultra-slow spreading Southwest Indian ridge (SWIR) shows an unexpected complexity in processes of generation of the oceanic lithosphere. There, detachment faulting is thought to be a mechanism for efficient exhumation of deep-seated mantle rocks. We present here a deep-tow geological-geophysical survey over smooth seafloor at the eastern SWIR (62-64°N) combining magnetic data, geology mapping from side-scan sonar images and results from dredge sampling. We introduce a new type of calibration approach for deep-tow fluxgate magnetometer. We show that magnetic data can be corrected from the magnetic effect of the vehicle with no recourse to its attitude (pitch, roll and heading) but only using the 3 components recorded by the magnetometer and an approximation of the scalar intensity of the Earth magnetic field. The collected dredge samples as well as the side-scan images confirm the presence of large areas of exhumed mantle-derived peridodites surrounded by a few volcanic constructions. This allows us to hypothesis that magnetic anomalies are caused by serpentinized peridotites or magmatic intrusions. We show that the magnetic signature of the smooth seafloor is clearly weaker than the surrounding volcanic areas. Moreover, the calculated magnetization of a source layer as well as the comparison between deep-tow and sea-surface magnetic data argue for strong East-West variability in the distribution of the magnetized sources. This variability may results from fluid-rocks interaction along the detachment faults as well as from the repartition of the volcanic material and thus questions the seafloor spreading origin of the corresponding magnetic anomalies. Finally, we provide magnetic arguments, as calculation of block rotation or spreading asymmetry in order to better constrain tectonic mechanisms that occur during the formation of this

Deep-tow geophysical survey above large exhumed mantle domains of the eastern Southwest Indian ridge

Science.gov (United States)

Bronner, A.; Munschy, M.; Sauter, D.; Carlut, J.; Searle, R.; Cannat, M.

2012-04-01

The recent discovery of a new type of seafloor, the "smooth seafloor", formed with no or very little volcanic activity along the easternmost part of the ultra-slow spreading Southwest Indian ridge (SWIR) shows an unexpected complexity in processes of generation of the oceanic lithosphere. There, detachment faulting is thought to be a mechanism for efficient exhumation of deep-seated mantle rocks. We present here a deep-tow geological-geophysical survey over smooth seafloor at the eastern SWIR (62-64°N) combining multibeam bathymetric data, magnetic data, geology mapping from sidescan sonar (TOBI) images and results from dredge sampling. We introduce a new type of calibration approach for deep-tow fluxgate magnetometer. We show that magnetic data can be corrected from the magnetic effect of the vehicle with no recourse to its attitude (pitch, roll and heading) but only using the 3 components recorded by the magnetometer and an approximation of the scalar intensity of the Earth magnetic field. The collected dredge samples as well as the sidescan sonar images confirm the presence of large areas of exhumed mantle-derived peridodites surrounded by a few volcanic constructions. We investigate the possibility that magnetic anomalies are either caused by serpentinized peridotites and/or magmatic intrusions. We show that the magnetic signature of the smooth seafloor is clearly weaker than the surrounding volcanic areas. Moreover, the calculated magnetization of a source layer as well as the comparison between deep-tow and sea-surface magnetic data argue for strong East-West variability in the distribution of the magnetized sources. This variability may result from fluid-rock interactions along the detachment faults as well as from the occurrence of small sized and thin volcanic patches and thus questions the seafloor spreading origin of the corresponding magnetic anomalies. Finally, we provide magnetic arguments, as calculation of block rotation or spreading asymmetry in

Desarrollo de un modelo de evaluación financiera de proyectos para BAC Credomatic Network

OpenAIRE

Sandí Piedra, Allan Adolfo

2016-01-01

Universidad de Costa Rica. Posgrado en Administración y Dirección de Empresas. Maestría Profesional en Administración y Dirección de Empresas con énfasis en Finanzas, 2016 El presente trabajo final de investigación contiene los aspectos que fundamentan un modelo de Evaluación Financiera de Proyectos que permite solventar la problemática identificada en BAC Credomatic Network respecto al limitado valor agregado del proceso existente de valoración financiera de los proyectos de la empresa. P...

Armenian media coverage of science topics

Science.gov (United States)

Mkhitaryan, Marie

2016-12-01

The article discusses features and issues of Armenian media coverage on scientific topics and provides recommendations on how to promote scientific topics in media. The media is more interested in social or public reaction rather than in scientific information itself. Medical science has a large share of the global media coverage. It is followed by articles about environment, space, technology, physics and other areas. Armenian media mainly tends to focus on a scientific topic if at first sight it contains something revolutionary. Media primarily reviews whether that scientific study can affect the Armenian economy and only then decides to refer to it. Unfortunately, nowadays the perception of science is a little distorted in media. We can often see headlines of news where is mentioned that the scientist has made "an invention". Nowadays it is hard to see the border between a scientist and an inventor. In fact, the technological term "invention" attracts the media by making illusionary sensation and ensuring large audience. The report also addresses the "Gitamard" ("A science-man") special project started in 2016 in Mediamax that tells about scientists and their motivations.

Single photon image from PET with insertable collimator for boron neutron capture therapy

International Nuclear Information System (INIS)

Jung, Jooyoung; Suh, Tae Suk; Hong, Key Jo

2014-01-01

Boron neutron capture therapy (BNCT) is a radiation therapy technique for treating deep-seated brain tumors by irradiation with a thermal neutron in which boron-labelled low molecular weight compounds. Once completed, a single photon emission computed tomography (SPECT) scan is conducted to investigate for the region of therapy using an isotope exclusive to SPECT. In the case of an existing PET/SPECT combination system, at least two types of isotopes should be used for each scan with their purposes. Recently, researchers examined the effects of PET/SPECT dual modality on animal imaging systems. They reported that the PET/SPECT combination system was effective for simultaneous achievement of a single event and coincidence. The aim of our proposed system is to confirm the feasibility of extraction of two types of images from one PET module with an insertable collimator for brain tumor treatment during the BNCT. We attempted to acquire the PET and SPECT images simultaneously using only PET without an additional isotope. Single photon images were acquired using an insertable collimator on a PET detector

Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells.

Science.gov (United States)

Luo, Wentian; Galvan, Daniel L; Woodard, Lauren E; Dorset, Dan; Levy, Shawn; Wilson, Matthew H

2017-08-21

Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes without requiring homologous recombination. We systematically compared four different engineered zinc finger proteins (ZFP), four transcription activator-like effector proteins (TALE), CRISPR associated protein 9 (SpCas9) and the catalytically inactive dSpCas9 protein fused to the amino-terminus of the transposase enzyme designed to target the hypoxanthine phosphoribosyltransferase (HPRT) gene located on human chromosome X. Chimeric transposases were evaluated for expression, transposition activity, chromatin immunoprecipitation at the target loci, and targeted knockout of the HPRT gene in human cells. One ZFP-PB and one TALE-PB chimera demonstrated notable HPRT gene targeting. In contrast, Cas9/dCas9-PB chimeras did not result in gene targeting. Instead, the HPRT locus appeared to be protected from transposon integration. Supplied separately, PB permitted highly efficient isolation of Cas9-mediated knockout of HPRT, with zero transposon integrations in HPRT by deep sequencing. In summary, these tools may allow isolation of 'targeted-only' cells, be utilized to protect a genomic locus from transposon integration, and enrich for Cas9-mutated cells. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

THE CITY IN CULTURAL JOURNALISM: A PERSPECTIVE OF PORTO ALEGRE IN THE COVERAGE OF DIÁRIO DO SUL (1986-1988

Directory of Open Access Journals (Sweden)

Sara Keller

2012-06-01

Full Text Available The article discusses the representation of the city in cultural journalism, examining how the cultural section of the newspaper Diário do Sul (which belonged to Gazeta Mercantil’s group offered a perspective of Porto Alegre from 1986 to 1988. The study summarizes a large part of the research results conducted by means of content analysis and thematic oral history techniques. It was perceived that the coverage, anchored in positivity, builds up the city as a place of consumption, of novelty, of updating and of the continuous movement of external flows. It reveals the geographic centralization of the circuit, investments in culture institutionalization and in the renewal of the city`s infrastructure. In the tension between the references that create belonging and those that expand the territory, journalism represents the city as the center of the show, inserted in a phenomenon of the recent decades, when cities became decisive agents in the realm of culture.

A Novel Deployment Scheme Based on Three-Dimensional Coverage Model for Wireless Sensor Networks

Science.gov (United States)

Xiao, Fu; Yang, Yang; Wang, Ruchuan; Sun, Lijuan

2014-01-01

Coverage pattern and deployment strategy are directly related to the optimum allocation of limited resources for wireless sensor networks, such as energy of nodes, communication bandwidth, and computing power, and quality improvement is largely determined by these for wireless sensor networks. A three-dimensional coverage pattern and deployment scheme are proposed in this paper. Firstly, by analyzing the regular polyhedron models in three-dimensional scene, a coverage pattern based on cuboids is proposed, and then relationship between coverage and sensor nodes' radius is deduced; also the minimum number of sensor nodes to maintain network area's full coverage is calculated. At last, sensor nodes are deployed according to the coverage pattern after the monitor area is subdivided into finite 3D grid. Experimental results show that, compared with traditional random method, sensor nodes number is reduced effectively while coverage rate of monitor area is ensured using our coverage pattern and deterministic deployment scheme. PMID:25045747

Recognition of large scale deep-seated landslides in vegetated areas of Taiwan

Science.gov (United States)

Lin, C. W.; Tarolli, P.; Tseng, C. M.; Tseng, Y. H.

2012-04-01

In August 2009, Typhoon Morakot triggered thousands of landslides and debris flows, and according to government reports, 619 people were dead and 76 missing and the economic loss was estimated at hundreds million of USD. In particular, the large deep-seated landslides are critical and deserve attention, since they can be affected by a reactivation during intense events, that usually can evolve in destructive failures. These are also difficult to recognize in the field, especially under dense forest areas. A detailed and constantly updated inventory map of such phenomena, and the recognition of their topographic signatures really represents a key tool for landslide risk mitigation, and mapping. The aim of this work is to test the performance of a new developed method for the automatic extraction of geomorphic features related to landslide crowns developed by Tarolli et al. (2010), in support to field surveys in order to develop a detailed and accurate inventory map of such phenomena. The methodology is based on the detection of thresholds derived by the statistical analysis of variability of landform curvature from high resolution LiDAR derived topography. The analysis suggested that the method allowed a good performance in localization and extraction, respect to field analysis, of features related to deep-seated landslides. Thanks to LiDAR capabilty to detect the bare ground elevation data also in forested areas, it was possible to recognize in detail landslide features also in remote regions difficult to access. Reference Tarolli, P., Sofia, G., Dalla Fontana, G. (2010). Geomorphic features extraction from high-resolution topography: landslide crowns and bank erosion, Natural Hazards, doi:10.1007/s11069-010-9695-2

Proceso para transferir el conocimiento en la adquisición de software en la Gerencia de Tecnologías de Información del BAC San José

OpenAIRE

Castillo Rivera, Roberto

2016-01-01

Proyecto final de graduación, Maestría profesional El presente proyecto es el resultado de la aplicación de las mejores prácticas tomando como base la metodología de ITIL en su versión 3 para la liberación final de productos de software, específicamente en cuanto a la transferencia del conocimiento obtenido durante el proceso de adquisición de software aplicativo en la Gerencia de Tecnologías de Información del Banco BAC San José. El Banco BAC San José es una entidad financiera privada,...

Differences in Endothelial Injury After Balloon Angioplasty, Insertion of Balloon-Expanded Stents or Release of Self-Expanding Stents: An Electron Microscopic Experimental Study

International Nuclear Information System (INIS)

Harnek, Jan; Zoucas, Evita; Carlemalm, Erik; Cwikiel, Wojciech

1999-01-01

Purpose: To evaluate which of six different commonly available stents inserted into an artery without percutaneous transluminal angioplasty (PTA) causes the least endothelial damage. To compare the degree of endothelial injury after insertion of such a stent with injury caused by PTA. Methods: Twelve healthy pigs were used in the experiments. In the first part of the study six different types of stents were inserted into the common iliac arteries. In the second part of the study self-expanding stents with large spaces between the wires were used. PTA was performed in the contralateral iliac artery. The pigs were killed immediately after the procedure and resected specimens examined after fixation, using scanning electron microscopy. Results: All procedures but two were accomplished successfully. More endothelium was preserved after insertion of self-expanding stents with large spaces between the wires, compared with stents with small spaces and balloon-expanded stents. After insertion of self-expanding stents with large spaces, 50.1% ± 16.4% of the endothelium remained intact, compared with only 5.6% ± 7.7% after PTA. The difference was statistically significant (p < 0.001). Conclusion: Self-expanding stents with large spaces between the wires, inserted without PTA, cause less damage to the endothelium than other stents and significantly less damage than PTA

Modelling the dispersion and transport of reactive pollutants in a deep urban street canyon: Using large-eddy simulation

International Nuclear Information System (INIS)

Zhong, Jian; Cai, Xiao-Ming; Bloss, William James

2015-01-01

This study investigates the dispersion and transport of reactive pollutants in a deep urban street canyon with an aspect ratio of 2 under neutral meteorological conditions using large-eddy simulation. The spatial variation of pollutants is significant due to the existence of two unsteady vortices. The deviation of species abundance from chemical equilibrium for the upper vortex is greater than that for the lower vortex. The interplay of dynamics and chemistry is investigated using two metrics: the photostationary state defect, and the inferred ozone production rate. The latter is found to be negative at all locations within the canyon, pointing to a systematic negative offset to ozone production rates inferred by analogous approaches in environments with incomplete mixing of emissions. This study demonstrates an approach to quantify parameters for a simplified two-box model, which could support traffic management and urban planning strategies and personal exposure assessment. - Highlights: • Large-eddy simulation reproduces two unsteady vortices seen in a lab experiment. • Reactive pollutants in an urban street canyon exhibit significant spatial variation. • O 3 production rate inferred by the NO x -O 3 -steady-state-defect approach is discussed. • Ground level sourced pollutants are largely trapped within the lower vortex. • A method of quantifying parameters of a two-box model is developed. - Reactive pollutants in a deep street canyon exhibit significant spatial variation driven by two unsteady vortices. A method of quantifying parameters of a two-box model is developed

Women's Health Insurance Coverage

Science.gov (United States)

... Women's Health Policy Women’s Health Insurance Coverage Women’s Health Insurance Coverage Published: Oct 31, 2017 Facebook Twitter LinkedIn ... that many women continue to face. Sources of Health Insurance Coverage Employer-Sponsored Insurance: Approximately 57.9 million ...

Heterogeneous transgene expression in the retinas of the TH-RFP, TH-Cre, TH-BAC-Cre and DAT-Cre mouse lines.

Science.gov (United States)

Vuong, H E; Pérez de Sevilla Müller, L; Hardi, C N; McMahon, D G; Brecha, N C

2015-10-29

Transgenic mouse lines are essential tools for understanding the connectivity, physiology and function of neuronal circuits, including those in the retina. This report compares transgene expression in the retina of a tyrosine hydroxylase (TH)-red fluorescent protein (RFP) mouse line with three catecholamine-related Cre recombinase mouse lines [TH-bacterial artificial chromosome (BAC)-, TH-, and dopamine transporter (DAT)-Cre] that were crossed with a ROSA26-tdTomato reporter line. Retinas were evaluated and immunostained with commonly used antibodies including those directed to TH, GABA and glycine to characterize the RFP or tdTomato fluorescent-labeled amacrine cells, and an antibody directed to RNA-binding protein with multiple splicing to identify ganglion cells. In TH-RFP retinas, types 1 and 2 dopamine (DA) amacrine cells were identified by their characteristic cellular morphology and type 1 DA cells by their expression of TH immunoreactivity. In the TH-BAC-, TH-, and DAT-tdTomato retinas, less than 1%, ∼ 6%, and 0%, respectively, of the fluorescent cells were the expected type 1 DA amacrine cells. Instead, in the TH-BAC-tdTomato retinas, fluorescently labeled AII amacrine cells were predominant, with some medium diameter ganglion cells. In TH-tdTomato retinas, fluorescence was in multiple neurochemical amacrine cell types, including four types of polyaxonal amacrine cells. In DAT-tdTomato retinas, fluorescence was in GABA immunoreactive amacrine cells, including two types of bistratified and two types of monostratified amacrine cells. Although each of the Cre lines was generated with the intent to specifically label DA cells, our findings show a cellular diversity in Cre expression in the adult retina and indicate the importance of careful characterization of transgene labeling patterns. These mouse lines with their distinctive cellular labeling patterns will be useful tools for future studies of retinal function and visual processing. Published by Elsevier

Construction of a Bacterial Artificial Chromosome Library of TM-1, a Standard Line for Genetics and Genomics in Upland Cotton

Institute of Scientific and Technical Information of China (English)

Yan Hu; Wang-Zhen Guo; Tian-Zhen Zhang

2009-01-01

A bacterial artificial chromosome (BAC) library was constructed for Gossyplum hirsutum acc. TM-1, a genetic and genomic standard line for Upland cotton. The library consists of 147 456 clones with an average insert size of 122.8 kb ranging from 97 to 240 kb. About 96.0% of the clones have inserts over 100 kb. Therefore, this library represents theoretically 7.4 haploid genome equivalents based on an AD genome size of 2 425 Mb. Clones were stored in 384 384- well plates and arrayed into multiplex pools for rapid and reliable library screening. BAC screening was carded out by four-round polymerase chain reactions using 23 simple sequence repeats (SSR) markers, three sequence-related amplified polymorphism markers and one pair of pdmere for a gene associated with fiber development to test the quality of the library. Correspondingly, in total 92 positive BAC clones were Identified with an average four positive clones per SSR marker, ranging from one to eight hits. Additionally, since these SSR markers have been localized to chromosome 12 (A12) and 26 (D12) according to the genetic map, these BAC clonee are expected to serve as seeds for the physical mapping of these two homologous chromosomes, sequentially map-based cloning of quantitative trait loci or genes associated with Important agronomic traits.

Religious subgroups influencing vaccination coverage in the Dutch Bible belt: an ecological study.

Science.gov (United States)

Ruijs, Wilhelmina L M; Hautvast, Jeannine L A; van der Velden, Koos; de Vos, Sjoerd; Knippenberg, Hans; Hulscher, Marlies E J L

2011-02-14

The Netherlands has experienced epidemics of vaccine preventable diseases largely confined to the Bible belt, an area where -among others- orthodox protestant groups are living. Lacking information on the vaccination coverage in this minority, and its various subgroups, control of vaccine preventable diseases is focused on the geographical area of the Bible belt. However, the adequacy of this strategy is questionable. This study assesses the influence of presence of various orthodox protestant subgroups (orthodox protestant denominations, OPDs) on municipal vaccination coverage in the Bible belt. We performed an ecological study at municipality level. Data on number of inhabitants, urbanization level, socio-economical status, immigration and vaccination coverage were obtained from national databases. As religion is not registered in the Netherlands, membership numbers of the OPDs had to be obtained from church year books and via church offices. For all municipalities in the Netherlands, the effect of presence or absence of OPDs on vaccination coverage was assessed by comparing mean vaccination coverage. For municipalities where OPDs were present, the effect of each of them (measured as membership ratio, the number of members proportional to total number of inhabitants) on vaccination coverage was assessed by bivariate correlation and multiple regression analysis in a model containing the determinants immigration, socio-economical status and urbanization as well. Mean vaccination coverage (93.5% ± 4.7) in municipalities with OPDs (n = 135) was significantly lower (p < 0.001) than in 297 municipalities without OPDs (96.9% ± 2.1). Multiple regression analyses showed that in municipalities with OPDs 84% of the variance in vaccination coverage was explained by the presence of these OPDs. Immigration had a significant, but small explanatory effect as well. Membership ratios of all OPDs were negatively related to vaccination coverage; this relationship was strongest for

[Comparison of the Latissimus dorsi insertions on the iliac crest in chimpanzee (Pan troglodytes) and in man].

Science.gov (United States)

Vacher, C; Ben Hadj Yahia, S; Braun, M; Journeau, P

2014-03-01

Comparing to other primates, one of the most important specificities of the human anatomy are consequences of bipedalism. Although bone consequences are well known (lumbar lordosis, horizontal position of the foramen magnum, lengthening of the lower limbs, reduction of the pelvis, specialization of the foot), consequences of our locomotion on the Latissimus dorsi are still unclear. One dissection of a chimpanzee Latissimus dorsi (Pan troglodytes) has been performed and compared to 30 human Latissimus dorsi dissections (10 fresh cadavers and 20 formoled cadavers). In each dissection, the existence of direct muscular insertions on the iliac crest has been investigated and the constitution of the thoracolumbar fascia has been described. In chimpanzee dissection, a muscular direct insertion of the Latissimus dorsi was present on the iliac crest of 9 cm long. The TLF was made of the superficial and the deep fascias of the Latissimus dorsi and the superficial fascia of the erector spinae muscles which was deeper. In man, there was no direct muscular insertion of the Latissimus dorsi in 90 % of cases, the TLF was constituted the same way. This study suggests that the Latissimus dorsi has been separated from the iliac crest in man during the evolution because of the permanent bipedalism and that it stayed inserted on the iliac crest in chimpanzee because of the brachiation. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

ISABELLE insertion quadrupoles

International Nuclear Information System (INIS)

Kaugerts, J.; Polk, I.; Sampson, W.; Dahl, P.F.

1979-01-01

Beam focussing and control at the beam intersection regions of ISABELLE is accomplished by a number of superconducting insertion quadrupoles. These magnets differ from the standard ISABELLE quadrupoles in various ways. In particular, the requirements of limited space near the intersections and aperture for beam extraction impose constraints on their configuration. To achieve optimum beam focussing and provide tuning flexibility calls for stronger quadrupole trim windings than those in the standard quadrupoles. The magnetic and mechanical design of the insertion quadrupoles and their associated correction and steering windings to accomplish the above tasks is presented

A multiple objective magnet sorting algorithm for the Advanced Light Source insertion devices

International Nuclear Information System (INIS)

Humphries, D.; Goetz, F.; Kownacki, P.; Marks, S.; Schlueter, R.

1995-01-01

Insertion devices for the Advanced Light Source (ALS) incorporate large numbers of permanent magnets which have a variety of magnetization orientation errors. These orientation errors can produce field errors which affect both the spectral brightness of the insertion devices and the storage ring electron beam dynamics. A perturbation study was carried out to quantify the effects of orientation errors acting in a hybrid magnetic structure. The results of this study were used to develop a multiple stage sorting algorithm which minimizes undesirable integrated field errors and essentially eliminates pole excitation errors. When applied to a measured magnet population for an existing insertion device, an order of magnitude reduction in integrated field errors was achieved while maintaining near zero pole excitation errors

Generating resources for genomics of wheat homoeologous chromosome group 3: 3AS- and 3DS-specific BAC libraries

Czech Academy of Sciences Publication Activity Database

Šafář, Jan; Šimková, Hana; Kubaláková, Marie; Suchánková, Pavla; Čihalíková, Jarmila; Bartoš, Jan; Fiocchetti, F.; Roselli, M.; Gill, B. S.; Doležel, Jaroslav; Lucretti, S.

2009-01-01

Roč. 61, 1-2 (2009), s. 151-160 ISSN 0394-9257 R&D Projects: GA ČR GD521/05/H013; GA ČR GA521/06/1723; GA ČR GA521/07/1573; GA MŠk(CZ) LC06004; GA MŠk OC08025 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC library * Flow sorting * Homoeologous chromosomes Subject RIV: GE - Plant Breeding

Investigating the Influences of Tree Coverage and Road Density on Property Crime

Directory of Open Access Journals (Sweden)

Chengming Ye

2018-03-01

Full Text Available With the development of Geographic Information Systems (GIS, crime mapping has become an effective approach for investigating the spatial pattern of crime in a defined area. Understanding the relationship between crime and its surrounding environment reveals possible strategies for reducing crime in a neighborhood. The relationship between vegetation density and crime has long been under debate. The convenience of a road network is another important factor that can influence a criminal’s selection of locations. This research is conducted to investigate the correlations between tree coverage and property crime, and road density and property crime in the City of Vancouver. High spatial resolution airborne LiDAR data and road network data collected in 2013 were used to extract tree covered areas for cross-sectional analysis. The independent variables were inserted into Ordinary Least-Squares (OLS regression, Spatial Lag regression, and Geographically Weighted Regression (GWR models to examine their relationships to property crime rates. The results of the cross-sectional analysis provide statistical evidence that there are negative correlations between property crime rates and both tree coverage and road density, with the stronger correlations occurring around Downtown Vancouver.

Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster

Science.gov (United States)

Adrion, Jeffrey R.; Song, Michael J.; Schrider, Daniel R.; Hahn, Matthew W.

2017-01-01

Abstract Knowing the rate at which transposable elements (TEs) insert and delete is critical for understanding their role in genome evolution. We estimated spontaneous rates of insertion and deletion for all known, active TE superfamilies present in a set of Drosophila melanogaster mutation-accumulation (MA) lines using whole genome sequence data. Our results demonstrate that TE insertions far outpace TE deletions in D. melanogaster. We found a significant effect of background genotype on TE activity, with higher rates of insertions in one MA line. We also found significant rate heterogeneity between the chromosomes, with both insertion and deletion rates elevated on the X relative to the autosomes. Further, we identified significant associations between TE activity and chromatin state, and tested for associations between TE activity and other features of the local genomic environment such as TE content, exon content, GC content, and recombination rate. Our results provide the most detailed assessment of TE mobility in any organism to date, and provide a useful benchmark for both addressing theoretical predictions of TE dynamics and for exploring large-scale patterns of TE movement in D. melanogaster and other species. PMID:28338986

A Max-Flow Based Algorithm for Connected Target Coverage with Probabilistic Sensors

Directory of Open Access Journals (Sweden)

Anxing Shan

2017-05-01

Full Text Available Coverage is a fundamental issue in the research field of wireless sensor networks (WSNs. Connected target coverage discusses the sensor placement to guarantee the needs of both coverage and connectivity. Existing works largely leverage on the Boolean disk model, which is only a coarse approximation to the practical sensing model. In this paper, we focus on the connected target coverage issue based on the probabilistic sensing model, which can characterize the quality of coverage more accurately. In the probabilistic sensing model, sensors are only be able to detect a target with certain probability. We study the collaborative detection probability of target under multiple sensors. Armed with the analysis of collaborative detection probability, we further formulate the minimum ϵ-connected target coverage problem, aiming to minimize the number of sensors satisfying the requirements of both coverage and connectivity. We map it into a flow graph and present an approximation algorithm called the minimum vertices maximum flow algorithm (MVMFA with provable time complex and approximation ratios. To evaluate our design, we analyze the performance of MVMFA theoretically and also conduct extensive simulation studies to demonstrate the effectiveness of our proposed algorithm.

Azimuthal asymmetries in semi-inclusive deep-inelastic hadron muoproduction on longitudinally polarized protons

Energy Technology Data Exchange (ETDEWEB)

Sirtl, Stefan

2016-06-27

In recent years, measuring azimuthal asymmetries in semi-inclusive deep-inelastic scattering (SIDIS) off polarized targets emerged as a powerful tool to investigate the nucleon spin structure, one of the main objectives of the COMPASS physics program. The two-stage COMPASS spectrometer at the CERN SPS is characterized by a large acceptance and a broad kinematic coverage. It makes use of a tertiary longitudinally polarized high-energetic μ{sup +} beam, impinging on a transversely or longitudinally polarized ammonia target. This thesis is dedicated to the analysis of both leading and subleading longitudinal target spin dependent asymmetries arising in the SIDIS cross section of one hadron and hadron pair production. The results provide new insights to the longitudinal spin structure of the nucleon, addressing the role of spin-orbit couplings and quark-gluon correlations in the framework of collinear or transverse momentum dependent factorization.

Fine mapping of the sunflower resistance locus Pl(ARG) introduced from the wild species Helianthus argophyllus.

Science.gov (United States)

Wieckhorst, S; Bachlava, E; Dussle, C M; Tang, S; Gao, W; Saski, C; Knapp, S J; Schön, C-C; Hahn, V; Bauer, E

2010-11-01

Downy mildew, caused by Plasmopara halstedii, is one of the most destructive diseases in cultivated sunflower (Helianthus annuus L.). The dominant resistance locus Pl(ARG) originates from silverleaf sunflower (H. argophyllus Torrey and Gray) and confers resistance to all known races of P. halstedii. We mapped Pl(ARG) on linkage group (LG) 1 of (cms)HA342 × ARG1575-2, a population consisting of 2,145 F(2) individuals. Further, we identified resistance gene candidates (RGCs) that cosegregated with Pl(ARG) as well as closely linked flanking markers. Markers from the target region were mapped with higher resolution in NDBLOS(sel) × KWS04, a population consisting of 2,780 F(2) individuals that does not segregate for Pl(ARG). A large-insert sunflower bacterial artificial chromosome (BAC) library was screened with overgo probes designed for markers RGC52 and RGC151, which cosegregated with Pl(ARG). Two RGC-containing BAC contigs were anchored to the Pl(ARG) region on LG 1.

Sequential cooling insert for turbine stator vane

Science.gov (United States)

Jones, Russel B

2017-04-04

A sequential flow cooling insert for a turbine stator vane of a small gas turbine engine, where the impingement cooling insert is formed as a single piece from a metal additive manufacturing process such as 3D metal printing, and where the insert includes a plurality of rows of radial extending impingement cooling air holes alternating with rows of radial extending return air holes on a pressure side wall, and where the insert includes a plurality of rows of chordwise extending second impingement cooling air holes on a suction side wall. The insert includes alternating rows of radial extending cooling air supply channels and return air channels that form a series of impingement cooling on the pressure side followed by the suction side of the insert.

Deletion of the budBAC operon in Klebsiella pneumoniae to understand the physiological role of 2,3-butanediol biosynthesis.

Science.gov (United States)

Jeong, Daun; Yang, Jeongmo; Lee, Soojin; Kim, Borim; Um, Youngsoon; Kim, Youngrok; Ha, Kyoung-Su; Lee, Jinwon

2016-05-18

Klebsiella pneumoniae is known to produce 2,3-butanediol (2,3-BDO), a valuable chemical. In K. pneumoniae, the 2,3-BDO operon (budBAC) is involved in the production of 2,3-BDO. To observe the physiological role of the 2,3-BDO operon in a mixed acid fermentation, we constructed a budBAC-deleted strain (SGSB109). The production of extracellular metabolites, CO2 emission, carbon distribution, and NADH/NAD(+) balance of SGSB109 were compared with the parent strain (SGSB100). When comparing the carbon distribution at 15 hr, four significant differences were observed: in 2,3-BDO biosynthesis, lactate and acetate production (lactate and acetate production increased 2.3-fold and 4.1-fold in SGSB109 compared to SGSB100), CO2 emission (higher in SGSB100), and carbon substrate uptake (higher in SGSB100). Previous studies on the inactivation of the 2,3-BDO operon were focused on the increase of 1,3-propanediol production. Few studies have been done observing the role of 2,3-BDO biosynthesis. This study provides a prime insight into the role of 2,3-BDO biosynthesis of K. pneumoniae.

Fuel insert shuffler

International Nuclear Information System (INIS)

Naser, J.; Colley, R.; Gaiser, J.; Brookmire, T.; Engle, S.

1987-01-01

The potential for the use of expert systems in the nuclear power industry is widely recognized. The benefits of such systems include consistency of reasoning during off-normal situations when humans are under great stress, the reduction of time required to perform certain functions and the retention of human expertise in performing specialized functions. As the potential benefits are more and more demonstrated and realized, the development of expert systems becomes a necessary part of the nuclear power industry. The development of the fuel insert shuffle expert system is used as a case study. In fact, it shows that the potential benefits are realizable. Currently, the development of the insert shuffle plan requires three to four man-weeks of effort. Further modifications to this plan are sometimes required dur to either changes in the desired core load pattern or damaged fuel assemblies or inserts. These changes generally require two to four man-days of effort and could be stressful if they are critical path items on the outage schedule

Contemporary deep recurrent learning for recognition

Science.gov (United States)

Iftekharuddin, K. M.; Alam, M.; Vidyaratne, L.

2017-05-01

Large-scale feed-forward neural networks have seen intense application in many computer vision problems. However, these networks can get hefty and computationally intensive with increasing complexity of the task. Our work, for the first time in literature, introduces a Cellular Simultaneous Recurrent Network (CSRN) based hierarchical neural network for object detection. CSRN has shown to be more effective to solving complex tasks such as maze traversal and image processing when compared to generic feed forward networks. While deep neural networks (DNN) have exhibited excellent performance in object detection and recognition, such hierarchical structure has largely been absent in neural networks with recurrency. Further, our work introduces deep hierarchy in SRN for object recognition. The simultaneous recurrency results in an unfolding effect of the SRN through time, potentially enabling the design of an arbitrarily deep network. This paper shows experiments using face, facial expression and character recognition tasks using novel deep recurrent model and compares recognition performance with that of generic deep feed forward model. Finally, we demonstrate the flexibility of incorporating our proposed deep SRN based recognition framework in a humanoid robotic platform called NAO.

CoverageAnalyzer (CAn: A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles

Directory of Open Access Journals (Sweden)

Ralf Hauenschild

2016-11-01

Full Text Available Combination of reverse transcription (RT and deep sequencing has emerged as a powerful instrument for the detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures of modified ribonucleotides relying on both sequence-dependent mismatch patterns and reverse transcription arrests. Common alignment viewers lack specialized functionality, such as filtering, tailored visualization, image export and differential analysis. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer (CAn was developed in response to the demand for a powerful inspection tool. It is freely available for all three main operating systems. With SAM file format as standard input, CAn is an intuitive and user-friendly tool that is generally applicable to the large community of biomedical users, starting from simple visualization of RNA sequencing (RNA-Seq data, up to sophisticated modification analysis with significance-based modification candidate calling.

Files synchronization from a large number of insertions and deletions

Science.gov (United States)

Ellappan, Vijayan; Kumari, Savera

2017-11-01

Synchronization between different versions of files is becoming a major issue that most of the applications are facing. To make the applications more efficient a economical algorithm is developed from the previously used algorithm of “File Loading Algorithm”. I am extending this algorithm in three ways: First, dealing with non-binary files, Second backup is generated for uploaded files and lastly each files are synchronized with insertions and deletions. User can reconstruct file from the former file with minimizing the error and also provides interactive communication by eliminating the frequency without any disturbance. The drawback of previous system is overcome by using synchronization, in which multiple copies of each file/record is created and stored in backup database and is efficiently restored in case of any unwanted deletion or loss of data. That is, to introduce a protocol that user B may use to reconstruct file X from file Y with suitably low probability of error. Synchronization algorithms find numerous areas of use, including data storage, file sharing, source code control systems, and cloud applications. For example, cloud storage services such as Drop box synchronize between local copies and cloud backups each time users make changes to local versions. Similarly, synchronization tools are necessary in mobile devices. Specialized synchronization algorithms are used for video and sound editing. Synchronization tools are also capable of performing data duplication.

Constructing Long Short-Term Memory based Deep Recurrent Neural Networks for Large Vocabulary Speech Recognition

OpenAIRE

Li, Xiangang; Wu, Xihong

2014-01-01

Long short-term memory (LSTM) based acoustic modeling methods have recently been shown to give state-of-the-art performance on some speech recognition tasks. To achieve a further performance improvement, in this research, deep extensions on LSTM are investigated considering that deep hierarchical model has turned out to be more efficient than a shallow one. Motivated by previous research on constructing deep recurrent neural networks (RNNs), alternative deep LSTM architectures are proposed an...

Building high-coverage monolayers of covalently bound magnetic nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Williams, Mackenzie G.; Teplyakov, Andrew V., E-mail: andrewt@udel.edu

2016-12-01

Graphical abstract: - Highlights: • A method for forming a layer of covalently bound nanoparticles is offered. • A nearly perfect monolayer of covalently bound magnetic nanoparticles was formed on gold. • Spectroscopic techniques confirmed covalent binding by the “click” reaction. • The influence of the functionalization scheme on surface coverage was investigated. - Abstract: This work presents an approach for producing a high-coverage single monolayer of magnetic nanoparticles using “click chemistry” between complementarily functionalized nanoparticles and a flat substrate. This method highlights essential aspects of the functionalization scheme for substrate surface and nanoparticles to produce exceptionally high surface coverage without sacrificing selectivity or control over the layer produced. The deposition of one single layer of magnetic particles without agglomeration, over a large area, with a nearly 100% coverage is confirmed by electron microscopy. Spectroscopic techniques, supplemented by computational predictions, are used to interrogate the chemistry of the attachment and to confirm covalent binding, rather than attachment through self-assembly or weak van der Waals bonding. Density functional theory calculations for the surface intermediate of this copper-catalyzed process provide mechanistic insight into the effects of the functionalization scheme on surface coverage. Based on this analysis, it appears that steric limitations of the intermediate structure affect nanoparticle coverage on a flat solid substrate; however, this can be overcome by designing a functionalization scheme in such a way that the copper-based intermediate is formed on the spherical nanoparticles instead. This observation can be carried over to other approaches for creating highly controlled single- or multilayered nanostructures of a wide range of materials to result in high coverage and possibly, conformal filling.

Proteolytic cleavage orchestrates cofactor insertion and protein assembly in [NiFe]-hydrogenase biosynthesis.

Science.gov (United States)

Senger, Moritz; Stripp, Sven T; Soboh, Basem

2017-07-14

Metalloenzymes catalyze complex and essential processes, such as photosynthesis, respiration, and nitrogen fixation. For example, bacteria and archaea use [NiFe]-hydrogenases to catalyze the uptake and release of molecular hydrogen (H 2 ). [NiFe]-hydrogenases are redox enzymes composed of a large subunit that harbors a NiFe(CN) 2 CO metallo-center and a small subunit with three iron-sulfur clusters. The large subunit is synthesized with a C-terminal extension, cleaved off by a specific endopeptidase during maturation. The exact role of the C-terminal extension has remained elusive; however, cleavage takes place exclusively after assembly of the [NiFe]-cofactor and before large and small subunits form the catalytically active heterodimer. To unravel the functional role of the C-terminal extension, we used an enzymatic in vitro maturation assay that allows synthesizing functional [NiFe]-hydrogenase-2 of Escherichia coli from purified components. The maturation process included formation and insertion of the NiFe(CN) 2 CO cofactor into the large subunit, endoproteolytic cleavage of the C-terminal extension, and dimerization with the small subunit. Biochemical and spectroscopic analysis indicated that the C-terminal extension of the large subunit is essential for recognition by the maturation machinery. Only upon completion of cofactor insertion was removal of the C-terminal extension observed. Our results indicate that endoproteolytic cleavage is a central checkpoint in the maturation process. Here, cleavage temporally orchestrates cofactor insertion and protein assembly and ensures that only cofactor-containing protein can continue along the assembly line toward functional [NiFe]-hydrogenase. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Regulatory issues for deep borehole plutonium disposition

International Nuclear Information System (INIS)

Halsey, W.G.

1995-03-01

As a result of recent changes throughout the world, a substantial inventory of excess separated plutonium is expected to result from dismantlement of US nuclear weapons. The safe and secure management and eventual disposition of this plutonium, and of a similar inventory in Russia, is a high priority. A variety of options (both interim and permanent) are under consideration to manage this material. The permanent solutions can be categorized into two broad groups: direct disposal and utilization. The deep borehole disposition concept involves placing excess plutonium deep into old stable rock formations with little free water present. Issues of concern include the regulatory, statutory and policy status of such a facility, the availability of sites with desirable characteristics and the technologies required for drilling deep holes, characterizing them, emplacing excess plutonium and sealing the holes. This white paper discusses the regulatory issues. Regulatory issues concerning construction, operation and decommissioning of the surface facility do not appear to be controversial, with existing regulations providing adequate coverage. It is in the areas of siting, licensing and long term environmental protection that current regulations may be inappropriate. This is because many current regulations are by intent or by default specific to waste forms, facilities or missions significantly different from deep borehole disposition of excess weapons usable fissile material. It is expected that custom regulations can be evolved in the context of this mission

[Effects of slow twisting needle insertion and tubing needle insertion at Neiguan (PC 6) on cardiovascular function: a comparative study].

Science.gov (United States)

Ning, Shaoli; Zhao, Lihua; Xu, Lingjun; Huang, Yu; Pang, Yong; Huang, Dingjian

2016-01-01

To compare the effects between slow twisting needle insertion and tubing needle insertion. With cross-over design, 100 healthy young subjects (half male and half female) aged from 19 to 23 years were randomly divided into two groups by random digital table, 50 cases in each one. At the first stage, subjects in the group A were treated with slow twisting needle insertion while, subjects in,the group B were treated with tubing needle insertion. One week later, the procedure of second stage was performed alternately. The needle was inserted into Neiguan (PC 6) with two methods by one acupuncturist. The needle was retained for 5 min before removal. Five min before needle insertion as well as needle withdrawal and 30 min after needle withdrawal, ZXG-E automatic cardiovascular diagnostic apparatus was used to test cardiovascular function. At the tim of needle withdrawal, slow twisting needle insertion could improve effect work of kinetics (EWK), effective blood volume (BV) and reduce elastic expansion coefficient of blood vessel (FEK) and left ventricular spray blood impedance (VER), which was significantly different from tubing needle insertion (all P 0.05). The slow twisting needle insertion is significantly superior to tubing needle insertion on lowering vascular tension and VER, improving EWK and BV.

The characteristics of laser welded magnesium alloy using silver nanoparticles as insert material

International Nuclear Information System (INIS)

Ishak, M.; Maekawa, K.; Yamasaki, K.

2012-01-01

Highlights: ► Ag nanoparticles are used as insert material for welding Mg alloy with laser. ► We examine the microstructure and mechanical properties of welded Mg alloys. ► Nananoparticle promote grain refinement to the weld structure. ► Finer nanoparticle produces high weld efficiency and mechanical properties. - Abstract: This paper describes the characteristics of the laser welding of thin-sheet magnesium alloys using silver (Ag) nanoparticles as an insert material. The experiment was conducted using nanoparticles with 5 nm and 100 nm diameters that were welded with a Nd:YAG laser. The microstructure and mechanical properties of the specimens welded using inserts with different sizes of nanoparticles and without an insert material, were examined. Electron probe micro-analyzer (EPMA) analysis was conducted to confirm the existence of Ag in the welded area. The introduction of the Ag nanoparticle insert promoted large area of fine grain and broadened the acceptable range of scanning speed parameters compared to welds without an insert. Welds with 5 nm nanoparticles yielded the highest fracture load of up to 818 N while the lowest fracture load was found for weld specimens with 100 nm nanoparticles. This lower fracture load was due to larger voids and a smaller throat length, which contributed to a lower fracture load when using larger nanoparticles.

DNA immunization with a herpes simplex virus 2 bacterial artificial chromosome

International Nuclear Information System (INIS)

Meseda, Clement A.; Schmeisser, Falko; Pedersen, Robin; Woerner, Amy; Weir, Jerry P.

2004-01-01

Construction of a herpes simplex virus 2 (HSV-2) bacterial artificial chromosome (BAC) is described. BAC vector sequences were inserted into the thymidine kinase gene of HSV-2 by homologous recombination. DNA from cells infected with the resulting recombinant virus was transformed into E. coli, and colonies containing the HSV-2 BAC (HSV2-BAC) were isolated and analyzed for the expected genotype. HSV2-BAC DNA was infectious when transfected back into mammalian cells and the resulting virus was thymidine kinase negative. When used to immunize mice, the HSV2-BAC DNA elicited a strong HSV-2 specific antibody response that was equal to or greater than live virus immunization. Further, HSV2-BAC immunization was protective when animals were challenged with a lethal dose of virus. The utility of the HSV2-BAC for construction of recombinant virus genomes was demonstrated by elimination of the HSV-2 glycoprotein D (gD) gene. A recombinant HSV-2 BAC with the gD gene deleted was isolated and shown to be incapable of producing infectious virus following transfection unless an HSV gD gene was expressed in a complementing cell line. Immunization of mice with the HSV2 gD-BAC also elicited an HSV-2 specific antibody response and was protective. The results demonstrate the feasibility of DNA immunization with HSV-2 bacterial artificial chromosomes for replicating and nonreplicating candidate HSV-2 vaccines, as well as the utility of BAC technology for construction and maintenance of novel HSV-2 vaccines. The results further suggest that such technology will be a powerful tool for dissecting the immune response to HSV-2

Timing of insertion of levonorgestrel-releasing intrauterine system : a randomised controlled trial

NARCIS (Netherlands)

van der Heijden, Pahh; Geomini, Pmaj; Herman, M C; Veersema, S; Bongers, M Y

OBJECTIVE: The objective was to assess whether patient-perceived pain during the insertion of the levonorgestrel-releasing intrauterine system (LNG-IUS) depends on the timing during the menstrual cycle. DESIGN: A stratified two-armed non-inferiority randomised controlled trial. SETTING: Large

Deep long-period earthquakes beneath Washington and Oregon volcanoes

Science.gov (United States)

Nichols, M.L.; Malone, S.D.; Moran, S.C.; Thelen, W.A.; Vidale, J.E.

2011-01-01

Deep long-period (DLP) earthquakes are an enigmatic type of seismicity occurring near or beneath volcanoes. They are commonly associated with the presence of magma, and found in some cases to correlate with eruptive activity. To more thoroughly understand and characterize DLP occurrence near volcanoes in Washington and Oregon, we systematically searched the Pacific Northwest Seismic Network (PNSN) triggered earthquake catalog for DLPs occurring between 1980 (when PNSN began collecting digital data) and October 2009. Through our analysis we identified 60 DLPs beneath six Cascade volcanic centers. No DLPs were associated with volcanic activity, including the 1980-1986 and 2004-2008 eruptions at Mount St. Helens. More than half of the events occurred near Mount Baker, where the background flux of magmatic gases is greatest among Washington and Oregon volcanoes. The six volcanoes with DLPs (counts in parentheses) are Mount Baker (31), Glacier Peak (9), Mount Rainier (9), Mount St. Helens (9), Three Sisters (1), and Crater Lake (1). No DLPs were identified beneath Mount Adams, Mount Hood, Mount Jefferson, or Newberry Volcano, although (except at Hood) that may be due in part to poorer network coverage. In cases where the DLPs do not occur directly beneath the volcanic edifice, the locations coincide with large structural faults that extend into the deep crust. Our observations suggest the occurrence of DLPs in these areas could represent fluid and/or magma transport along pre-existing tectonic structures in the middle crust. ?? 2010 Elsevier B.V.

The O(α{sub s}{sup 2}) heavy quark corrections to charged current deep-inelastic scattering at large virtualities

Energy Technology Data Exchange (ETDEWEB)

Blümlein, Johannes, E-mail: Johannes.Bluemlein@desy.de [Deutsches Elektronen–Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Hasselhuhn, Alexander [Deutsches Elektronen–Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Pfoh, Torsten [Deutsches Elektronen–Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany)

2014-04-15

We calculate the O(α{sub s}{sup 2}) heavy flavor corrections to charged current deep-inelastic scattering at large scales Q{sup 2}≫m{sup 2}. The contributing Wilson coefficients are given as convolutions between massive operator matrix elements and massless Wilson coefficients. Foregoing results in the literature are extended and corrected. Numerical results are presented for the kinematic region of the HERA data.

A Novel Nonlinear Multitarget k-Degree Coverage Preservation Protocol in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Zeyu Sun

2016-01-01

Full Text Available Due to the existence of a large number of redundant data in the process of covering multiple targets, the effective coverage of monitored region decreases, causing the network to consume more energy. To solve this problem, this paper proposes a multitarget k-degree coverage preservation protocol. Firstly, the affiliation between the sensor nodes and target nodes is established in the network model; meanwhile the method used to calculate the coverage expectation value of the monitored region is put forward; secondly, in the aspect of the network energy conversion, use scheduling mechanisms on the sensor nodes to balance the network energy and achieve different network coverage quality with energy conversion between different nodes. Finally, simulation results show that NMCP can improve the network lifetime by effectively reducing the number of active nodes to meet certain coverage requirements.

Evolution of the large Deep Space Network antennas

Science.gov (United States)

Imbriale, William A.

1991-12-01

The evolution of the largest antenna of the US NASA Deep Space Network (DSN) is described. The design, performance analysis, and measurement techniques, beginning with its initial 64-m operation at S-band (2295 MHz) in 1966 and continuing through the present ka-band (32-GHz) operation at 70 m, is described. Although their diameters and mountings differ, these parabolic antennas all employ a Cassegrainian feed system, and each antenna dish surface is constructed of precision-shaped perforated-aluminum panels that are secured to an open steel framework

Postcolonial partnerships: deep sea research, media coverage and (inter)national narratives on the Galathea Deep Sea Expedition from 1950 to 1952.

Science.gov (United States)

Nielsen, Kristian Hvidtfelt

2010-03-01

The Danish Galathea Deep Sea Expedition between 1950 and 1952 combined scientific and official objectives with the production of national and international narratives distributed through the daily press and other media. Dispatched by the Danish government on a newly acquired naval ship, the expedition undertook groundbreaking deep sea research while also devoting efforts to showing the flag, public communication of science, and international cooperation. The expedition was conceived after the war as a way in which to rehabilitate Denmark's reputation internationally and to rebuild national pride. To this end, the expedition included an onboard press section reporting the expedition to the Danish public and to an international audience. The press section mediated the favourable, post-war and postcolonial image of Denmark as an internationalist, scientific, modernizing and civilizing nation for which the expedition planners and many others were hoping. The expedition, therefore, was highly relevant to, indeed fed on, the emerging internationalist agenda in Denmark's foreign policy. Bringing out these aspects of the historical context of the expedition, this paper adds important perspectives to our knowledge about the expedition in particular and, more generally, about scientific exploration in the immediate post-war and postcolonial period.