Unjoined primary and secondary neural tubes: junctional neural tube defect, a new form of spinal dysraphism caused by disturbance of junctional neurulation.

PubMed

Eibach, Sebastian; Moes, Greg; Hou, Yong Jin; Zovickian, John; Pang, Dachling

2017-10-01

Primary and secondary neurulation are the two known processes that form the central neuraxis of vertebrates. Human phenotypes of neural tube defects (NTDs) mostly fall into two corresponding categories consistent with the two types of developmental sequence: primary NTD features an open skin defect, an exposed, unclosed neural plate (hence an open neural tube defect, or ONTD), and an unformed or poorly formed secondary neural tube, and secondary NTD with no skin abnormality (hence a closed NTD) and a malformed conus caudal to a well-developed primary neural tube. We encountered three cases of a previously unrecorded form of spinal dysraphism in which the primary and secondary neural tubes are individually formed but are physically separated far apart and functionally disconnected from each other. One patient was operated on, in whom both the lumbosacral spinal cord from primary neurulation and the conus from secondary neurulation are each anatomically complete and endowed with functioning segmental motor roots tested by intraoperative triggered electromyography and direct spinal cord stimulation. The remarkable feature is that the two neural tubes are unjoined except by a functionally inert, probably non-neural band. The developmental error of this peculiar malformation probably occurs during the critical transition between the end of primary and the beginning of secondary neurulation, in a stage aptly called junctional neurulation. We describe the current knowledge concerning junctional neurulation and speculate on the embryogenesis of this new class of spinal dysraphism, which we call junctional neural tube defect.

Hardware-in-the-loop grid simulator system and method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fox, John Curtiss; Collins, Edward Randolph; Rigas, Nikolaos

A hardware-in-the-loop (HIL) electrical grid simulation system and method that combines a reactive divider with a variable frequency converter to better mimic and control expected and unexpected parameters in an electrical grid. The invention provides grid simulation in a manner to allow improved testing of variable power generators, such as wind turbines, and their operation once interconnected with an electrical grid in multiple countries. The system further comprises an improved variable fault reactance (reactive divider) capable of providing a variable fault reactance power output to control a voltage profile, therein creating an arbitrary recovery voltage. The system further comprises anmore » improved isolation transformer designed to isolate zero-sequence current from either a primary or secondary winding in a transformer or pass the zero-sequence current from a primary to a secondary winding.« less

Dynamics in supercooled polyalcohols: Primary and secondary relaxation

NASA Astrophysics Data System (ADS)

Döß, A.; Paluch, M.; Sillescu, H.; Hinze, G.

2002-10-01

We have studied details of the molecular dynamics in a series of pure polyalcohols by means of dielectric spectroscopy and 2H nuclear magnetic resonance (NMR). From glycerol to threitol, xylitol and sorbitol a systematic change in the dynamics of the primary and secondary relaxation is found. With increasing molecular weight and fragility an increase in the width of the α-peak is observed. Details of the molecular reorientation process responsible for the α-relaxation were exploited by two-dimensional NMR experiments. It is found that in the same sequence of polyalcohols the appearance of the secondary relaxation changes gradually from a wing type scenario to a pronounced β-peak. From NMR experiments using selectively deuterated samples the molecular origin of the secondary relaxation could be elucidated in more detail.

Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas.

PubMed

Phi, Ji Hoon; Park, Ae Kyung; Lee, Semin; Choi, Seung Ah; Baek, In-Pyo; Kim, Pora; Kim, Eun-Hye; Park, Hee Chul; Kim, Byung Chul; Bhak, Jong; Park, Sung-Hye; Lee, Ji Yeoun; Wang, Kyu-Chang; Kim, Dong-Seok; Shim, Kyu Won; Kim, Se Hoon; Kim, Chae-Yong; Kim, Seung-Ki

2018-06-01

Despite great advances in understanding of molecular pathogenesis and achievement of a high cure rate in medulloblastoma, recurrent medulloblastomas are still dismal. Additionally, misidentification of secondary malignancies due to histological ambiguity leads to misdiagnosis and eventually to inappropriate treatment. Nevertheless, the genomic characteristics of recurrent medulloblastomas are poorly understood, largely due to a lack of matched primary and recurrent tumor tissues. We performed a genomic analysis of recurrent tumors from 17 pediatric medulloblastoma patients. Whole transcriptome sequencing revealed that a subset of recurrent tumors initially diagnosed as locally recurrent medulloblastomas are secondary glioblastomas after radiotherapy, showing high similarity to the non-G-CIMP proneural subtype of glioblastoma. Further analysis, including whole exome sequencing, revealed missense mutations or complex gene fusion events in PDGFRA with augmented expression in the secondary glioblastomas after radiotherapy, implicating PDGFRA as a putative driver in the development of secondary glioblastomas after treatment exposure. This result provides insight into the possible application of PDGFRA-targeted therapy in these second malignancies. Furthermore, genomic alterations of TP53 including 17p loss or germline/somatic mutations were also found in most of the secondary glioblastomas after radiotherapy, indicating a crucial role of TP53 alteration in the process. On the other hand, analysis of recurrent medulloblastomas revealed that the most prevalent alterations are the loss of 17p region including TP53 and gain of 7q region containing EZH2 which already exist in primary tumors. The 7q gain events are frequently accompanied by high expression levels of EZH2 in both primary and recurrent medulloblastomas, which provides a clue to a new therapeutic target to prevent recurrence. Considering the fact that it is often challenging to differentiate between recurrent medulloblastomas and secondary glioblastomas after radiotherapy, our findings have major clinical implications both for correct diagnosis and for potential therapeutic interventions in these devastating diseases.

Zygotic amplification of secondary piRNAs during silkworm embryogenesis

PubMed Central

Kawaoka, Shinpei; Arai, Yuji; Kadota, Koji; Suzuki, Yutaka; Hara, Kahori; Sugano, Sumio; Shimizu, Kentaro; Tomari, Yukihide; Shimada, Toru; Katsuma, Susumu

2011-01-01

PIWI-interacting RNAs (piRNAs) are 23–30-nucleotide-long small RNAs that act as sequence-specific silencers of transposable elements in animal gonads. In flies, genetics and deep sequencing data have led to a hypothesis for piRNA biogenesis called the ping-pong cycle, where antisense primary piRNAs initiate an amplification loop to generate sense secondary piRNAs. However, to date, the process of the ping-pong cycle has never been monitored at work. Here, by large-scale profiling of piRNAs from silkworm ovary and embryos of different developmental stages, we demonstrate that maternally inherited antisense-biased piRNAs trigger acute amplification of secondary sense piRNA production in zygotes, at a time coinciding with zygotic transcription of sense transposon mRNAs. These results provide on-site evidence for the ping-pong cycle. PMID:21628432

Unraveling systematic inventory of Echinops (Asteraceae) with special reference to nrDNA ITS sequence-based molecular typing of Echinops abuzinadianus.

PubMed

Ali, M A; Al-Hemaid, F M; Lee, J; Hatamleh, A A; Gyulai, G; Rahman, M O

2015-10-02

The present study explored the systematic inventory of Echinops L. (Asteraceae) of Saudi Arabia, with special reference to the molecular typing of Echinops abuzinadianus Chaudhary, an endemic species to Saudi Arabia, based on the internal transcribed spacer (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA. A sequence similarity search using BLAST and a phylogenetic analysis of the ITS sequence of E. abuzinadianus revealed a high level of sequence similarity with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. abuzinadianus could potentially be used for molecular genotyping.

Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa

PubMed Central

2010-01-01

Background With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of genes that play specialized functions during each of these phases of growth. Results Using a genomic microarray representing the majority of the transcriptome, we profiled gene expression in stem segments that spanned primary to secondary growth. We found 3,016 genes that were differentially expressed during stem development (Q-value ≤ 0.05; >2-fold expression variation), and 15% of these genes encode proteins with no significant identities to known genes. We identified all gene family members putatively involved in secondary growth for carbohydrate active enzymes, tubulins, actins, actin depolymerizing factors, fasciclin-like AGPs, and vascular development-associated transcription factors. Almost 70% of expressed transcription factors were upregulated during the transition to secondary growth. The primary shoot elongation region of the stem contained specific carbohydrate active enzyme and expansin family members that are likely to function in primary cell wall synthesis and modification. Genes involved in plant defense and protective functions were also dominant in the primary growth region. Conclusion Our results describe the global patterns of gene expression that occur during the transition from primary to secondary stem growth. We were able to identify three major patterns of gene expression and over-represented gene ontology categories during stem development. The new regulatory factors and cell wall biogenesis genes that we identified provide candidate genes for further functional characterization, as well as new tools for molecular breeding and biotechnology aimed at improvement of tree growth rate, crown form, and wood quality. PMID:20199690

Finding the target sites of RNA-binding proteins

PubMed Central

Li, Xiao; Kazan, Hilal; Lipshitz, Howard D; Morris, Quaid D

2014-01-01

RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201 PMID:24217996

Origin of secondary potash deposits; a case from Miocene evaporites of NW Central Iran

NASA Astrophysics Data System (ADS)

Rahimpour-Bonab, H.; Kalantarzadeh, Z.

2005-04-01

In early Miocene times, an extensive carbonate shelf developed in Central Iran and during several cycles of sea-level fluctuations, evaporite-bearing carbonate sequences of the Qom Formation were deposited. However, in the early-middle Miocene, development of restricted marine conditions led to a facies change from shelf carbonates of the Qom Formation to the evaporite series of the M 1 member of the overlying Lower Red Formation. This member is a facies mosaic of lagoonal and salina evaporites (mainly halite beds) admixed with wadi siliciclastics. The purpose of this study, which focuses on two salt mines in the northwestern portion of Central Iran in the Zanjan province, was to reveal the origin, sedimentary environment, and diagenesis of these potash-bearing evaporite sequences. Petrographic examination revealed the following mineral assemblage: halite, gypsum, anhydrite and carnallite as primary precipitates, and langbeinite and aphthitalite as secondary metamorphic potash salts. In the Iljaq mine, distorted halite beds are dominated by burial and deformational textures and a great deal of secondary potash salts. In the Qarah-Aghaje mine, however, the bedded halite shows pristine primary textures and is devoid of the secondary potash salts. High bromine content of most evaporite minerals suggests their marine origin, and confirms the absence of the extensive meteoric alterations and subsequent bromine depletions. Potash salts are mainly secondary, and resulted from diagenetic replacements of distorted halite beds during thermal and dynamic metamorphism in a burial setting.

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

Curriculum for the Intellectually Disabled Trainable.

ERIC Educational Resources Information Center

Magnolia Special Education Center, Orlando, FL.

The curriculum guide presents a developmental sequence of learning activities to achieve specific goals for primary, intermediate, and secondary age level trainable mentally retarded students. Six major areas of learning are covered: self care (bathroom, grooming, food, clothing, safety), body usage (gross motor, health, fitness, eye-hand…

Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation

PubMed Central

Albritton, Sarah Elizabeth; Kranz, Anna-Lena; Winterkorn, Lara Heermans; Street, Lena Annika; Ercan, Sevinc

2017-01-01

In many organisms, it remains unclear how X chromosomes are specified for dosage compensation, since DNA sequence motifs shown to be important for dosage compensation complex (DCC) recruitment are themselves not X-specific. Here, we addressed this problem in C. elegans. We found that the DCC recruiter, SDC-2, is required to maintain open chromatin at a small number of primary DCC recruitment sites, whose sequence and genomic context are X-specific. Along the X, primary recruitment sites are interspersed with secondary sites, whose function is X-dependent. A secondary site can ectopically recruit the DCC when additional recruitment sites are inserted either in tandem or at a distance (>30 kb). Deletion of a recruitment site on the X results in reduced DCC binding across several megabases surrounded by topologically associating domain (TAD) boundaries. Our work elucidates that hierarchy and long-distance cooperativity between gene-regulatory elements target a single chromosome for regulation. DOI: http://dx.doi.org/10.7554/eLife.23645.001 PMID:28562241

BE Ursae Majoris: A detached binary with a unique reprocessing spectrum

NASA Technical Reports Server (NTRS)

Steiner, Joao E.; Ferguson, Donald H.; Liebert, James; Tokarz, Susan; Cutri, Roc; Green, Richard F.; Willner, S. P.

1987-01-01

New infrared photometry, optical and UV spectrophotometry, and a photographic ephemeris are presented for the detached binary BE UMa. Results show the primary to be a DO white dwarf with an effective temperature of 80,000 + or - 15,000 K and a mass of 0.6 + or - 0.1 solar masses. No evidence is found for variability of the primary. The main sequence secondary star is shown to be of early M spectral type, with a formal range of M1 to M5 being possible. A reflection effect in reprocessed line and continuum radiation is produced by EUV radiation from the primary incident on the secondary atmosphere. It is suggested that the temperature of the reprocessed component of the secondary's atmosphere is in the 5000 to 8500 K range, and that emission lines of decreasing ionization form deeper in the irradiated envelope. Relatively narrow He II and high excitation metal lines are formed from recombination and continuum fluorescence processes.

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential.

PubMed

Choque, Elodie; Klopp, Christophe; Valiere, Sophie; Raynal, José; Mathieu, Florence

2018-03-15

Black Aspergilli represent one of the most important fungal resources of primary and secondary metabolites for biotechnological industry. Having several black Aspergilli sequenced genomes should allow targeting the production of certain metabolites with bioactive properties. In this study, we report the draft genome of a black Aspergilli, A. tubingensis G131, isolated from a French Mediterranean vineyard. This 35 Mb genome includes 10,994 predicted genes. A genomic-based discovery identifies 80 secondary metabolites biosynthetic gene clusters. Genomic sequences of these clusters were blasted on 3 chosen black Aspergilli genomes: A. tubingensis CBS 134.48, A. niger CBS 513.88 and A. kawachii IFO 4308. This comparison highlights different levels of clusters conservation between the four strains. It also allows identifying seven unique clusters in A. tubingensis G131. Moreover, the putative secondary metabolites clusters for asperazine and naphtho-gamma-pyrones production were proposed based on this genomic analysis. Key biosynthetic genes required for the production of 2 mycotoxins, ochratoxin A and fumonisin, are absent from this draft genome. Even if intergenic sequences of these mycotoxins biosynthetic pathways are present, this could not lead to the production of those mycotoxins by A. tubingensis G131. Functional and bioinformatics analyses of A. tubingensis G131 genome highlight its potential for metabolites production in particular for TAN-1612, asperazine and naphtho-gamma-pyrones presenting antioxidant, anticancer or antibiotic properties.

Mineral paragenesis on Mars: The roles of reactive surface area and diffusion

PubMed Central

Gil‐Lozano, Carolina; Uceda, Esther R.; Losa‐Adams, Elisabeth; Davila, Alfonso F.; Gago‐Duport, Luis

2017-01-01

Abstract Geochemical models of secondary mineral precipitation on Mars generally assume semiopen systems (open to the atmosphere but closed at the water‐sediment interface) and equilibrium conditions. However, in natural multicomponent systems, the reactive surface area of primary minerals controls the dissolution rate and affects the precipitation sequences of secondary phases, and simultaneously, the transport of dissolved species may occur through the atmosphere‐water and water‐sediment interfaces. Here we present a suite of geochemical models designed to analyze the formation of secondary minerals in basaltic sediments on Mars, evaluating the role of (i) reactive surface areas and (ii) the transport of ions through a basalt sediment column. We consider fully open conditions, both to the atmosphere and to the sediment, and a kinetic approach for mineral dissolution and precipitation. Our models consider a geochemical scenario constituted by a basin (i.e., a shallow lake) where supersaturation is generated by evaporation/cooling and the starting point is a solution in equilibrium with basaltic sediments. Our results show that cation removal by diffusion, along with the input of atmospheric volatiles and the influence of the reactive surface area of primary minerals, plays a central role in the evolution of the secondary mineral sequences formed. We conclude that precipitation of evaporites finds more restrictions in basaltic sediments of small grain size than in basaltic sediments of greater grain size. PMID:29104844

Mineral paragenesis on Mars: The roles of reactive surface area and diffusion.

PubMed

Fairén, Alberto G; Gil-Lozano, Carolina; Uceda, Esther R; Losa-Adams, Elisabeth; Davila, Alfonso F; Gago-Duport, Luis

2017-09-01

Geochemical models of secondary mineral precipitation on Mars generally assume semiopen systems (open to the atmosphere but closed at the water-sediment interface) and equilibrium conditions. However, in natural multicomponent systems, the reactive surface area of primary minerals controls the dissolution rate and affects the precipitation sequences of secondary phases, and simultaneously, the transport of dissolved species may occur through the atmosphere-water and water-sediment interfaces. Here we present a suite of geochemical models designed to analyze the formation of secondary minerals in basaltic sediments on Mars, evaluating the role of (i) reactive surface areas and (ii) the transport of ions through a basalt sediment column. We consider fully open conditions, both to the atmosphere and to the sediment, and a kinetic approach for mineral dissolution and precipitation. Our models consider a geochemical scenario constituted by a basin (i.e., a shallow lake) where supersaturation is generated by evaporation/cooling and the starting point is a solution in equilibrium with basaltic sediments. Our results show that cation removal by diffusion, along with the input of atmospheric volatiles and the influence of the reactive surface area of primary minerals, plays a central role in the evolution of the secondary mineral sequences formed. We conclude that precipitation of evaporites finds more restrictions in basaltic sediments of small grain size than in basaltic sediments of greater grain size.

EMR Behavioral Curriculum and Student Record.

ERIC Educational Resources Information Center

Hartnett, John J.

Intended for use as a curriculum guide, a source for objectives for the individualized educational plan, and an evaluation instrument to measure handicapped students' learning, the guide lists sequences of developmental tasks. Tasks are outlined for primary, intermediate, and secondary levels in the following areas (sample subskills in…

Elementary Science 1-6.

ERIC Educational Resources Information Center

Adams, Yvonne H.; And Others

In this guide for teaching science in the Duval County Public Schools, Jacksonville, Florida, the following items are included for each grade level from one to six: (1) county-adopted resources; (2) supplementary resources; (3) scope and sequence; (4) primary ideas, secondary ideas, and performance objectives; and (5) correlation with…

Photometric Investigation of Novae T Pyx, BT Mon and V574 Pup at Quiescence by using the 2.4-m Thai National Telescope

NASA Astrophysics Data System (ADS)

Thipboon, Ritthichai; Kaewrakmuk, Metichai; Surina, Farung; Sanguansak, Nuanwan

2017-09-01

Recurrent novae (RNe) are novae with multiple recorded outbursts powered by a thermonuclear runaway. The outburst occurs on the surface of the white dwarf which accompanies with a late type main-sequence or giant secondary star transferring material onto the white dwarf primary star. They resemble classical novae (CNe) outbursts but only RNe has more than one recorded outbursts. RNe play an important role as one of the suspected progenitor systems of Type Ia supernovae (SNe) which are used as primary distance indicators in cosmology. Thus, it is important to investigate the outburst type of CNe and RNe and finally ascertain the population of objects that might ultimately be candidates for Type Ia SNe explosions. The proposal that RNe occupy a region separated from CNe in an outburst amplitude versus speed class diagram was adopted. Since the low amplitude results from the existence of an evolved secondary and/or high mass transfer rate in the quiescent system, RNe candidates should accordingly have low amplitude. We selected 3 preliminary targets including T Pyx, BT Mon and V574 Pup. Their amplitudes are not that low but the lowest amplitude that can be observed with Thai National Telescope (TNT). We obtained their magnitudes at quiescence using ULTRASPEC camera on the 2.4-m TNT. The positions of three targets on optical and near-infrared color-magnitude diagrams suggest that all three should have main-sequence secondary stars. This is true for T Pyx, whose secondary star has been confirmed its spectroscopy to be a main-sequence star, but not yet confirmed for BT Mon and V574 Pup.

Highly diverse microbiota in dental root canals in cases of apical periodontitis (data of illumina sequencing).

PubMed

Vengerfeldt, Veiko; Špilka, Katerina; Saag, Mare; Preem, Jens-Konrad; Oopkaup, Kristjan; Truu, Jaak; Mändar, Reet

2014-11-01

Chronic apical periodontitis (CAP) is a frequent condition that has a considerable effect on a patient's quality of life. We aimed to reveal root canal microbial communities in antibiotic-naive patients by applying Illumina sequencing (Illumina Inc, San Diego, CA). Samples were collected under strict aseptic conditions from 12 teeth (5 with primary CAP, 3 with secondary CAP, and 4 with a periapical abscess [PA]) and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products. Root canal specimens displayed highly polymicrobial communities in all 3 patient groups. One sample contained 5-8 (mean = 6.5) phyla of bacteria. The most numerous were Firmicutes and Bacteroidetes, but Actinobacteria, Fusobacteria, Proteobacteria, Spirochaetes, Tenericutes, and Synergistetes were also present in most of the patients. One sample contained 30-70 different operational taxonomic units; the mean (± standard deviation) was lower in the primary CAP group (36 ± 4) than in the PA (45 ± 4) and secondary CAP (43 ± 13) groups (P < .05). The communities were individually different, but anaerobic bacteria predominated as the rule. Enterococcus faecalis was found only in patients with secondary CAP. One PA sample displayed a significantly high proportion (47%) of Proteobacteria, mainly at the expense of Janthinobacterium lividum. This study provided an in-depth characterization of the microbiota of periapical tissues, revealing highly polymicrobial communities and minor differences between the study groups. A full understanding of the etiology of periodontal disease will only be possible through further in-depth systems-level analyses of the host-microbiome interaction. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Sequence of the chloroplast 16S rRNA gene and its surrounding regions of Chlamydomonas reinhardii.

PubMed Central

Dron, M; Rahire, M; Rochaix, J D

1982-01-01

The sequence of a 2 kb DNA fragment containing the chloroplast 16S ribosomal RNA gene from Chlamydomonas reinhardii and its flanking regions has been determined. The algal 16S rRNA sequence (1475 nucleotides) and secondary structure are highly related to those found in bacteria and in the chloroplasts of higher plants. In contrast, the flanking regions are very different. In C. reinhardii the 16S rRNA gene is surrounded by AT rich segments of about 180 bases, which are followed by a long stretch of complementary bases separated from each other by 1833 nucleotides. It is likely that these structures play an important role in the folding and processing of the precursor of 16S rRNA. The primary and secondary structures of the binding sites of two ribosomal proteins in the 16SrRNAs of E. coli and C. reinhardii are considerably related. Images PMID:6296784

Absolute properties of the eclipsing binary VV CORVI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fekel, Francis C.; Henry, Gregory W.; Sowell, James R., E-mail: fekel@evans.tsuniv.edu, E-mail: gregory.w.henry@gmail.com, E-mail: jim.sowell@physics.gatech.edu

2013-12-01

We have obtained red-wavelength spectroscopy and Johnson B and V differential photoelectric photometry of the eclipsing binary VV Crv = HR 4821. The system is the secondary of the common proper motion double star ADS 8627, which has a separation of 5.''2. VV Crv has an orbital period of 3.144536 days and a low but non-zero eccentricity of 0.085. With the Wilson-Devinney program we have determined a simultaneous solution of our spectroscopic and photometric observations. Those orbital elements produce masses of M {sub 1} = 1.978 ± 0.010 M {sub ☉} and M {sub 2} = 1.513 ± 0.008 Mmore » {sub ☉}, and radii of R {sub 1} = 3.375 ± 0.010 R {sub ☉} and R {sub 2} = 1.650 ± 0.008 R {sub ☉} for the primary and secondary, respectively. The effective temperatures of the two components are 6500 K (fixed) and 6638 K, so the star we call the primary is the more massive but cooler and larger component. A comparison with evolutionary tracks indicates that the components are metal rich with [Fe/H] = 0.3, and the system has an age of 1.2 Gyr. The primary is near the end of its main-sequence lifetime and is rotating significantly faster than its pseudosynchronous velocity. The secondary is still well ensconced on the main sequence and is rotating more slowly than its pseudosynchronous rate.« less

SSMART: Sequence-structure motif identification for RNA-binding proteins.

PubMed

Munteanu, Alina; Mukherjee, Neelanjan; Ohler, Uwe

2018-06-11

RNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized. We developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3'UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP. Availability: SSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/. Supplementary data are available at Bioinformatics online.

Theoretical investigation about secondary deposition of thin-film formation by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Chen, Huawei; Hagiwara, Ichiro; Kiet Tieu, A.; Kishimoto, Kikuo; Liu, Qiang

2007-05-01

The thin-film growth has been confirmed to be assembled by an enormous number of clusters in experiments of CVD. Sequence of clusters' depositions proceeds to form the thin-film in short time as gas fluids through surface of substrate. Such growth mechanism has been mainly investigated on the basis of experiment. Due to immense cost of the experimental equipment and low level of current measurement technology, the comprehension about authentic effect of formation condition on properties of nanomaterial is limited in qualitative manner. Three quantitative items: flatness of primary deposition, adhesion between cluster and substrate, and degree of epitaxial growth were proposed to evaluate the property of thin-film. In this simulation, three different cluster sizes of 203, 653, and 1563 atoms with different velocities (0, 10, 100, 1000, and 3000 m/s) were deposited on a Cu(0 0 1) substrate whose temperatures were set between 300 and 1000 K. Four clusters and one cluster were used in primary deposition and secondary deposition, respectively. To increase initial velocity not only enhanced the speed of epitaxial growth, adhesion between clusters and substrate, but also increased the degree of epitaxy for primary deposition and secondary deposition. Exfoliation pattern of thin-film was profoundly dependent on initial velocity through comparison between adhesion of primary and secondary deposition. Moreover, the epitaxial growth became well as the temperature of substrate was raised, and the degree of epitaxy of small cluster was larger than that of larger cluster, no matter of primary and secondary deposition.

SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.

PubMed

Polishchuk, Maya; Paz, Inbal; Yakhini, Zohar; Mandel-Gutfreund, Yael

2018-05-25

Gene expression regulation is highly dependent on binding of RNA-binding proteins (RBPs) to their RNA targets. Growing evidence supports the notion that both RNA primary sequence and its local secondary structure play a role in specific Protein-RNA recognition and binding. Despite the great advance in high-throughput experimental methods for identifying sequence targets of RBPs, predicting the specific sequence and structure binding preferences of RBPs remains a major challenge. We present a novel webserver, SMARTIV, designed for discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from in-vivo experiments. The uniqueness of SMARTIV is that it predicts motifs from enriched k-mers that combine information from ranked RNA sequences and their predicted secondary structure, obtained using various folding methods. Consequently, SMARTIV generates Position Weight Matrices (PWMs) in a combined sequence and structure alphabet with assigned P-values. SMARTIV concisely represents the sequence and structure motif content as a single graphical logo, which is informative and easy for visual perception. SMARTIV was examined extensively on a variety of high-throughput binding experiments for RBPs from different families, generated from different technologies, showing consistent and accurate results. Finally, SMARTIV is a user-friendly webserver, highly efficient in run-time and freely accessible via http://smartiv.technion.ac.il/.

MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.

PubMed

Fang, Chao; Shang, Yi; Xu, Dong

2018-05-01

Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neural network architecture, named the Deep inception-inside-inception (Deep3I) network, is proposed for protein secondary structure prediction and implemented as a software tool MUFOLD-SS. The input to MUFOLD-SS is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio-chemical properties of amino acids, PSI-BLAST profile, and HHBlits profile. MUFOLD-SS is composed of a sequence of nested inception modules and maps the input matrix to either eight states or three states of secondary structures. The architecture of MUFOLD-SS enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, MUFOLD-SS outperformed the best existing methods and other deep neural networks significantly. MUFold-SS can be downloaded from http://dslsrv8.cs.missouri.edu/~cf797/MUFoldSS/download.html. © 2018 Wiley Periodicals, Inc.

Genomic and clinical profiling of a national nephrotic syndrome cohort advocates a precision medicine approach to disease management.

PubMed

Bierzynska, Agnieszka; McCarthy, Hugh J; Soderquest, Katrina; Sen, Ethan S; Colby, Elizabeth; Ding, Wen Y; Nabhan, Marwa M; Kerecuk, Larissa; Hegde, Shivram; Hughes, David; Marks, Stephen; Feather, Sally; Jones, Caroline; Webb, Nicholas J A; Ognjanovic, Milos; Christian, Martin; Gilbert, Rodney D; Sinha, Manish D; Lord, Graham M; Simpson, Michael; Koziell, Ania B; Welsh, Gavin I; Saleem, Moin A

2017-04-01

Steroid Resistant Nephrotic Syndrome (SRNS) in children and young adults has differing etiologies with monogenic disease accounting for 2.9-30% in selected series. Using whole exome sequencing we sought to stratify a national population of children with SRNS into monogenic and non-monogenic forms, and further define those groups by detailed phenotypic analysis. Pediatric patients with SRNS were identified via a national United Kingdom Renal Registry. Whole exome sequencing was performed on 187 patients, of which 12% have a positive family history with a focus on the 53 genes currently known to be associated with nephrotic syndrome. Genetic findings were correlated with individual case disease characteristics. Disease causing variants were detected in 26.2% of patients. Most often this occurred in the three most common SRNS-associated genes: NPHS1, NPHS2, and WT1 but also in 14 other genes. The genotype did not always correlate with expected phenotype since mutations in OCRL, COL4A3, and DGKE associated with specific syndromes were detected in patients with isolated renal disease. Analysis by primary/presumed compared with secondary steroid resistance found 30.8% monogenic disease in primary compared with none in secondary SRNS permitting further mechanistic stratification. Genetic SRNS progressed faster to end stage renal failure, with no documented disease recurrence post-transplantation within this cohort. Primary steroid resistance in which no gene mutation was identified had a 47.8% risk of recurrence. In this unbiased pediatric population, whole exome sequencing allowed screening of all current candidate genes. Thus, deep phenotyping combined with whole exome sequencing is an effective tool for early identification of SRNS etiology, yielding an evidence-based algorithm for clinical management. Copyright © 2016 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia.

PubMed

Engle, E K; Fisher, D A C; Miller, C A; McLellan, M D; Fulton, R S; Moore, D M; Wilson, R K; Ley, T J; Oh, S T

2015-04-01

Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single-nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML.

The number of reduced alignments between two DNA sequences

PubMed Central

2014-01-01

Background In this study we consider DNA sequences as mathematical strings. Total and reduced alignments between two DNA sequences have been considered in the literature to measure their similarity. Results for explicit representations of some alignments have been already obtained. Results We present exact, explicit and computable formulas for the number of different possible alignments between two DNA sequences and a new formula for a class of reduced alignments. Conclusions A unified approach for a wide class of alignments between two DNA sequences has been provided. The formula is computable and, if complemented by software development, will provide a deeper insight into the theory of sequence alignment and give rise to new comparison methods. AMS Subject Classification Primary 92B05, 33C20, secondary 39A14, 65Q30 PMID:24684679

DNA sequence analysis of simian virus 40 mutants with deletions mapping in the leader region of the late viral mRNA's: mutants with deletions similar in size and position exhibit varied phenotypes.

PubMed

Barkan, A; Mertz, J E

1981-02-01

The nucleotide sequences of 10 viable yet partially defective deletion mutants of simian virus 40 were determined. The deletions mapped within, and, in many cases, 5' to, the predominant leader sequence of the late viral mRNA's. They ranged from 74 to 187 nucleotide pairs in length. Six of the mutants had lost the sequence that corresponds to the "cap" site (5' terminus) of the most abundant class of 16S mRNA's. One of these mutants had a deletion that extended 103 nucleotide pairs into the region preceding this primary cap site and, therefore, was missing many secondary cap sites as well. A seventh mutant lacked the entire major 16S leader sequence except for the first six nucleotides at its 5' end and the last nine at its 3' end. Although these mutants differed in the size and position of their deletions, we were unable to discover any simple correlations between their growth characteristics and their DNA sequences. This finding indicates that the secondary structures of the RNA transcripts may play a more important role than the exact nucleotide sequence of the RNAs in determining how they function within the cell.

School belongingness and mental health functioning across the primary-secondary transition in a mainstream sample: multi-group cross-lagged analyses.

PubMed

Vaz, Sharmila; Falkmer, Marita; Parsons, Richard; Passmore, Anne Elizabeth; Parkin, Timothy; Falkmer, Torbjörn

2014-01-01

The relationship between school belongingness and mental health functioning before and after the primary-secondary school transition has not been previously investigated in students with and without disabilities. This study used a prospective longitudinal design to test the bi-directional relationships between these constructs, by surveying 266 students with and without disabilities and their parents, 6-months before and after the transition to secondary school. Cross-lagged multi-group analyses found student perception of belongingness in the final year of primary school to contribute to change in their mental health functioning a year later. The beneficial longitudinal effects of school belongingness on subsequent mental health functioning were evident in all student subgroups; even after accounting for prior mental health scores and the cross-time stability in mental health functioning and school belongingness scores. Findings of the current study substantiate the role of school contextual influences on early adolescent mental health functioning. They highlight the importance for primary and secondary schools to assess students' school belongingness and mental health functioning and transfer these records as part of the transition process, so that appropriate scaffolds are in place to support those in need. Longer term longitudinal studies are needed to increase the understanding of the temporal sequencing between school belongingness and mental health functioning of all mainstream students.

School Belongingness and Mental Health Functioning across the Primary-Secondary Transition in a Mainstream Sample: Multi-Group Cross-Lagged Analyses

PubMed Central

Vaz, Sharmila; Falkmer, Marita; Parsons, Richard; Passmore, Anne Elizabeth; Parkin, Timothy; Falkmer, Torbjörn

2014-01-01

The relationship between school belongingness and mental health functioning before and after the primary-secondary school transition has not been previously investigated in students with and without disabilities. This study used a prospective longitudinal design to test the bi-directional relationships between these constructs, by surveying 266 students with and without disabilities and their parents, 6-months before and after the transition to secondary school. Cross-lagged multi-group analyses found student perception of belongingness in the final year of primary school to contribute to change in their mental health functioning a year later. The beneficial longitudinal effects of school belongingness on subsequent mental health functioning were evident in all student subgroups; even after accounting for prior mental health scores and the cross-time stability in mental health functioning and school belongingness scores. Findings of the current study substantiate the role of school contextual influences on early adolescent mental health functioning. They highlight the importance for primary and secondary schools to assess students’ school belongingness and mental health functioning and transfer these records as part of the transition process, so that appropriate scaffolds are in place to support those in need. Longer term longitudinal studies are needed to increase the understanding of the temporal sequencing between school belongingness and mental health functioning of all mainstream students. PMID:24967580

Predicting residue-wise contact orders in proteins by support vector regression.

PubMed

Song, Jiangning; Burrage, Kevin

2006-10-03

The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

KOI-1003: A New Spotted, Eclipsing RS CVn Binary in the Kepler Field

NASA Astrophysics Data System (ADS)

Roettenbacher, Rachael M.; Kane, Stephen R.; Monnier, John D.; Harmon, Robert O.

2016-12-01

Using the high-precision photometry from the Kepler space telescope, thousands of stars with stellar and planetary companions have been observed. The characterization of stars with companions is not always straightforward and can be contaminated by systematic and stellar influences on the light curves. Here, through a detailed analysis of starspots and eclipses, we identify KOI-1003 as a new, active RS CVn star—the first identified with data from Kepler. The Kepler light curve of this close binary system exhibits the system’s primary transit, secondary eclipse, and starspot evolution of two persistent active longitudes. The near equality of the system’s orbital and rotation periods indicates the orbit and primary star’s rotation are nearly synchronized ({P}{orb}=8.360613+/- 0.000003 {days}; {P}{rot}˜ 8.23 {days}). By assuming the secondary star is on the main sequence, we suggest the system consists of a {1.45}-0.19+0.11 {M}⊙ subgiant primary and a {0.59}-0.04+0.03 {M}⊙ main-sequence companion. Our work gives a distance of 4400 ± 600 pc and an age of t={3.0}+2.0-0.5 {Gyr}, parameters which are discrepant with previous studies that included the star as a member of the open cluster NGC 6791.

R-chie: a web server and R package for visualizing RNA secondary structures

PubMed Central

Lai, Daniel; Proctor, Jeff R.; Zhu, Jing Yun A.; Meyer, Irmtraud M.

2012-01-01

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems. PMID:22434875

Herpesvirus systematics☆

PubMed Central

Davison, Andrew J.

2010-01-01

This paper is about the taxonomy and genomics of herpesviruses. Each theme is presented as a digest of current information flanked by commentaries on past activities and future directions. The International Committee on Taxonomy of Viruses recently instituted a major update of herpesvirus classification. The former family Herpesviridae was elevated to a new order, the Herpesvirales, which now accommodates 3 families, 3 subfamilies, 17 genera and 90 species. Future developments will include revisiting the herpesvirus species definition and the criteria used for taxonomic assignment, particularly in regard to the possibilities of classifying the large number of herpesviruses detected only as DNA sequences by polymerase chain reaction. Nucleotide sequence accessions in primary databases, such as GenBank, consist of the sequences plus annotations of the genetic features. The quality of these accessions is important because they provide a knowledge base that is used widely by the research community. However, updating the accessions to take account of improved knowledge is essentially reserved to the original depositors, and this activity is rarely undertaken. Thus, the primary databases are likely to become antiquated. In contrast, secondary databases are open to curation by experts other than the original depositors, thus increasing the likelihood that they will remain up to date. One of the most promising secondary databases is RefSeq, which aims to furnish the best available annotations for complete genome sequences. Progress in regard to improving the RefSeq herpesvirus accessions is discussed, and insights into particular aspects of herpesvirus genomics arising from this work are reported. PMID:20346601

T2 relaxation times of the glenohumeral joint at 3.0 T MRI in patients with and without primary and secondary osteoarthritis.

PubMed

Lee, So-Yeon; Park, Hee-Jin; Kwon, Heon-Ju; Kim, Mi Sung; Choi, Seon Hyeong; Choi, Yoon Jung; Kim, Eugene

2015-11-01

Quantitative magnetic resonance imaging (MRI) of cartilage has recently been applied to patients with osteoarthritis (OA). T2 mapping is a sensitive method of detecting changes in the chemical composition and structure of cartilage. To establish baseline T2 values of glenohumeral joint cartilage at 3.0 T and compare T2 values among subjects with and without OA. The study involved 30 patients (18 women, 12 men; median age, 67 years; age range, 51-78 years) with primary (n = 7) and secondary OA (n = 23) in the glenohumeral joint and 34 subjects without OA (19 women, 15 men; median age, 49 years; age range, 23-63 years). All subjects were evaluated by radiography and 3.0 T MRI including a multi-echo T2-weighted spin echo pulse sequence. The T2 value of the cartilage was measured by manually drawing the region of interest on the T2 map. Per-zone comparison of T2 values was performed using Mann-Whitney U test. Median T2 values differed significantly between subjects without OA (36.00 ms [interquartile range, 33.89-37.31 ms]) and those with primary (37.52 ms [36.84-39.11], P = 0.028), but not secondary (36.87 ms [34.70-41.10], P = 0.160) OA. Glenohumeral cartilage T2 values were higher in different zones between patients with primary and secondary OA than in subjects without OA. These T2 values can be used for comparison to assess cartilage degeneration in patients with shoulder OA. Significant differences in T2 were observed among subjects without OA and those with primary and secondary OA. © The Foundation Acta Radiologica 2014.

Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays.

PubMed

Horn, T; Chang, C A; Urdea, M S

1997-12-01

The divergent synthesis of bDNA structures is described. This new type of branched DNA contains one unique oligonucleotide, the primary sequence, covalently attached through a comb-like branching network to many identical copies of a different oligonucleotide, the secondary sequence. The bDNA comb molecules were assembled on a solid support using parameters optimized for bDNA synthesis. The chemistry was used to synthesize bDNA comb molecules containing 15 secondary sequences. The bDNA comb molecules were elaborated by enzymatic ligation into branched amplification multimers, large bDNA molecules (a total of 1068 nt) containing an average of 36 repeated DNA oligomer sequences, each capable of hybridizing specifically to an alkaline phosphatase-labeled oligonucleotide. The bDNA comb molecules were characterized by electrophoretic methods and by controlled cleavage at periodate-cleavable moieties incorporated during synthesis. The branched amplification multimers have been used as signal amplifiers in nucleic acid quantification assays for detection of viral infection. It is possible to detect as few as 50 molecules with bDNA technology.

Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays.

PubMed Central

Horn, T; Chang, C A; Urdea, M S

1997-01-01

The divergent synthesis of bDNA structures is described. This new type of branched DNA contains one unique oligonucleotide, the primary sequence, covalently attached through a comb-like branching network to many identical copies of a different oligonucleotide, the secondary sequence. The bDNA comb molecules were assembled on a solid support using parameters optimized for bDNA synthesis. The chemistry was used to synthesize bDNA comb molecules containing 15 secondary sequences. The bDNA comb molecules were elaborated by enzymatic ligation into branched amplification multimers, large bDNA molecules (a total of 1068 nt) containing an average of 36 repeated DNA oligomer sequences, each capable of hybridizing specifically to an alkaline phosphatase-labeled oligonucleotide. The bDNA comb molecules were characterized by electrophoretic methods and by controlled cleavage at periodate-cleavable moieties incorporated during synthesis. The branched amplification multimers have been used as signal amplifiers in nucleic acid quantification assays for detection of viral infection. It is possible to detect as few as 50 molecules with bDNA technology. PMID:9365266

Impact of peer review on reports of randomised trials published in open peer review journals: retrospective before and after study

PubMed Central

Collins, Gary S; Boutron, Isabelle; Yu, Ly-Mee; Cook, Jonathan; Shanyinde, Milensu; Wharton, Rose; Shamseer, Larissa; Altman, Douglas G

2014-01-01

Objective To investigate the effectiveness of open peer review as a mechanism to improve the reporting of randomised trials published in biomedical journals. Design Retrospective before and after study. Setting BioMed Central series medical journals. Sample 93 primary reports of randomised trials published in BMC-series medical journals in 2012. Main outcome measures Changes to the reporting of methodological aspects of randomised trials in manuscripts after peer review, based on the CONSORT checklist, corresponding peer reviewer reports, the type of changes requested, and the extent to which authors adhered to these requests. Results Of the 93 trial reports, 38% (n=35) did not describe the method of random sequence generation, 54% (n=50) concealment of allocation sequence, 50% (n=46) whether the study was blinded, 34% (n=32) the sample size calculation, 35% (n=33) specification of primary and secondary outcomes, 55% (n=51) results for the primary outcome, and 90% (n=84) details of the trial protocol. The number of changes between manuscript versions was relatively small; most involved adding new information or altering existing information. Most changes requested by peer reviewers had a positive impact on the reporting of the final manuscript—for example, adding or clarifying randomisation and blinding (n=27), sample size (n=15), primary and secondary outcomes (n=16), results for primary or secondary outcomes (n=14), and toning down conclusions to reflect the results (n=27). Some changes requested by peer reviewers, however, had a negative impact, such as adding additional unplanned analyses (n=15). Conclusion Peer reviewers fail to detect important deficiencies in reporting of the methods and results of randomised trials. The number of these changes requested by peer reviewers was relatively small. Although most had a positive impact, some were inappropriate and could have a negative impact on reporting in the final publication. PMID:24986891

Research on the co-movement between high-end talent and economic growth: A complex network approach

NASA Astrophysics Data System (ADS)

Zhang, Zhen; Wang, Minggang; Xu, Hua; Zhang, Wenbin; Tian, Lixin

2018-02-01

The major goal of this paper is to focus on the co-movement between high-end talent and economic growth by a complex network approach. Firstly, the national high-end talent development efficiency from 1990 to 2015 is taken as the quantitative index to measure the development of high-end talent. The added values of the primary industry, secondary industry, tertiary industry are selected as economic growth indexes, and all the selected sample data are standardized by the mean value processing method. Secondly, let seven months as the length of the sliding window, and one month as the sliding step, then the grey correlation degrees between systems are measured using the slope correlation degrees, and the grey correlation degree sequence is mapped into the symbol series composed by three symbols { Y , O , N } based on the coarse graining method. Let three characters as a mode, the nodes are obtained by the modes according to the time sequence. Let the transformation between the modal be the edge, and the times of the transformation be weight, then the co-movement networks between national high-end talent development efficiency and the added values of the primary industry, secondary industry, tertiary industry are built respectively. Finally, the dynamic characteristics of the networks are analysed by the node strength, strength distribution, weighted clustering coefficient, conversion cycle of the modes and the transition between the co-movement modes. The results indicate that there are mutual influence and promotion relations between the national high-end talent development efficiency and the added values of the primary, secondary and tertiary industry.

Approximate matching of structured motifs in DNA sequences.

PubMed

El-Mabrouk, Nadia; Raffinot, Mathieu; Duchesne, Jean-Eudes; Lajoie, Mathieu; Luc, Nicolas

2005-04-01

Several methods have been developed for identifying more or less complex RNA structures in a genome. All these methods are based on the search for conserved primary and secondary sub-structures. In this paper, we present a simple formal representation of a helix, which is a combination of sequence and folding constraints, as a constrained regular expression. This representation allows us to develop a well-founded algorithm that searches for all approximate matches of a helix in a genome. The algorithm is based on an alignment graph constructed from several copies of a pushdown automaton, arranged one on top of another. This is a first attempt to take advantage of the possibilities of pushdown automata in the context of approximate matching. The worst time complexity is O(krpn), where k is the error threshold, n the size of the genome, p the size of the secondary expression, and r its number of union symbols. We then extend the algorithm to search for pseudo-knots and secondary structures containing an arbitrary number of helices.

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.

PubMed

Edvardsson, Sverker; Gardner, Paul P; Poole, Anthony M; Hendy, Michael D; Penny, David; Moulton, Vincent

2003-05-01

Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date. We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.

Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma

PubMed Central

Kondrashova, Olga; Nguyen, Minh; Shield-Artin, Kristy; Tinker, Anna V.; Teng, Nelson N.H.; Harrell, Maria I.; Kuiper, Michael J.; Ho, Gwo-Yaw; Barker, Holly; Jasin, Maria; Prakash, Rohit; Kass, Elizabeth M.; Sullivan, Meghan R.; Brunette, Gregory J.; Bernstein, Kara A.; Coleman, Robert L.; Floquet, Anne; Friedlander, Michael; Kichenadasse, Ganessan; O'Malley, David M.; Oza, Amit; Sun, James; Robillard, Liliane; Maloney, Lara; Giordano, Heidi; Wakefield, Matthew J.; Kaufmann, Scott H.; Simmons, Andrew D.; Harding, Thomas C.; Raponi, Mitch; McNeish, Iain A.; Swisher, Elizabeth M.; Lin, Kevin K.; Scott, Clare L.

2017-01-01

High-grade epithelial ovarian carcinomas containing mutated BRCA1 or BRCA2 (BRCA1/2) homologous recombination (HR) genes are sensitive to platinum-based chemotherapy and PARP inhibitors (PARPi), while restoration of HR function due to secondary mutations in BRCA1/2 has been recognized as an important resistance mechanism. We sequenced core HR pathway genes in 12 pairs of pretreatment and postprogression tumor biopsy samples collected from patients in ARIEL2 Part 1, a phase II study of the PARPi rucaparib as treatment for platinum-sensitive, relapsed ovarian carcinoma. In 6 of 12 pretreatment biopsies, a truncation mutation in BRCA1, RAD51C, or RAD51D was identified. In five of six paired postprogression biopsies, one or more secondary mutations restored the open reading frame. Four distinct secondary mutations and spatial heterogeneity were observed for RAD51C. In vitro complementation assays and a patient-derived xenograft, as well as predictive molecular modeling, confirmed that resistance to rucaparib was associated with secondary mutations. Significance Analyses of primary and secondary mutations in RAD51C and RAD51D provide evidence for these primary mutations in conferring PARPi sensitivity and secondary mutations as a mechanism of acquired PARPi resistance. PARPi resistance due to secondary mutations underpins the need for early delivery of PARPi therapy and for combination strategies. PMID:28588062

Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes

NASA Technical Reports Server (NTRS)

Woese, C. R.; Luehrsen, K. R.; Pribula, C. D.; Fox, G. E.

1976-01-01

Complete nucleotide sequences are presented for 5S rRNA from Bacillus subtilis, B. firmus, B. pasteurii, B. brevis, Lactobacillus brevis, and Streptococcus faecalis, and 5S rRNA oligonucleotide catalogs and partial sequence data are given for B. cereus and Sporosarcina ureae. These data demonstrate a striking consistency of 5S rRNA primary and secondary structure within a given bacterial grouping. An exception is B. brevis, in which the 5S rRNA sequence varies significantly from that of other bacilli in the tuned helix and the procaryotic loop. The localization of these variations suggests that B. brevis occupies an ecological niche that selects such changes. It is noted that this organism produces antibiotics which affect ribosome function.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Complete genomic sequence of Powassan virus: evaluation of genetic elements in tick-borne versus mosquito-borne flaviviruses.

PubMed

Mandl, C W; Holzmann, H; Kunz, C; Heinz, F X

1993-05-01

The complete nucleotide sequence of the positive-stranded RNA genome of the tick-borne flavivirus Powassan (10,839 nucleotides) was elucidated and the amino acid sequence of all viral proteins was derived. Based on this sequence as well as serological data, Powassan virus represents the most divergent member of the tick-borne serocomplex within the genus flaviviruses, family Flaviviridae. The primary nucleotide sequence and potential RNA secondary structures of the Powassan virus genome as well as the protein sequences and the reactivities of the virion with a panel of monoclonal antibodies were compared to other tick-borne and mosquito-borne flaviviruses. These analyses corroborated significant differences between tick-borne and mosquito-borne flaviviruses, but also emphasized structural elements that are conserved among both vector groups. The comparisons among tick-borne flaviviruses revealed conserved sequence elements that might represent important determinants of the tick-borne flavivirus phenotype.

The developmental dynamics of the Populus stem transcriptome.

PubMed

Chao, Qing; Gao, Zhi-Fang; Zhang, Dong; Zhao, Biligen-Gaowa; Dong, Feng-Qin; Fu, Chun-Xiang; Liu, Li-Jun; Wang, Bai-Chen

2018-05-31

The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87,150 full-length transcripts, including 2,081 new isoforms and 62,058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1,187 long noncoding RNAs and 356 fusion genes. Using this annotation, we found 15,838 differentially expressed transcripts along the shoot developmental gradient, of which 1,216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloging and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Alterations of p53 in tumorigenic human bronchial epithelial cells correlate with metastatic potential

NASA Technical Reports Server (NTRS)

Piao, C. Q.; Willey, J. C.; Hei, T. K.; Hall, E. J. (Principal Investigator)

1999-01-01

The cellular and molecular mechanisms of radiation-induced lung cancer are not known. In the present study, alterations of p53 in tumorigenic human papillomavirus-immortalized human bronchial epithelial (BEP2D) cells induced by a single low dose of either alpha-particles or 1 GeV/nucleon (56)Fe were analyzed by PCR-single-stranded conformation polymorphism (SSCP) coupled with sequencing analysis and immunoprecipitation assay. A total of nine primary and four secondary tumor cell lines, three of which were metastatic, together with the parental BEP2D and primary human bronchial epithelial (NHBE) cells were studied. The immunoprecipitation assay showed overexpression of mutant p53 proteins in all the tumor lines but not in NHBE and BEP2D cells. PCR-SSCP and sequencing analysis found band shifts and gene mutations in all four of the secondary tumors. A G-->T transversion in codon 139 in exon 5 that replaced Lys with Asn was detected in two tumor lines. One mutation each, involving a G-->T transversion in codon 215 in exon 6 (Ser-->lle) and a G-->A transition in codon 373 in exon 8 (Arg-->His), was identified in the remaining two secondary tumors. These results suggest that p53 alterations correlate with tumorigenesis in the BEP2D cell model and that mutations in the p53 gene may be indicative of metastatic potential.

Sequencing and comparison of the Rickettsia genomes from the whitefly Bemisia tabaci Middle East Asia Minor I.

PubMed

Zhu, Dan-Tong; Xia, Wen-Qiang; Rao, Qiong; Liu, Shu-Sheng; Ghanim, Murad; Wang, Xiao-Wei

2016-08-01

The whitefly, Bemisia tabaci, harbors the primary symbiont 'Candidatus Portiera aleyrodidarum' and a variety of secondary symbionts. Among these secondary symbionts, Rickettsia is the only one that can be detected both inside and outside the bacteriomes. Infection with Rickettsia has been reported to influence several aspects of the whitefly biology, such as fitness, sex ratio, virus transmission and resistance to pesticides. However, mechanisms underlying these differences remain unclear, largely due to the lack of genomic information of Rickettsia. In this study, we sequenced the genome of two Rickettsia strains isolated from the Middle East Asia Minor 1 (MEAM1) species of the B. tabaci complex in China and Israel. Both Rickettsia genomes were of high coding density and AT-rich, containing more than 1000 coding sequences, much larger than that of the coexisted primary symbiont, Portiera. Moreover, the two Rickettsia strains isolated from China and Israel shared most of the genes with 100% identity and only nine genes showed sequence differences. The phylogenetic analysis using orthologs shared in the genus, inferred the proximity of Rickettsia in MEAM1 and Rickettsia bellii. Functional analysis revealed that Rickettsia was unable to synthesize amino acids required for complementing the whitefly nutrition. Besides, a type IV secretion system and a number of virulence-related genes were detected in the Rickettsia genome. The presence of virulence-related genes might benefit the symbiotic life of the bacteria, and hint on potential effects of Rickettsia on whiteflies. The genome sequences of Rickettsia provided a basis for further understanding the function of Rickettsia in whiteflies. © 2016 Institute of Zoology, Chinese Academy of Sciences.

Developmental and Subcellular Organization of Single-Cell C₄ Photosynthesis in Bienertia sinuspersici Determined by Large-Scale Proteomics and cDNA Assembly from 454 DNA Sequencing.

PubMed

Offermann, Sascha; Friso, Giulia; Doroshenk, Kelly A; Sun, Qi; Sharpe, Richard M; Okita, Thomas W; Wimmer, Diana; Edwards, Gerald E; van Wijk, Klaas J

2015-05-01

Kranz C4 species strictly depend on separation of primary and secondary carbon fixation reactions in different cell types. In contrast, the single-cell C4 (SCC4) species Bienertia sinuspersici utilizes intracellular compartmentation including two physiologically and biochemically different chloroplast types; however, information on identity, localization, and induction of proteins required for this SCC4 system is currently very limited. In this study, we determined the distribution of photosynthesis-related proteins and the induction of the C4 system during development by label-free proteomics of subcellular fractions and leaves of different developmental stages. This was enabled by inferring a protein sequence database from 454 sequencing of Bienertia cDNAs. Large-scale proteome rearrangements were observed as C4 photosynthesis developed during leaf maturation. The proteomes of the two chloroplasts are different with differential accumulation of linear and cyclic electron transport components, primary and secondary carbon fixation reactions, and a triose-phosphate shuttle that is shared between the two chloroplast types. This differential protein distribution pattern suggests the presence of a mRNA or protein-sorting mechanism for nuclear-encoded, chloroplast-targeted proteins in SCC4 species. The combined information was used to provide a comprehensive model for NAD-ME type carbon fixation in SCC4 species.

Mechanisms of Exchange Reactions of Primary and Secondary Alkyl Iodides with Elementary Iodine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bujake, John E.; Pratt, M. W. T.; Noyes, Richard M.

1961-04-01

Several primary and secondary alkyl iodides exchange thermally with I/ sup 131/ in hexachlorobutadiene between 130 and 200 deg . If the solutions are saturated with oxygen at one atmosphere, rates of exchange fit the kinetic expression k/sub b/STARI! STAl/sub 2/!1/2. Degassed solutions always exchange faster than oxygen saturated ones, but methyl, ethyl, and n-propyl iodides show the same kinetics as with oxygen. Exchange rates of degassed isopropyl and neopentyl iodides also show contributions from a k/sub a/STARI! term. Exchange in degassed ethylene dichloride is 3 to 4 times as fast as in degassed hexachlorobutadiene. Activation energies for k/sub b/more » are usually about 27 to 31 kcal/mole. Effects of substitution on alpha carbon are illustrated by the rate sequence methyl < ethyl < i-propyl = sec-butyl. Effects of substitution on beta carbon are illustrated by the rate sequence ethyl < npropyl>> neopentyl. Since the rates of exchange of methyl, ethyl, and i-propyl iodides vary in the opposite direction from the sequence for bimolecular nucleophilic substitution, the explanation proposed suggests that for nucleophilic substitution the effect of added methyl groups on an alpha carbon is a steric hindrance to solvation by solvent dipoles rather than a steric hindrance to the group attacking the carbon atom itself.« less

Measuring moment-to-moment pilot workload using synchronous presentations of secondary tasks in a motion-base trainer

NASA Technical Reports Server (NTRS)

Bortolussi, Michael R.; Hart, Sandra G.; Shively, Robert J.

1987-01-01

A simulation was conducted to determine whether the sensitivity of secondary task measures of pilot workload could be improved by synchronizing their presentation to the occurrence of specific events or pilot actions. This synchronous method of presentation was compared to the more typical asynchronous method, where secondary task presentations are independent of pilot's flight-related activities. Twelve pilots flew low- and high-difficulty scenarios in a motion-base trainer with and without concurrent secondary tasks (e.g., choice reaction time and time production). The difficulty of each scenario was manipulated by the addition of 21 flight-related tasks superimposed on a standard approach and landing sequence. The insertion of the secondary tasks did not affect primary flight performance. However, secondary task performance did reflect workload differences between scenarios and among flight segments within scenarios, replicating the results of an earlier study in which the secondary tasks were presented asynchronously (Bortolussi et al., 1986).

The nucleotide sequence of Beneckea harveyi 5S rRNA. [bioluminescent marine bacterium

NASA Technical Reports Server (NTRS)

Luehrsen, K. R.; Fox, G. E.

1981-01-01

The primary sequence of the 5S ribosomal RNA isolated from the free-living bioluminescent marine bacterium Beneckea harveyi is reported and discussed in regard to indications of phylogenetic relationships with the bacteria Escherichia coli and Photobacterium phosphoreum. Sequences were determined for oligonucleotide products generated by digestion with ribonuclease T1, pancreatic ribonuclease and ribonuclease T2. The presence of heterogeneity is indicated for two sites. The B. harveyi sequence can be arranged into the same four helix secondary structures as E. coli and other prokaryotic 5S rRNAs. Examination of the 5S-RNS sequences of the three bacteria indicates that B. harveyi and P. phosphoreum are specifically related and share a common ancestor which diverged from an ancestor of E. coli at a somewhat earlier time, consistent with previous studies.

Pairwise amino acid secondary structural propensities

NASA Astrophysics Data System (ADS)

Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

2015-04-01

We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

PubMed

D'Souza, Alicia D; Belotserkovskii, Boris P; Hanawalt, Philip C

2018-02-01

The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription. Copyright © 2018 Elsevier B.V. All rights reserved.

Purification and characterization of a primary-secondary alcohol dehydrogenase from two strains of Clostridium beijerinckii.

PubMed Central

Ismaiel, A A; Zhu, C X; Colby, G D; Chen, J S

1993-01-01

Two primary alcohols (1-butanol and ethanol) are major fermentation products of several clostridial species. In addition to these two alcohols, the secondary alcohol 2-propanol is produced to a concentration of about 100 mM by some strains of Clostridium beijerinckii. An alcohol dehydrogenase (ADH) has been purified to homogeneity from two strains (NRRL B593 and NESTE 255) of 2-propanol-producing C. beijerinckii. When exposed to air, the purified ADH was stable, whereas the partially purified ADH was inactivated. The ADHs from the two strains had similar structural and kinetic properties. Each had a native M(r) of between 90,000 and 100,000 and a subunit M(r) of between 38,000 and 40,000. The ADHs were NADP(H) dependent, but a low level of NAD(+)-linked activity was detected. They were equally active in reducing aldehydes and 2-ketones, but a much lower oxidizing activity was obtained with primary alcohols than with secondary alcohols. The kcat/Km value for the alcohol-forming reaction appears to be a function of the size of the larger alkyl substituent on the carbonyl group. ADH activities measured in the presence of both acetone and butyraldehyde did not exceed activities measured with either substrate present alone, indicating a common active site for both substrates. There was no similarity in the N-terminal amino acid sequence between that of the ADH and those of fungi and several other bacteria. However, the N-terminal sequence had 67% identity with those of two other anaerobes, Thermoanaerobium brockii and Methanobacterium palustre. Furthermore, conserved glycine and tryptophan residues are present in ADHs of these three anaerobic bacteria and ADHs of mammals and green plants. Images PMID:8349550

A comparative study of methanol as a supplementary carbon source for enhancing denitrification in primary and secondary anoxic zones.

PubMed

Ginige, Maneesha P; Bowyer, Jocelyn C; Foley, Leah; Keller, Jürg; Yuan, Zhiguo

2009-04-01

A comparative study on the use of methanol as a supplementary carbon source to enhance denitrification in primary and secondary anoxic zones is reported. Three lab-scale sequencing batch reactors (SBR) were operated to achieve nitrogen and carbon removal from domestic wastewater. Methanol was added to the primary anoxic period of the first SBR, and to the secondary anoxic period of the second SBR. No methanol was added to the third SBR, which served as a control. The extent of improvement on the denitrification performance was found to be dependent on the reactor configuration. Addition to the secondary anoxic period is more effective when very low effluent nitrate levels are to be achieved and hence requires a relatively large amount of methanol. Adding a small amount of methanol to the secondary anoxic period may cause nitrite accumulation, which does not improve overall nitrogen removal. In the latter case, methanol should be added to the primary anoxic period. The addition of methanol can also improve biological phosphorus removal by creating anaerobic conditions and increasing the availability of organic carbon in wastewater for polyphosphate accumulating organisms. This potentially provides a cost-effective approach to phosphorus removal from wastewater with a low carbon content. New fluorescence in situ hybridisation (FISH) probes targeting methanol-utilising denitrifiers were designed using stable isotope probing. Microbial structure analysis of the sludges using the new and existing FISH probes clearly showed that the addition of methanol stimulated the growth of specific methanol-utilizing denitrifiers, which improved the capability of sludge to use methanol and ethanol for denitrification, but reduced its capability to use wastewater COD for denitrification. Unlike acetate, long-term application of methanol has no negative impact on the settling properties of the sludge.

The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila.

PubMed

Olivieri, Daniel; Senti, Kirsten-André; Subramanian, Sailakshmi; Sachidanandam, Ravi; Brennecke, Julius

2012-09-28

In animal gonads, PIWI proteins and their bound 23-30 nt piRNAs guard genome integrity by the sequence specific silencing of transposons. Two branches of piRNA biogenesis, namely primary processing and ping-pong amplification, have been proposed. Despite an overall conceptual understanding of piRNA biogenesis, identity and/or function of the involved players are largely unknown. Here, we demonstrate an essential role for the female sterility gene shutdown in piRNA biology. Shutdown, an evolutionarily conserved cochaperone collaborates with Hsp90 during piRNA biogenesis, potentially at the loading step of RNAs into PIWI proteins. We demonstrate that Shutdown is essential for both primary and secondary piRNA populations in Drosophila. An extension of our study to previously described piRNA pathway members revealed three distinct groups of biogenesis factors. Together with data on how PIWI proteins are wired into primary and secondary processing, we propose a unified model for piRNA biogenesis. Copyright © 2012 Elsevier Inc. All rights reserved.

[Transforming gene in human esophageal carcinoma tissue].

PubMed

Jiang, W

1988-09-01

The transforming gene in human esophageal carcinoma (HEC) tissues collected from Lin-xian county, a high incidence area of esophageal cancer was studied. Eight primary HEC tissues were used as sources for the preparation of DNA. High molecular weight DNAs were separately added to NIH 3T3 cells by the calcium phosphate coprecipitation method. Of the 8 HEC tissues examined, 3 DNAs showed transforming activity and produced secondary transformants. The use of uncloned NIH 3T3 cells resulted in the appearances of non-transforming. The efficiency of primary transfection foci was low (0.025--0.05 focus per ug of DNA). In the secondary transfection, the efficiency was increased (0.30 focus per ug of DNA). The primary and secondary transformants were capable of forming colonies in soft agar (0.33%) in contrast to the control NIH 3T3 cells, which did not show any anchorage-independent growth. About 1 X 10(6) cells of the cloned secondary transformants were injected subcutaneously into athymic BALB/c nude mice. The mice developed large tumors (approximately 20-30 mm in diameter) within 5--15 days after injection. No tumor developed in mice injected with control NIH 3T3 cells even after 2 months. The transforming DNA had a linkage to the Alu sequence, indicating that a common human DNA fragment is conserved in the tumors. H-ras was found in the transforming DNA using Southern blot assay.

Iron-catalyzed synthesis of secondary amines: on the way to green reductive aminations.

PubMed

Stemmler, Tobias; Surkus, Annette-Enrika; Pohl, Marga-Martina; Junge, Kathrin; Beller, Matthias

2014-11-01

Amines represent important intermediates in chemical and biological processes. Herein, we describe the use of a nanostructured iron-based catalyst for the tandem reductive amination between nitroarenes and aldehydes using hydrogen as reductant. The nanostructured iron-catalyst is prepared by immobilization of an iron-phenanthroline complex onto a commercially available carbon support. In the reaction sequence a primary amine is formed in situ from the corresponding nitro compound. Reversible condensation with aldehydes forms the respective imines, which are finally reduced to the desired secondary amine. This synthesis of secondary amines is atom-economical and environmentally attractive using cheap and readily available organic compounds as starting materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The calcium isotope evolution of Lake Lisan, the Dead Sea glacial precursor

NASA Astrophysics Data System (ADS)

Bradbury, H. J.; Turchyn, A. V.; Wong, K.; Torfstein, A.

2016-12-01

Calcium is a stoichiometric component of carbonate minerals whose calcium isotopic composition reflects changes in the calcium isotope composition of the water from which it precipitates as well as the calcium isotope fractionation factor during precipitation. The lacustrine deposits of the last glacial Dead Sea (Lisan Formation) are dominated by carbonate minerals (aragonite) that record the geochemical history of the lake. The sediment sequence comprises alternating laminae of aragonite and clay-rich marls, interspersed with primary gypsum beds and disseminated secondary gypsum crystals. The aragonite precipitated annually during high lake stands associated with wet periods, while the primary gypsum precipitated during low lake conditions (arid periods). We report the calcium isotopic composition (δ44Ca in ‰ relative to bulk silicate earth) of primary aragonite laminae, primary gypsum and secondary gypsum at 1-5kyr resolution throughout the Lisan Formation sampled at the Masada section (70 - 14.5 ka). The δ44Ca of the primary gypsum averages +0.29‰, and displays smaller temporal variations than the aragonite, which averages -0.35‰ but ranges between +0.18‰ and -0.68‰. The aragonite δ44Ca changes temporally in sync with the previously reconstructed lake level suggesting the aragonite δ44Ca reflects changes in the lake calcium balance during lake level changes. The secondary gypsum composition (-0.3‰) corresponds to coeval aragonite samples. For the secondary gypsum to have a similar δ44Ca to the aragonite it is likely that the calcium derived from the aragonite in a near quantitative fashion through recrystallization of the aragonite to gypsum. A numerical box model is used to explore the effect of changing lake water levels on the calcium isotope composition of the aragonite and gypsum over the time interval studied.

HII 2407: AN ECLIPSING BINARY REVEALED BY K2 OBSERVATIONS OF THE PLEIADES

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, Trevor J.; Hillenbrand, Lynne A.; Zhang, Celia

2015-11-20

The star HII 2407 is a member of the relatively young Pleiades star cluster and was previously discovered to be a single-lined spectroscopic binary. It is newly identified here within Kepler/K2 photometric time series data as an eclipsing binary system. Mutual fitting of the radial velocity and photometric data leads to an orbital solution and constraints on fundamental stellar parameters. While the primary has arrived on the main sequence, the secondary is still pre-main sequence and we compare our results for the M/M{sub ⊙} and R/R{sub ⊙} values with stellar evolutionary models. We also demonstrate that the system is likelymore » to be tidally synchronized. Follow-up infrared spectroscopy is likely to reveal the lines of the secondary, allowing for dynamically measured masses and elevating the system to benchmark eclipsing binary status.« less

Genetic influences on ovulation of primary oocytes in LT/Sv strain mice.

PubMed

Everett, Clare A; Auchincloss, Catherine A; Kaufman, Matthew H; Abbott, Catherine M; West, John D

2004-11-01

A high proportion of LT/Sv strain oocytes arrest in meiotic metaphase I (MI) and are ovulated as diploid primary oocytes rather than haploid secondary oocytes. (Mus musculus castaneus x LT/SvKau)F1 x LT/SvKau backcross females were analysed for the proportion of oocytes that arrested in MI and typed by PCR for a panel of microsatellite DNA sequences (simple sequence repeat polymorphisms) that differed between strain LT/SvKau and M. m. castaneus. This provided a whole genome scan of 86 genetic markers distributed over all 19 autosomes and the X chromosome, and revealed genetic linkage of the MI arrest phenotype to markers on chromosomes 1 and 9. Identification of these two chromosomal regions should facilitate the identification of genes involved in mammalian oocyte maturation and the control of meiosis.

Elevated immunoglobulin G antibodies to the proline-rich amino-terminal region of Epstein-Barr virus nuclear antigen-2 in sera from patients with systemic connective tissue diseases and from a subgroup of Sjögren's syndrome patients with pulmonary involvements.

PubMed

Yamazaki, M; Kitamura, R; Kusano, S; Eda, H; Sato, S; Okawa-Takatsuji, M; Aotsuka, S; Yanagi, K

2005-03-01

Associations of Epstein-Barr virus (EBV) and autoimmune diseases have been hypothesized. We have analysed IgG antibodies to EBV nuclear antigen (EBNA)-2 in sera from Japanese patients with autoimmune systemic connective tissue diseases (CTD), exemplified by systemic lupus erythematosus (SLE), primary Sjogren's syndrome (SS), rheumatoid arthritis (RA), systemic sclerosis (SSc) and secondary SS (classical CTDs complicated with SS). An enzyme-linked immunosorbent assay (ELISA) which uses glutathione-S-transferase polypeptides fused to EBV nuclear antigen (EBNA)-2 and EBNA-1 was developed. Ratios of IgG antibody reactivity to whole IgG concentrations of sera were calculated to normalize EBNA-2 and EBNA-1 antibody levels to the hypergammaglobulinaemia that occurs in CTD. The ELISA optical density OD(450) readings of IgG antibodies to both the amino-terminal aa 1-116 of EBNA-2 and carboxyl-terminal aa 451-641 of EBNA-1 were elevated significantly in patients with SLE, primary SS, RA, SSc and secondary SS when compared to EBNA-1. The OD readings were divided by serum IgG concentrations to normalize for the hypergammaglobulinaemia. The specific levels of IgG antibodies to the amino-terminal region of EBNA-2 were elevated in patients with SLE, primary SS or RA, as well as those with secondary SS complicated with SLE or RA. The EBNA-2 amino-terminal region contains a polyproline tract and a proline-rich sequence and has considerable amino acid sequence homology with many cellular proline-rich proteins. High ratios of EBNA-2 aa 1-116 to EBNA-1 aa 451-641 IgG antibody levels which probably suggest reactivation of EBV latent infection were associated significantly with pulmonary involvement in SS patients. These results are consistent with the hypothesis that the sequence similarity between the amino-terminal region of EBNA-2 and proline-rich cellular proteins is associated with pathogenesis in a subpopulation of CTD patients, possibly by the molecular mimicry-epitope shift mechanism.

Kottamia 74-inch telescope discovery of the new eclipsing binary KAO-EGYPT J225702.44+523222.1.: First CCD photometry and light curve analysis

NASA Astrophysics Data System (ADS)

Shokry, A.; Darwish, M. S.; Saad, S. M.; Eldepsy, M.; Zead, I.

2017-08-01

We present the first multicolor CCD photometry for the newly discovered binary system KAO-EGYPT J225702.44+523222.1. New times of light minimum and new ephemeris were obtained. The VR I light curves were analyzed using WD code, the difference in maximum light at phase 0.25 is modeled with a cool spot on the secondary component. The solution show that the system is A-subtype, overcontact binary with fill-out factor = 42% and low mass ratio, q = 0.275. The two components of spectral types K0 and K1 and the primary component is the massive one. The position of both components on the M-L and M-R relations revealed that the primary component is a main sequence star while the secondary is an evolved component.

Conserved and variable domains of RNase MRP RNA.

PubMed

Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

2009-01-01

Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

A Comparative Analysis of the Sugar Phosphate Cyclase Superfamily Involved in Primary and Secondary Metabolism

PubMed Central

Wu, Xiumei; Flatt, Patricia M.; Schlörke, Oliver; Zeeck, Axel; Dairi, Tohru

2011-01-01

Sugar Phosphate Cyclases (SPCs) catalyze the cyclization of sugar phosphates to produce a variety of cyclitol intermediates that serve as the building blocks of many primary metabolites, e.g., aromatic amino acids, and clinically relevant secondary metabolites, e.g., aminocyclitol/aminoglycoside and ansamycin antibiotics. Feeding experiments with isotopically-labeled cyclitols revealed that cetoniacytone A, a unique C7N-aminocyclitol antibiotic isolated from an insect endophytic Actinomyces sp., is derived from 2-epi-5-epi-valiolone, a product of SPC. Using heterologous probes from the 2-epi-5-epi-valiolone synthase class of SPCs, an SPC homolog gene, cetA, was isolated from the cetoniacytone producer. CetA is closely related to BE-orf9 found in the BE-40644 biosynthetic gene cluster from Actinoplanes sp. strain A40644. Recombinant expression of cetA and BE-orf9 and biochemical characterization of the gene products confirmed their function as 2-epi-5-epi-valiolone synthases. Further phylogenetic analysis of SPC sequences revealed a new clade of SPCs that may regulate the biosynthesis of a novel set of secondary metabolites. PMID:17195255

The primary structure of rat liver ribosomal protein L37. Homology with yeast and bacterial ribosomal proteins.

PubMed

Lin, A; McNally, J; Wool, I G

1983-09-10

The covalent structure of the rat liver 60 S ribosomal subunit protein L37 was determined. Twenty-four tryptic peptides were purified and the sequence of each was established; they accounted for all 111 residues of L37. The sequence of the first 30 residues of L37, obtained previously by automated Edman degradation of the intact protein, provided the alignment of the first 9 tryptic peptides. Three peptides (CN1, CN2, and CN3) were produced by cleavage of protein L37 with cyanogen bromide. The sequence of CN1 (65 residues) was established from the sequence of secondary peptides resulting from cleavage with trypsin and chymotrypsin. The sequence of CN1 in turn served to order tryptic peptides 1 through 14. The sequence of CN2 (15 residues) was determined entirely by a micromanual procedure and allowed the alignment of tryptic peptides 14 through 18. The sequence of the NH2-terminal 28 amino acids of CN3 (31 residues) was determined; in addition the complete sequences of the secondary tryptic and chymotryptic peptides were done. The sequence of CN3 provided the order of tryptic peptides 18 through 24. Thus the sequence of the three cyanogen bromide peptides also accounted for the 111 residues of protein L37. The carboxyl-terminal amino acids were identified after carboxypeptidase A treatment. There is a disulfide bridge between half-cystinyl residues at positions 40 and 69. Rat liver ribosomal protein L37 is homologous with yeast YP55 and with Escherichia coli L34. Moreover, there is a segment of 17 residues in rat L37 that occurs, albeit with modifications, in yeast YP55 and in E. coli S4, L20, and L34.

Immunodominance changes as a function of the infecting dengue virus serotype and primary versus secondary infection.

PubMed

Weiskopf, Daniela; Angelo, Michael A; Sidney, John; Peters, Bjoern; Shresta, Sujan; Sette, Alessandro

2014-10-01

Dengue virus (DENV) is the causative agent of dengue fever (DF). This disease can be caused by any of four DENV serotypes (DENV1 to -4) which share 67 to 75% sequence homology with one another. The effect of subsequent infections with different serotypes on the T cell repertoire is not fully understood. We utilized mice transgenic for human leukocyte antigens (HLA) lacking the alpha/beta interferon (IFN-α/β) receptor to study responses to heterologous DENV infection. First, we defined the primary T cell response to DENV3 in the context of a wide range of HLA molecules. The primary DENV3 immune response recognized epitopes derived from all 10 DENV proteins, with a significant fraction of the response specific for structural proteins. This is in contrast to primary DENV2 infection, in which structural proteins are a minor component of the response, suggesting differential antigen immunodominance as a function of the infecting serotype. We next investigated the effect of secondary heterologous DENV infection on the T cell repertoire. In the case of both DENV2/3 and DENV3/2 heterologous infections, recognition of conserved/cross-reactive epitopes was either constant or expanded compared to that in homologous infection. Furthermore, in heterologous infection, previous infection with a different serotype impaired the development of responses directed to serotype-specific but not conserved epitopes. Thus, a detrimental effect of previous heterotypic responses might not be due to dysfunctional and weakly cross-reactive epitopes dominating the response. Rather, responses to the original serotype might limit the magnitude of responses directed against epitopes that are either cross-reactive to or specific for the most recently infecting serotype. DENV transmission occurs in more than 100 countries and is an increasing public health problem in tropical and subtropical regions. At present, no effective antiviral therapy or licensed vaccine exists, and treatment is largely supportive in nature. Disease can be caused by any of the four DENV serotypes (DENV1 to -4), which share a high degree of sequence homology with one another. In this study, we have addressed the question of how the T cell repertoire changes as a function of infections with different serotypes and of subsequent heterologous secondary infections. This is of particular interest in the field of dengue viruses, in which secondary infections with different DENV serotypes increase the risk of severe disease. Our results on the evolution of the immune response after primary and secondary infections provide new insights into HLA-restricted T cell responses against DENV relevant for the design of a vaccine against DENV. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Simultaneous Photometric and Spectroscopic Solution for AW Cam

NASA Astrophysics Data System (ADS)

Frey, J. R.; Angione, R. J.; Sievers, J. R.

2010-07-01

We present the first four color Stromgren uvby photometric observations of the eclipsing binary system AW Cam along with the first simultaneous photometric and spectroscopic solution. This solution produced a detached system with a mass ratio of 0.45 consisting of an A1 primary and an F8 secondary, both in the main sequence band. The Hipparcos/Tycho Catalogue gives V = 8.24 and a parallax = 2.17 mas.

DGs for Service Restoration to Critical Loads in a Secondary Network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Yin; Liu, Chen-Ching; Wang, Zhiwen

During a major outage in a secondary network distribution system, distributed generators (DGs) connected to the primary feeders as well as the secondary network can be used to serve critical loads. This paper proposed a resilience-oriented method to determine restoration strategies for secondary network distribution systems after a major disaster. Technical issues associated with the restoration process are analyzed, including the operation of network protectors, inrush currents caused by the energization of network transformers, synchronization of DGs to the network, and circulating currents among DGs. A look-ahead load restoration framework is proposed, incorporating technical issues associated with secondary networks, limitsmore » on DG capacity and generation resources, dynamic constraints, and operational limits. The entire outage duration is divided into a sequence of periods. Restoration strategies can be adjusted at the beginning of each period using the latest information. Finally, numerical simulation of the modified IEEE 342-node low voltage networked test system is performed to validate the effectiveness of the proposed method.« less

DGs for Service Restoration to Critical Loads in a Secondary Network

DOE PAGES

Xu, Yin; Liu, Chen-Ching; Wang, Zhiwen; ...

2017-08-25

During a major outage in a secondary network distribution system, distributed generators (DGs) connected to the primary feeders as well as the secondary network can be used to serve critical loads. This paper proposed a resilience-oriented method to determine restoration strategies for secondary network distribution systems after a major disaster. Technical issues associated with the restoration process are analyzed, including the operation of network protectors, inrush currents caused by the energization of network transformers, synchronization of DGs to the network, and circulating currents among DGs. A look-ahead load restoration framework is proposed, incorporating technical issues associated with secondary networks, limitsmore » on DG capacity and generation resources, dynamic constraints, and operational limits. The entire outage duration is divided into a sequence of periods. Restoration strategies can be adjusted at the beginning of each period using the latest information. Finally, numerical simulation of the modified IEEE 342-node low voltage networked test system is performed to validate the effectiveness of the proposed method.« less

TU-H-CAMPUS-IeP1-05: A Framework for the Analytic Calculation of Patient-Specific Dose Distribution Due to CBCT Scan for IGRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Youn, H; Jeon, H; Nam, J

Purpose: To investigate the feasibility of an analytic framework to estimate patients’ absorbed dose distribution owing to daily cone-beam CT scan for image-guided radiation treatment. Methods: To compute total absorbed dose distribution, we separated the framework into primary and scattered dose calculations. Using the source parameters such as voltage, current, and bowtie filtration, for the primary dose calculation, we simulated the forward projection from the source to each voxel of an imaging object including some inhomogeneous inserts. Then we calculated the primary absorbed dose at each voxel based on the absorption probability deduced from the HU values and Beer’s law.more » In sequence, all voxels constructing the phantom were regarded as secondary sources to radiate scattered photons for scattered dose calculation. Details of forward projection were identical to that of the previous step. The secondary source intensities were given by using scatter-to- primary ratios provided by NIST. In addition, we compared the analytically calculated dose distribution with their Monte Carlo simulation results. Results: The suggested framework for absorbed dose estimation successfully provided the primary and secondary dose distributions of the phantom. Moreover, our analytic dose calculations and Monte Carlo calculations were well agreed each other even near the inhomogeneous inserts. Conclusion: This work indicated that our framework can be an effective monitor to estimate a patient’s exposure owing to cone-beam CT scan for image-guided radiation treatment. Therefore, we expected that the patient’s over-exposure during IGRT might be prevented by our framework.« less

Numerical calculation of a sea water heta exchanger using Simulink softwear

NASA Astrophysics Data System (ADS)

Preda, A.; Popescu, L. L.; Popescu, R. S.

2017-08-01

To highlight the heat exchange taking place between seawater as primary agent and the working fluid (water, glycol or Freon) as secondary agent, I have used the Simulink softwear in order to creat a new sequence for numerical calculation of heat exchanging. For optimum heat transfer we opted for a counter movement. The model developed to view the dynamic behavior of the exchanger consists of four interconnected levelsess. In the simulations was found that a finer mesh of the whole exchanger lead to results much closer to reality. There have been various models meshing, starting from a single cell and then advancing noticed an improvement in resultsSimulations were made in both the summer and the winter, using as a secondary agent process water and glycol solution. Studying heat transfer that occurs in the primary exchanger of a heat pump, having the primary fluid sea water with this program, we get the data plausible and worthy of consideration. Inserting into the program, the seasonal water temperatures of Black Sea water layers, we get a encouraging picture about storage capacity and heat transfer of sea water.

Mind the Gap when Data Mining the Ritter-Kolb Cataclysmic Variable Catalogue

NASA Astrophysics Data System (ADS)

Sparks, Warren M.; Sion, Edward M.

2017-01-01

The cataclysmic variable (CV) binary consists of a white dwarf primary and a low-mass secondary which overflows its Roche lobe. The Ritter-Kolb catalogue (2003, A&A, 404, 301) is a collection (~1000) of CV binaries and related objects. We have mined this catalogue for CVs with unevolved secondaries whose mass ratio (secondary/primary) is known (~130). A plot of the secondary mass verses the log of the orbital period exhibits the well-known period gap at 2-3 hrs. In addition, this plot shows that the secondary masses just above the period gap are collectively much larger than those just below. The average of the first ten secondary masses above the period is 180% larger than the average below the gap.The disrupted magnetic braking hypothesis (Howell, Nelson, and Rappaport 2001, ApJ, 550, 897 [HNR]) predicts that when the secondary becomes fully convective, the magnetic braking, which has driven the secondary out of thermal equilibrium, stops. In adjusting to thermal equilibrium the secondary shrinks below its Roche lobe and no longer loses mass. The binary system ceases to appear as a CV until gravitational radiation loss brings the secondary back in contact with its Roche lobe. This scenario is at odds with the apparent secondary mass loss across the period gap. Either the secondary continues to lose mass while crossing the period gap or the secondary masses are miscalculated!Magnetic braking causes the secondary to expand or inflate larger than its single star counterpart. Any orbital parameter calculation which assumes a radius-mass relationship based on single main-sequence stars will overestimate the mass of the secondary. We can approximate this mass overestimation from calculations by HNR which take into account the thermal heating from magnetic braking. Using this approximation as a first-order correction to the secondary mass, we replot the deflated secondary mass versus the binary period. The deflated masses immediately above and below the period gap are similar and do not indicate secondary mass loss across the gap. Thus, magnetic braking not only explains the period gap but the apparent secondary mass shift across it. Orbital parameters must be based upon actual secondary mass-radius observations.

Binary progenitors of supernovae

NASA Astrophysics Data System (ADS)

Trimble, V.

1984-12-01

Among the massive stars that are expected to produce Type II, hydrogen-rich supernovae, the presence of a close companion can increase the main sequence mass needed to yield a collapsing core. In addition, due to mass transfer from the primary to the secondary, the companion enhances the stripping of the stellar hydrogen envelope produced by single star winds and thereby makes it harder for the star to give rise to a typical SN II light curve. Among the less massive stars that may be the basis for Type I, hydrogen-free supernovae, a close companion could be an innocent bystander to carbon detonation/deflagration in the primary. It may alternatively be a vital participant which transfers material to a white dwarf primary and drives it to explosive conditions.

A high-throughput approach to profile RNA structure.

PubMed

Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano

2017-03-17

Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2΄-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database). The algorithm uses primary structure information alone to predict experimental structural profiles with >80% accuracy, showing high performances on large RNAs such as Xist (17 900 nucleotides; Area Under the ROC Curve AUC of 0.75 on dimethyl sulfate (DMS) experiments). We integrated CROSS in thermodynamics-based methods to predict secondary structure and observed an increase in their predictive power by up to 30%. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterization of a Mutant Diphtheria Toxin that is Defective in Binding to Cell Membrane Receptors on Vero Cells

DTIC Science & Technology

1982-08-13

phospholipid, such as phosphatidyllnositolphosphate or phosphatidic acid , or some other phosphorylated membrane molecule. 34 Clearly, it has not been...metabolize lactic acid (40), all represented secondary changes which followed a rapid and irreversible primary Injury (73, 142). Pappenheimer...CR>1197 is taken as 100. Determined from the amino acid sequence (42), From Holmes (74). and lysogeny was demonstrated (11, 66, reviewed in 6, 8

Data processing system for the Sneg-2MP experiment

NASA Technical Reports Server (NTRS)

Gavrilova, Y. A.

1980-01-01

The data processing system for scientific experiments on stations of the "Prognoz" type provides for the processing sequence to be broken down into a number of consecutive stages: preliminary processing, primary processing, secondary processing. The tasks of each data processing stage are examined for an experiment designed to study gamma flashes of galactic origin and solar flares lasting from several minutes to seconds in the 20 kev to 1000 kev energy range.

Primary and secondary structural analyses of glutathione S-transferase pi from human placenta.

PubMed

Ahmad, H; Wilson, D E; Fritz, R R; Singh, S V; Medh, R D; Nagle, G T; Awasthi, Y C; Kurosky, A

1990-05-01

The primary structure of glutathione S-transferase (GST) pi from a single human placenta was determined. The structure was established by chemical characterization of tryptic and cyanogen bromide peptides as well as automated sequence analysis of the intact enzyme. The structural analysis indicated that the protein is comprised of 209 amino acid residues and gave no evidence of post-translational modifications. The amino acid sequence differed from that of the deduced amino acid sequence determined by nucleotide sequence analysis of a cDNA clone (Kano, T., Sakai, M., and Muramatsu, M., 1987, Cancer Res. 47, 5626-5630) at position 104 which contained both valine and isoleucine whereas the deduced sequence from nucleotide sequence analysis identified only isoleucine at this position. These results demonstrated that in the one individual placenta studied at least two GST pi genes are coexpressed, probably as a result of allelomorphism. Computer assisted consensus sequence evaluation identified a hydrophobic region in GST pi (residues 155-181) that was predicted to be either a buried transmembrane helical region or a signal sequence region. The significance of this hydrophobic region was interpreted in relation to the mode of action of the enzyme especially in regard to the potential involvement of a histidine in the active site mechanism. A comparison of the chemical similarity of five known human GST complete enzyme structures, one of pi, one of mu, two of alpha, and one microsomal, gave evidence that all five enzymes have evolved by a divergent evolutionary process after gene duplication, with the microsomal enzyme representing the most divergent form.

Multimode Directional Coupler

NASA Technical Reports Server (NTRS)

Simons, Rainee N. (Inventor); Wintucky, Edwin G. (Inventor)

2016-01-01

A multimode directional coupler is provided. In some embodiments, the multimode directional coupler is configured to receive a primary signal and a secondary signal at a first port of a primary waveguide. The primary signal is configured to propagate through the primary waveguide and be outputted at a second port of the primary waveguide. The multimode directional coupler also includes a secondary waveguide configured to couple the secondary signal from the primary waveguide with no coupling of the primary signal into the secondary waveguide. The secondary signal is configured to propagate through the secondary waveguide and be outputted from a port of the secondary waveguide.

Web-Beagle: a web server for the alignment of RNA secondary structures.

PubMed

Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2015-07-01

Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

New bacterial composition in primary and persistent/secondary endodontic infections with respect to clinical and radiographic findings.

PubMed

Tennert, Christian; Fuhrmann, Maximilian; Wittmer, Annette; Karygianni, Lamprini; Altenburger, Markus J; Pelz, Klaus; Hellwig, Elmar; Al-Ahmad, Ali

2014-05-01

The aim of the present study was to analyze the microbiota of primary and secondary/persistent endodontic infections of patients undergoing endodontic treatment with respect to clinical and radiographic findings. Samples from the root canals of 21 German patients were taken using 3 sequential sterile paper points. In the case of a root canal filling, gutta-percha was removed with sterile files, and samples were taken using sterile paper points. The samples were plated, and microorganisms were then isolated and identified morphologically by biochemical analysis and sequencing the 16S rRNA genes of isolated microorganisms. In 12 of 21 root canals, 33 different species could be isolated. Six (50%) of the cases with isolated microorganisms were primary, and 6 (50%) cases were endodontic infections associated with root-filled teeth. Twelve of the isolated species were facultative anaerobic and 21 obligate anaerobic. Monomicrobial infections were found for Enterococcus faecalis and Actinomyces viscosus. E. faecalis was most frequently isolated in secondary endodontic infections (33%). Moraxella osloensis was isolated from a secondary endodontic infection that had an insufficient root canal filling accompanied by a mild sensation of pain. A new bacterial composition compromising Atopobium rimae, Anaerococcus prevotii, Pseudoramibacter alactolyticus, Dialister invisus, and Fusobacterium nucleatum was recovered from teeth with chronic apical abscesses. New bacterial combinations were found and correlated to clinical and radiographic findings, particularly to chronic apical abscesses. M. osloensis was detected in root canals for the second time and only in German patients. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.12 National primary and secondary ambient air quality standards for lead. (a) National primary and secondary...

Learning of pitch and time structures in an artificial grammar setting.

PubMed

Prince, Jon B; Stevens, Catherine J; Jones, Mari Riess; Tillmann, Barbara

2018-04-12

Despite the empirical evidence for the power of the cognitive capacity of implicit learning of structures and regularities in several modalities and materials, it remains controversial whether implicit learning extends to the learning of temporal structures and regularities. We investigated whether (a) an artificial grammar can be learned equally well when expressed in duration sequences as when expressed in pitch sequences, (b) learning of the artificial grammar in either duration or pitch (as the primary dimension) sequences can be influenced by the properties of the secondary dimension (invariant vs. randomized), and (c) learning can be boosted when the artificial grammar is expressed in both pitch and duration. After an exposure phase with grammatical sequences, learning in a subsequent test phase was assessed in a grammaticality judgment task. Participants in both the pitch and duration conditions showed incidental (not fully implicit) learning of the artificial grammar when the secondary dimension was invariant, but randomizing the pitch sequence prevented learning of the artificial grammar in duration sequences. Expressing the artificial grammar in both pitch and duration resulted in disproportionately better performance, suggesting an interaction between the learning of pitch and temporal structure. The findings are relevant to research investigating the learning of temporal structures and the learning of structures presented simultaneously in 2 dimensions (e.g., space and time, space and objects). By investigating learning, the findings provide further insight into the potential specificity of pitch and time processing, and their integrated versus independent processing, as previously debated in music cognition research. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

De novo Assembly of Leaf Transcriptome in the Medicinal Plant Andrographis paniculata

PubMed Central

Cherukupalli, Neeraja; Divate, Mayur; Mittapelli, Suresh R.; Khareedu, Venkateswara R.; Vudem, Dashavantha R.

2016-01-01

Andrographis paniculata is an important medicinal plant containing various bioactive terpenoids and flavonoids. Despite its importance in herbal medicine, no ready-to-use transcript sequence information of this plant is made available in the public data base, this study mainly deals with the sequencing of RNA from A. paniculata leaf using Illumina HiSeq™ 2000 platform followed by the de novo transcriptome assembly. A total of 189.22 million high quality paired reads were generated and 1,70,724 transcripts were predicted in the primary assembly. Secondary assembly generated a transcriptome size of ~88 Mb with 83,800 clustered transcripts. Based on the similarity searches against plant non-redundant protein database, gene ontology, and eukaryotic orthologous groups, 49,363 transcripts were annotated constituting upto 58.91% of the identified unigenes. Annotation of transcripts—using kyoto encyclopedia of genes and genomes database—revealed 5606 transcripts plausibly involved in 140 pathways including biosynthesis of terpenoids and other secondary metabolites. Transcription factor analysis showed 6767 unique transcripts belonging to 97 different transcription factor families. A total number of 124 CYP450 transcripts belonging to seven divergent clans have been identified. Transcriptome revealed 146 different transcripts coding for enzymes involved in the biosynthesis of terpenoids of which 35 contained terpene synthase motifs. This study also revealed 32,341 simple sequence repeats (SSRs) in 23,168 transcripts. Assembled sequences of transcriptome of A. paniculata generated in this study are made available, for the first time, in the TSA database, which provides useful information for functional and comparative genomic analysis besides identification of key enzymes involved in the various pathways of secondary metabolism. PMID:27582746

The RDE-10/RDE-11 complex triggers RNAi-induced mRNA degradation by association with target mRNA in C. elegans

PubMed Central

Yang, Huan; Zhang, Ying; Vallandingham, Jim; Li, Hau; Florens, Laurence; Mak, Ho Yi

2012-01-01

The molecular mechanisms for target mRNA degradation in Caenorhabditis elegans undergoing RNAi are not fully understood. Using a combination of genetic, proteomic, and biochemical approaches, we report a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. Genetic analysis indicates that the RDE-10/RDE-11 complex acts in parallel to nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary siRNA. Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Deep sequencing reveals a fivefold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, while primary siRNA and microRNA biogenesis is normal. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans. PMID:22508728

The RDE-10/RDE-11 complex triggers RNAi-induced mRNA degradation by association with target mRNA in C. elegans.

PubMed

Yang, Huan; Zhang, Ying; Vallandingham, Jim; Li, Hua; Li, Hau; Florens, Laurence; Mak, Ho Yi

2012-04-15

The molecular mechanisms for target mRNA degradation in Caenorhabditis elegans undergoing RNAi are not fully understood. Using a combination of genetic, proteomic, and biochemical approaches, we report a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. Genetic analysis indicates that the RDE-10/RDE-11 complex acts in parallel to nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary siRNA. Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Deep sequencing reveals a fivefold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, while primary siRNA and microRNA biogenesis is normal. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans.

1998 UBV Light Curves of Eclipsing Binary AI Draconis and Absolute Parameters

NASA Astrophysics Data System (ADS)

Jassur, D. M. Z.; Khaledian, M. S.; Kermani, M. H.

New UBV photometry of Algol-Type eclipsing binary star AI Dra and the absolute physical parameters of this system have been presented. The light curve analysis carried out by the method of differential corrections indicates that both components are inside their Roche-Lobes. From combining the photometric solution with spectroscopic data obtained from velocity curve analysis, it has been found that the system consist of a main sequence primary and an evolved (subgiant) secondary.

Foodborne hepatitis A outbreak associated with bakery products in northern Germany, 2012.

PubMed

Harries, M; Monazahian, M; Wenzel, J; Jilg, W; Weber, M; Ehlers, J; Dreesman, J; Mertens, E

2014-12-18

In October 2012, a hepatitis A (HA) outbreak with 83 laboratory-confirmed cases occurred in Lower Saxony. We defined primary outbreak cases as people with laboratory-confirmed HA and symptom onset between 8 October and 12 November 2012, residing in or visiting the affected districts. Secondary outbreak cases were persons with symptom onset after 12 November 2012 and close contact with primary cases. We identified 77 primary and six secondary cases. We enrolled 50 primary cases and 52 controls matched for age and sex, and found that 82% of cases and 60% of controls had consumed products from a particular bakery (OR=3.09; 95% CI: 1.15–8.68). Cases were more likely to have eaten sweet pastries (OR=5.74; 95% CI: 1.46–22.42). Viral isolates from five selected cases and three positively tested surfaces in the bakery had identical nucleotide sequences. One additional identical isolate derived from a salesperson of the bakery suffering from a chronic disease that required immunosuppressive treatment. Epidemiological and laboratory findings suggested that the salesperson contaminated products while packing and selling. Future risk assessment should determine whether food handlers with chronic diseases under immunosuppressive treatment could be more at risk of contaminating food and might benefit from HAV immunisation.

Unusual sugar specificity of banana lectin from Musa paradisiaca and its probable evolutionary origin. Crystallographic and modelling studies.

PubMed

Singh, D D; Saikrishnan, K; Kumar, Prashant; Surolia, A; Sekar, K; Vijayan, M

2005-10-01

The crystal structure of a complex of methyl-alpha-D-mannoside with banana lectin from Musa paradisiaca reveals two primary binding sites in the lectin, unlike in other lectins with beta-prism I fold which essentially consists of three Greek key motifs. It has been suggested that the fold evolved through successive gene duplication and fusion of an ancestral Greek key motif. In other lectins, all from dicots, the primary binding site exists on one of the three motifs in the three-fold symmetric molecule. Banana is a monocot, and the three motifs have not diverged enough to obliterate sequence similarity among them. Two Greek key motifs in it carry one primary binding site each. A common secondary binding site exists on the third Greek key. Modelling shows that both the primary sites can support 1-2, 1-3, and 1-6 linked mannosides with the second residue interacting in each case primarily with the secondary binding site. Modelling also readily leads to a bound branched mannopentose with the nonreducing ends of the two branches anchored at the two primary binding sites, providing a structural explanation for the lectin's specificity for branched alpha-mannans. A comparison of the dimeric banana lectin with other beta-prism I fold lectins, provides interesting insights into the variability in their quaternary structure.

Electromagnetic interference-aware transmission scheduling and power control for dynamic wireless access in hospital environments.

PubMed

Phunchongharn, Phond; Hossain, Ekram; Camorlinga, Sergio

2011-11-01

We study the multiple access problem for e-Health applications (referred to as secondary users) coexisting with medical devices (referred to as primary or protected users) in a hospital environment. In particular, we focus on transmission scheduling and power control of secondary users in multiple spatial reuse time-division multiple access (STDMA) networks. The objective is to maximize the spectrum utilization of secondary users and minimize their power consumption subject to the electromagnetic interference (EMI) constraints for active and passive medical devices and minimum throughput guarantee for secondary users. The multiple access problem is formulated as a dual objective optimization problem which is shown to be NP-complete. We propose a joint scheduling and power control algorithm based on a greedy approach to solve the problem with much lower computational complexity. To this end, an enhanced greedy algorithm is proposed to improve the performance of the greedy algorithm by finding the optimal sequence of secondary users for scheduling. Using extensive simulations, the tradeoff in performance in terms of spectrum utilization, energy consumption, and computational complexity is evaluated for both the algorithms.

Primary bacterial peritonitis in dogs and cats: 24 cases (1990-2006).

PubMed

Culp, William T N; Zeldis, Tracy E; Reese, Michael S; Drobatz, Kenneth J

2009-04-01

To determine clinical characteristics of primary bacterial peritonitis (infection of the peritoneal cavity with no identifiable intraperitoneal source of infection) and compare characteristics of primary and secondary peritonitis in dogs and cats. Retrospective case series. 24 (primary peritonitis) and 60 (secondary peritonitis) client-owned dogs and cats. Data from medical records of dogs and cats with primary and secondary peritonitis were reviewed for descriptive information regarding primary peritonitis and for comparison between the 2 forms of peritonitis. 15 dogs and 9 cats met inclusion criteria for primary peritonitis, and 49 dogs and 11 cats met inclusion criteria for secondary peritonitis. The most common historical findings in dogs and cats with primary and secondary peritonitis were lethargy, vomiting, and anorexia. Dogs with secondary peritonitis more often developed peritoneal exudates than those with primary peritonitis, and dogs with primary peritonitis were more often infected with gram-positive bacteria than those with secondary peritonitis. No difference in outcome was detected between all animals with primary versus secondary peritonitis; however, dogs with secondary peritonitis treated with surgery were more commonly discharged than those with primary peritonitis treated with surgery. Differences in primary and secondary peritonitis related to historical, physical examination, and clinical laboratory findings; bacteriologic findings; peritoneal effusion characteristics; and outcome were detected. However, larger case numbers are needed before alternative recommendations, such as avoidance of surgery, can be made.

Genomic sequencing of uric acid metabolizing and clearing genes in relationship to xanthine oxidase inhibitor dose.

PubMed

Carroll, Matthew B; Smith, Derek M; Shaak, Thomas L

2017-03-01

It remains unclear why the dose of xanthine oxidase inhibitors (XOI) allopurinol or febuxostat varies among patients though they reach similar serum uric acid (SUA) goal. We pursued genomic sequencing of XOI metabolism and clearance genes to identify single-nucleotide polymorphisms (SNPs) relate to differences in XOI dose. Subjects with a diagnosis of Gout based on the 1977 American College of Rheumatology Classification Criteria for the disorder, who were on stable doses of a XOI, and who were at their goal SUA level, were enrolled. The primary outcome was relationship between SNPs in any of these genes to XOI dose. The secondary outcome was relationship between SNPs and change in pre- and post-treatment SUA. We enrolled 100 subjects. The average patient age was 68.6 ± 10.6 years old. Over 80% were men and 77% were Caucasian. One SNP was associated with a higher XOI dose: rs75995567 (p = 0.031). Two SNPs were associated with 300 mg daily of allopurinol: rs11678615 (p = 0.022) and rs3731722 on Aldehyde Oxidase (AO) (His1297Arg) (p = 0.001). Two SNPs were associated with a lower dose of allopurinol: rs1884725 (p = 0.033) and rs34650714 (p = 0.006). For the secondary outcome, rs13415401 was the only SNP related to a smaller mean SUA change. Ten SNPs were identified with a larger change in SUA. Though multiple SNPs were identified in the primary and secondary outcomes of this study, rs3731722 is known to alter catalytic function for some aldehyde oxidase substrates.

Four Novel Cellulose Synthase (CESA) Genes from Birch (Betula platyphylla Suk.) Involved in Primary and Secondary Cell Wall Biosynthesis

PubMed Central

Liu, Xuemei; Wang, Qiuyu; Chen, Pengfei; Song, Funan; Guan, Minxiao; Jin, Lihua; Wang, Yucheng; Yang, Chuanping

2012-01-01

Cellulose synthase (CESA), which is an essential catalyst for the generation of plant cell wall biomass, is mainly encoded by the CesA gene family that contains ten or more members. In this study; four full-length cDNAs encoding CESA were isolated from Betula platyphylla Suk., which is an important timber species, using RT-PCR combined with the RACE method and were named as BplCesA3, −4, −7 and −8. These deduced CESAs contained the same typical domains and regions as their Arabidopsis homologs. The cDNA lengths differed among these four genes, as did the locations of the various protein domains inferred from the deduced amino acid sequences, which shared amino acid sequence identities ranging from only 63.8% to 70.5%. Real-time RT-PCR showed that all four BplCesAs were expressed at different levels in diverse tissues. Results indicated that BplCESA8 might be involved in secondary cell wall biosynthesis and floral development. BplCESA3 appeared in a unique expression pattern and was possibly involved in primary cell wall biosynthesis and seed development; it might also be related to the homogalacturonan synthesis. BplCESA7 and BplCESA4 may be related to the formation of a cellulose synthase complex and participate mainly in secondary cell wall biosynthesis. The extremely low expression abundance of the four BplCESAs in mature pollen suggested very little involvement of them in mature pollen formation in Betula. The distinct expression pattern of the four BplCesAs suggested they might participate in developments of various tissues and that they are possibly controlled by distinct mechanisms in Betula. PMID:23202892

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Statistical interior properties of globular proteins

NASA Astrophysics Data System (ADS)

Jiang, Zhou-Ting; Zhang, Lin-Xi; Sun, Ting-Ting; Wu, Tai-Quan

2009-10-01

The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories of globular proteins, the statistical properties are thoroughly discussed in this paper. Two parameters NC and ND are defined to confine the valid residues in detail. The relationship between hydrophobicity scales and valid residue percentage of each amino acid is given in the present work and the linear functions are shown in our statistical results. It is concluded that the hydrophobicity scale defined by chemical derivatives of the amino acids and nonpolar phase of large unilamellar vesicle membranes is the most effective technique to characterise the hydrophobic behavior of amino acid residues. Meanwhile, residue percentage Pi and sequential residue length Li of a certain protein i are calculated under different conditions. The statistical results show that the average value of Pi as well as Li of all-α proteins has a minimum among these 4 classes of globular proteins, indicating that all-α proteins are hardly capable of forming long-range contacts one by one along their linear amino acid sequences. All-β proteins have a higher tendency to construct long-range contacts along their primary sequences related to the secondary configurations, i.e. parallel and anti-parallel configurations of β sheets. The investigation of the interior properties of globular proteins give us the connection between the three-dimensional structure and its primary sequence data or secondary configurations, and help us to understand the structure of protein and its folding process well.

Formation of the black-hole binary M33 X-7 through mass exchange in a tight massive system.

PubMed

Valsecchi, Francesca; Glebbeek, Evert; Farr, Will M; Fragos, Tassos; Willems, Bart; Orosz, Jerome A; Liu, Jifeng; Kalogera, Vassiliki

2010-11-04

The X-ray source M33 X-7 in the nearby galaxy Messier 33 is among the most massive X-ray binary stellar systems known, hosting a rapidly spinning, 15.65M(⊙) black hole orbiting an underluminous, 70M(⊙) main-sequence companion in a slightly eccentric 3.45-day orbit (M(⊙), solar mass). Although post-main-sequence mass transfer explains the masses and tight orbit, it leaves unexplained the observed X-ray luminosity, the star's underluminosity, the black hole's spin and the orbital eccentricity. A common envelope phase, or rotational mixing, could explain the orbit, but the former would lead to a merger and the latter to an overluminous companion. A merger would also ensue if mass transfer to the black hole were invoked for its spin-up. Here we report simulations of evolutionary tracks which reveal that if M33 X-7 started as a primary body of 85M(⊙)-99M(⊙) and a secondary body of 28M(⊙)-32M(⊙), in a 2.8-3.1-d orbit, its observed properties can be consistently explained. In this model, the main-sequence primary transfers part of its envelope to the secondary and loses the rest in a wind; it ends its life as a ∼16M(⊙) helium star with an iron-nickel core that collapses to a black hole (with or without an accompanying supernova). The release of binding energy, and possibly collapse asymmetries, 'kick' the nascent black hole into an eccentric orbit. Wind accretion explains the X-ray luminosity, and the black-hole spin can be natal.

Laparoscopic evaluation of female factors in infertility.

PubMed

Aziz, Nousheen

2010-10-01

To find out different causes of female infertility with diagnostic laparoscopy and their comparative frequency in primary and secondary infertility. A case series. Department of Obstetric and Gynaecology, Liaquat University Hospital (LUH), Hyderabad, rom January 2006 to December 2007. All infertile women underwent diagnostic laparoscopy for primary and secondary infertility during the study period were included. Couples who had not lived together for at least 12 months, and those with male factor infertility were excluded. Data were collected on a proforma, and analysed on SPSS package for windows version 10. Frequencies were calculated for laparoscopic findings regarding primary and secondary infertility. Fifty infertile women underwent laparoscopy during the study period, 32 (64%) had primary infertility while 18 (36%) secondary infertility. Eight (25.0%) patients with primary and 2 (11.1%) patients with secondary infertility had no visible abnormality. The common finding was tubal blockage in 7 (21.9%) and 6 (33.3%) cases of primary and secondary infertility respectively. Five (15.6%) cases of primary infertility were detected as polycystic ovaries (PCO) which was not found in cases of secondary infertility. Endometriosis was found in 4 (12.5%) cases with primary infertility and 2 (11.1%) cases with secondary infertility. Pelvic inflammatory disease (PID) was found in 1 (3.1%) and 2 (16.7%) cases of primary and secondary infertility respectively. Peritubal and periovarian adhesions were detected in 2 (6.3%) cases with primary infertility and 4 (22.2%) cases with secondary infertility. Fibriod was found in 2 (6.3%) and 1 (5.6%) cases of primary and secondary infertility respectively. Ovarian cyst detected in 2 (6.3%) cases with primary infertility while none was found in cases of secondary infertility. Most common causes responsible for infertility were tubal occlusion, endometriosis, peritubal and periovarian adhesions. Ovarian causes were seen in primary infertility only.

Does Post-task Declarative Learning Have an Influence on Early Motor Memory Consolidation Over Day? An fMRI Study

PubMed Central

Rothkirch, Inken; Wolff, Stephan; Margraf, Nils G.; Pedersen, Anya; Witt, Karsten

2018-01-01

Previous studies demonstrated the influence of the post-learning period on procedural motor memory consolidation. In an early period after the acquisition, motor skills are vulnerable to modifications during wakefulness. Indeed, specific interventions such as world-list learning within this early phase of motor memory consolidation seem to enhance motor performance as an indicator for successful consolidation. This finding highlights the idea that manipulations of procedural and declarative memory systems during the early phase of memory consolidation over wakefulness may influence off-line consolidation. Using functional magnetic resonance imaging (fMRI) during initial motor sequence learning and motor sequence recall, we indirectly assess the influence of a secondary task taken place in the early phase of memory consolidation. All participants were scanned using fMRI during the learning phase of a serial reaction time task (SRTT) at 8 a.m. Afterwards, they were randomly assigned to one of five conditions. One group performed a declarative verbal, one a declarative nonverbal learning task. Two groups worked on attention tasks. A control group passed a resting condition. Participants stayed awake the whole day and performed the SRTT in the MRI scanner 12 h later at 8 p.m. At the behavioral level, the analysis of the reaction times failed to show a significant group difference. The primary analysis assessing fMRI data based on the contrast (sequence – random) between learning and retrieval also did not show any significant group differences. Therefore, our main analysis do not support the hypothesis that a secondary task influences the retrieval of the SRTT. In a more liberal fMRI analysis, we compared only the sequence blocks of the SRTT from learning to recall. BOLD signal decreased in the ipsilateral cerebellum and the supplementary motor area solely in the verbal learning group. Although our primary analysis failed to show significant changes between our groups, results of the secondary analysis could be an indication for a beneficial effect of the verbal declarative task in the early post-learning phase. A nonverbal learning task did not affect the activation within the motor network. Further studies are needed to replicate this finding and to assess the usefulness of this manipulation. PMID:29755315

Does Post-task Declarative Learning Have an Influence on Early Motor Memory Consolidation Over Day? An fMRI Study.

PubMed

Rothkirch, Inken; Wolff, Stephan; Margraf, Nils G; Pedersen, Anya; Witt, Karsten

2018-01-01

Previous studies demonstrated the influence of the post-learning period on procedural motor memory consolidation. In an early period after the acquisition, motor skills are vulnerable to modifications during wakefulness. Indeed, specific interventions such as world-list learning within this early phase of motor memory consolidation seem to enhance motor performance as an indicator for successful consolidation. This finding highlights the idea that manipulations of procedural and declarative memory systems during the early phase of memory consolidation over wakefulness may influence off-line consolidation. Using functional magnetic resonance imaging (fMRI) during initial motor sequence learning and motor sequence recall, we indirectly assess the influence of a secondary task taken place in the early phase of memory consolidation. All participants were scanned using fMRI during the learning phase of a serial reaction time task (SRTT) at 8 a.m. Afterwards, they were randomly assigned to one of five conditions. One group performed a declarative verbal, one a declarative nonverbal learning task. Two groups worked on attention tasks. A control group passed a resting condition. Participants stayed awake the whole day and performed the SRTT in the MRI scanner 12 h later at 8 p.m. At the behavioral level, the analysis of the reaction times failed to show a significant group difference. The primary analysis assessing fMRI data based on the contrast (sequence - random) between learning and retrieval also did not show any significant group differences. Therefore, our main analysis do not support the hypothesis that a secondary task influences the retrieval of the SRTT. In a more liberal fMRI analysis, we compared only the sequence blocks of the SRTT from learning to recall. BOLD signal decreased in the ipsilateral cerebellum and the supplementary motor area solely in the verbal learning group. Although our primary analysis failed to show significant changes between our groups, results of the secondary analysis could be an indication for a beneficial effect of the verbal declarative task in the early post-learning phase. A nonverbal learning task did not affect the activation within the motor network. Further studies are needed to replicate this finding and to assess the usefulness of this manipulation.

40 CFR 50.16 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.16 National primary and secondary ambient air quality standards for lead. (a) The national primary and...

Primary versus secondary achalasia: New signs on barium esophagogram

PubMed Central

Gupta, Pankaj; Debi, Uma; Sinha, Saroj Kant; Prasad, Kaushal Kishor

2015-01-01

Aim: To investigate new signs on barium swallow that can differentiate primary from secondary achalasia. Materials and Methods: Records of 30 patients with primary achalasia and 17 patients with secondary achalasia were reviewed. Clinical, endoscopic, and manometric data was recorded. Barium esophagograms were evaluated for peristalsis and morphology of distal esophageal segment (length, symmetry, nodularity, shouldering, filling defects, and “tram-track sign”). Results: Mean age at presentation was 39 years in primary achalasia and 49 years in secondary achalasia. The mean duration of symptoms was 3.5 years in primary achalasia and 3 months in secondary achalasia. False-negative endoscopic results were noted in the first instance in five patients. In the secondary achalasia group, five patients had distal esophageal segment morphology indistinguishable from that of primary achalasia. None of the patients with primary achalasia and 35% patients with secondary achalasia had a length of the distal segment approaching combined height of two vertebral bodies. None of the patients with secondary achalasia and 34% patients with primary achalasia had maximum caliber of esophagus approaching combined height of two vertebral bodies. Tertiary contractions were noted in 90% patients with primary achalasia and 24% patients with secondary achalasia. Tram-track sign was found in 55% patients with primary achalasia. Filling defects in the distal esophageal segment were noted in 94% patients with secondary achalasia. Conclusion: Length of distal esophageal segment, tertiary contractions, tram-track sign, and filling defects in distal esophageal segment are useful esophagographic features distinguishing primary from secondary achalasia. PMID:26288525

One-Pot Two-Step Multicomponent Process of Indole and Other Nitrogenous Heterocycles or Amines toward α-Oxo-acetamidines.

PubMed

Martinez-Ariza, Guillermo; McConnell, Nicholas; Hulme, Christopher

2016-04-15

A cesium carbonate promoted three-component reaction of N-H containing heterocycles, primary or secondary amines, arylglyoxaldehydes, and anilines is reported. The key step involves a tandem sequence of N-1 addition of a heterocycle or an amine to preformed α-iminoketones, followed by an air- or oxygen-mediated oxidation to form α-oxo-acetamidines. The scope of the reaction is enticingly broad, and this novel methodology is applied toward the synthesis of various polycyclic heterocycles.

Regions flanking ori sequences affect the replication efficiency of the mitochondrial genome of ori+ petite mutants from yeast.

PubMed

Rayko, E; Goursot, R; Cherif-Zahar, B; Melis, R; Bernardi, G

1988-03-31

The mitochondrial genomes of progenies from 26 crosses between 17 cytoplasmic, spontaneous, suppressive, ori+ petite mutants of Saccharomyces cerevisiae have been studied by electrophoresis of restriction fragments. Only parental genomes (or occasionally, genomes derived from them by secondary excisions) were found in the progenies of the almost 500 diploids investigated; no evidence for illegitimate, site-specific mitochondrial recombination was detected. One of the parental genomes was always found to be predominate over the other one, although to different extents in different crosses. This predominance appears to be due to a higher replication efficiency, which is correlated with a greater density of ori sequences on the mitochondrial genome (and with a shorter repeat unit size of the latter). Exceptions to the 'repeat-unit-size rule' were found, however, even when the parental mitochondrial genomes carried the same ori sequence. This indicates that noncoding, intergenic sequences outside ori sequences also play a role in modulating replication efficiency. Since in different petites such sequences differ in primary structure, size, and position relative to ori sequences, this modulation is likely to take place through an indirect effect on DNA and nucleoid structure.

Empirical analysis of RNA robustness and evolution using high-throughput sequencing of ribozyme reactions.

PubMed

Hayden, Eric J

2016-08-15

RNA molecules provide a realistic but tractable model of a genotype to phenotype relationship. This relationship has been extensively investigated computationally using secondary structure prediction algorithms. Enzymatic RNA molecules, or ribozymes, offer access to genotypic and phenotypic information in the laboratory. Advancements in high-throughput sequencing technologies have enabled the analysis of sequences in the lab that now rivals what can be accomplished computationally. This has motivated a resurgence of in vitro selection experiments and opened new doors for the analysis of the distribution of RNA functions in genotype space. A body of computational experiments has investigated the persistence of specific RNA structures despite changes in the primary sequence, and how this mutational robustness can promote adaptations. This article summarizes recent approaches that were designed to investigate the role of mutational robustness during the evolution of RNA molecules in the laboratory, and presents theoretical motivations, experimental methods and approaches to data analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

The rRNA evolution and procaryotic phylogeny

NASA Technical Reports Server (NTRS)

Fox, G. E.

1986-01-01

Studies of ribosomal RNA primary structure allow reconstruction of phylogenetic trees for prokaryotic organisms. Such studies reveal major dichotomy among the bacteria that separates them into eubacteria and archaebacteria. Both groupings are further segmented into several major divisions. The results obtained from 5S rRNA sequences are essentially the same as those obtained with the 16S rRNA data. In the case of Gram negative bacteria the ribosomal RNA sequencing results can also be directly compared with hybridization studies and cytochrome c sequencing studies. There is again excellent agreement among the several methods. It seems likely then that the overall picture of microbial phylogeny that is emerging from the RNA sequence studies is a good approximation of the true history of these organisms. The RNA data allow examination of the evolutionary process in a semi-quantitative way. The secondary structures of these RNAs are largely established. As a result it is possible to recognize examples of local structural evolution. Evolutionary pathways accounting for these events can be proposed and their probability can be assessed.

40 CFR 50.7 - National primary and secondary ambient air quality standards for PM2.5.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.7 National primary and secondary ambient air quality standards for PM2.5. (a) The national primary and...

40 CFR 50.13 - National primary and secondary ambient air quality standards for PM2.5.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.13 National primary and secondary ambient air quality standards for PM2.5. (a) The national primary...

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

PubMed Central

Chakrabarty, Prosanta; Warren, Melanie; Page, Lawrence M.; Baldwin, Carole C.

2013-01-01

Abstract An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the “Genetypes” naming system, which some have been reluctant to adopt because of the use of the “type” suffix in the terminology. In the new nomenclature, genetic sequences are labeled “genseq,” followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types – “genseq-1,” secondary types – “genseq-2,” collection-vouchered topotypes – “genseq-3,” collection-vouchered non-types – “genseq-4,” and non-types that lack specimen vouchers but have photo vouchers – “genseq-5.” To demonstrate use of the new nomenclature, we review recently published new-species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications. We encourage authors to adopt the GenSeq nomenclature (note capital “G” and “S” when referring to the nomenclatural program) to provide a searchable tag (e.g., “genseq”; note lowercase “g” and “s” when referring to sequences) for genetic sequences from types and other vouchered specimens. Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data. We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made. PMID:24223486

Sequence swapping does not result in conformation swapping for the beta4/beta5 and beta8/beta9 beta-hairpin turns in human acidic fibroblast growth factor.

PubMed

Kim, Jaewon; Lee, Jihun; Brych, Stephen R; Logan, Timothy M; Blaber, Michael

2005-02-01

The beta-turn is the most common type of nonrepetitive structure in globular proteins, comprising ~25% of all residues; however, a detailed understanding of effects of specific residues upon beta-turn stability and conformation is lacking. Human acidic fibroblast growth factor (FGF-1) is a member of the beta-trefoil superfold and contains a total of five beta-hairpin structures (antiparallel beta-sheets connected by a reverse turn). beta-Turns related by the characteristic threefold structural symmetry of this superfold exhibit different primary structures, and in some cases, different secondary structures. As such, they represent a useful system with which to study the role that turn sequences play in determining structure, stability, and folding of the protein. Two turns related by the threefold structural symmetry, the beta4/beta5 and beta8/beta9 turns, were subjected to both sequence-swapping and poly-glycine substitution mutations, and the effects upon stability, folding, and structure were investigated. In the wild-type protein these turns are of identical length, but exhibit different conformations. These conformations were observed to be retained during sequence-swapping and glycine substitution mutagenesis. The results indicate that the beta-turn structure at these positions is not determined by the turn sequence. Structural analysis suggests that residues flanking the turn are a primary structural determinant of the conformation within the turn.

RF transformer

DOEpatents

Smith, James L.; Helenberg, Harold W.; Kilsdonk, Dennis J.

1979-01-01

There is provided an improved RF transformer having a single-turn secondary of cylindrical shape and a coiled encapsulated primary contained within the secondary. The coil is tapered so that the narrowest separation between the primary and the secondary is at one end of the coil. The encapsulated primary is removable from the secondary so that a variety of different capacity primaries can be utilized with one secondary.

Primary and Secondary Abscission in Pisum sativum and Euphorbia pulcherrima—How Do They Compare and How Do They Differ?

PubMed Central

Hvoslef-Eide, Anne K.; Munster, Cristel M.; Mathiesen, Cecilie A.; Ayeh, Kwadwo O.; Melby, Tone I.; Rasolomanana, Paoly; Lee, YeonKyeong

2016-01-01

Abscission is a highly regulated and coordinated developmental process in plants. It is important to understand the processes leading up to the event, in order to better control abscission in crop plants. This has the potential to reduce yield losses in the field and increase the ornamental value of flowers and potted plants. A reliable method of abscission induction in poinsettia (Euphorbia pulcherrima) flowers has been established to study the process in a comprehensive manner. By correctly decapitating buds of the third order, abscission can be induced in 1 week. AFLP differential display (DD) was used to search for genes regulating abscission. Through validation using qRT-PCR, more information of the genes involved during induced secondary abscission have been obtained. A study using two pea (Pisum sativum) mutants in the def (Developmental funiculus) gene, which was compared with wild type peas (tall and dwarf in both cases) was performed. The def mutant results in a deformed, abscission-less zone instead of normal primary abscission at the funiculus. RNA in situ hybridization studies using gene sequences from the poinsettia differential display, resulted in six genes differentially expressed for abscission specific genes in both poinsettia and pea. Two of these genes are associated with gene up- or down-regulation during the first 2 days after decapitation in poinsettia. Present and previous results in poinsettia (biochemically and gene expressions), enables a more detailed division of the secondary abscission phases in poinsettia than what has previously been described from primary abscission in Arabidopsis. This study compares the inducible secondary abscission in poinsettia and the non-abscising mutants/wild types in pea demonstrating primary abscission zones. The results may have wide implications on the understanding of abscission, since pea and poinsettia have been separated for 94–98 million years in evolution, hence any genes or processes in common are bound to be widespread in the plant kingdom. PMID:26858724

Comparative effectiveness of next generation genomic sequencing for disease diagnosis: design of a randomized controlled trial in patients with colorectal cancer/polyposis syndromes.

PubMed

Gallego, Carlos J; Bennette, Caroline S; Heagerty, Patrick; Comstock, Bryan; Horike-Pyne, Martha; Hisama, Fuki; Amendola, Laura M; Bennett, Robin L; Dorschner, Michael O; Tarczy-Hornoch, Peter; Grady, William M; Fullerton, S Malia; Trinidad, Susan B; Regier, Dean A; Nickerson, Deborah A; Burke, Wylie; Patrick, Donald L; Jarvik, Gail P; Veenstra, David L

2014-09-01

Whole exome and whole genome sequencing are applications of next generation sequencing transforming clinical care, but there is little evidence whether these tests improve patient outcomes or if they are cost effective compared to current standard of care. These gaps in knowledge can be addressed by comparative effectiveness and patient-centered outcomes research. We designed a randomized controlled trial that incorporates these research methods to evaluate whole exome sequencing compared to usual care in patients being evaluated for hereditary colorectal cancer and polyposis syndromes. Approximately 220 patients will be randomized and followed for 12 months after return of genomic findings. Patients will receive findings associated with colorectal cancer in a first return of results visit, and findings not associated with colorectal cancer (incidental findings) during a second return of results visit. The primary outcome is efficacy to detect mutations associated with these syndromes; secondary outcomes include psychosocial impact, cost-effectiveness and comparative costs. The secondary outcomes will be obtained via surveys before and after each return visit. The expected challenges in conducting this randomized controlled trial include the relatively low prevalence of genetic disease, difficult interpretation of some genetic variants, and uncertainty about which incidental findings should be returned to patients. The approaches utilized in this study may help guide other investigators in clinical genomics to identify useful outcome measures and strategies to address comparative effectiveness questions about the clinical implementation of genomic sequencing in clinical care. Copyright © 2014 Elsevier Inc. All rights reserved.

Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies

PubMed Central

Timmermans, Marshall L.; Paudel, Yagya P.; Ross, Avena C.

2017-01-01

The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria. PMID:28762997

Preliminary examination of uranium deposits near Marysvale, Piute County, Utah

USGS Publications Warehouse

Granger, Harry C.; Bauer, Herman L.

1950-01-01

Autunite and other uranium minerals were discovered in 1948 by Pratt Seegmiller about 3 1/4 miles north of Marysvale, Piute County, Utah. Mining operations were begun in the summer of 1949 by the Vanadium Corporation of America on the Prospector and the Freedom claims, and by the Bullion Monarch Mining Company a the Bullion Monarch claims. These claims were examined briefly in December 1949 and January 1950 by the writers. The uranium deposits of the Marysvale district are in north-easterly striking fault zones in quartz monzonite that intrudes rocks of the "older" Tertiary volcanic sequence. Flows and tuffs of the "younger" Tertiary volcanic sequence uncomfortably overlie the earlier rocks. Autunite, tobernite, uranophane, schroeckingerite, and at least one unidentified secondary uranium mineral occur in the upper parts of the deposits. Pitchblende has been mined from the underground workings of the Prospector No. 1 mine. The uranium minerals are associated with dense quartz veins and intensely argillized wall rock. In the upper parts of the deposits pyrite is completely oxidized. The secondary uranium minerals probably were formed by the alteration of primary pitchblende by circulating meteoric waters.

Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies.

PubMed

Timmermans, Marshall L; Paudel, Yagya P; Ross, Avena C

2017-08-01

The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

40 CFR 421.300 - Applicability: Description of the primary and secondary titanium subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... primary and secondary titanium subcategory. 421.300 Section 421.300 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Titanium Subcategory § 421.300 Applicability: Description of the primary and secondary titanium subcategory. The provisions of this subpart are applicable to...

The mechanism of chromosome 7 inversion in human lymphocytes expressing chimeric gamma beta TCR.

PubMed

Retière, C; Halary, F; Peyrat, M A; Le Deist, F; Bonneville, M; Hallet, M M

1999-01-15

Functional chimeric TCR chains, encoded by V gamma J gamma C beta or V gamma J beta C beta hybrid gene TCR, are expressed at the surface of a small fraction of alpha beta T lymphocytes in healthy individuals. Their frequency is dramatically increased in patients with ataxia-telangiectasia, a syndrome associated with inherited genomic instability. As the TCR gamma and beta loci are in an inverted orientation on chromosome 7, the generation of such hybrid genes requires at least an inversion event. Until now, neither the sequences involved in this genetic mechanism nor the number of recombinations leading to the formation of functional transcriptional units have been characterized. In this manuscript, we demonstrate that at least two rearrangements, involving classical recombination signal sequence and the V(D)J recombinase complex, lead to the formation of productive hybrid genes. A primary inversion 7 event between D beta and J gamma genic segments generates C gamma V beta and C beta V gamma hybrid loci. Within the C gamma V beta locus, secondary rearrangements between V gamma and J gamma or V gamma and J beta elements generate functional genes. Besides, our results suggest that secondary rearrangements were blocked in the C beta V gamma locus of normal but not ataxia-telangiectasia T lymphocytes. We also provide formal evidence that the same D beta-3' recombination signal sequence can be used in successive rearrangements with J gamma and J beta genic segments, thus showing that a signal joint has been involved in a secondary recombination event.

Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

PubMed

Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying

2013-05-01

Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

Molecular responses to toxicological stressors: profiling microRNAs in wild Atlantic salmon (Salmo salar) exposed to acidic aluminum-rich water.

PubMed

Kure, Elin H; Sæbø, Mona; Stangeland, Astrid M; Hamfjord, Julian; Hytterød, Sigurd; Heggenes, Jan; Lydersen, Espen

2013-08-15

Atlantic salmon (Salmo salar) is among the most sensitive organisms toward acidic, aluminum exposure. Main documented responses to this type of stress are a combination of hypoxia and loss of blood plasma ions. Physiological responses to stress in fish are often grouped into primary, secondary and tertiary responses, where the above mentioned effects are secondary responses, while primary responses include endocrine changes as measurable levels of catecholamines and corticosteroids. In this study we have exposed young (14 months) Atlantic salmon to acid/Al water (pH ≈ 5.6, Al(i) ≈ 80 μg L⁻¹) for 3 days, and obtained clear and consistent decrease of Na⁺ and Cl⁻ ions, and increases of glucose in blood plasma, hematocrit and P(CO₂) in blood. We did not measure plasma cortisol (primary response compound), but analyzed effects on microRNA level (miRNA) in muscle tissue, as this may represent initial markers of primary stress responses. miRNAs regulate diverse biological processes, many are evolutionarily conserved, and hundreds have been identified in various animals, although only in a few fish species. We used a novel high-throughput sequencing (RNA-Seq) method to identify miRNAs in Atlantic salmon and specific miRNAs as potential early markers for stress. A total of 18 miRNAs were significantly differentially expressed (FDR<0.1) in exposed compared to control fish, four down-regulated and 14 up-regulated. An unsupervised hierarchical clustering of significant miRNAs revealed two clusters representing exposed and non-exposed individuals. Utilizing the genome of the zebrafish and bioinformatic tools, we identified 224 unique miRNAs in the Atlantic salmon samples sequenced. Additional laboratory studies focusing on function, stress dose-responses and temporal expression of the identified miRNAs will facilitate their use as initial markers for stress responses. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Petrologic evolution of CM chondrites: The difficulty of discriminating between nebular and parent-body effects

NASA Astrophysics Data System (ADS)

Kerridge, J. F.; McSween, H. Y., Jr.; Bunch, T. E.

1994-07-01

We wish to draw attention to a major controversy that has arisen in the area of CM-chondrite petrology. The problem is important because its resolution will have profound implications for ideas concerning nebular dynamics, gas-solid interactions in the nebula, and accretionary processes in the nebula, among other issues. On the one hand, cogent arguments have been presented that 'accretionary dust mantles,' were formed in the solar nebula prior to accretion of the CM parent asteroid(s). On the other hand, no-less-powerful arguments have been advanced that a significant fraction of the CM lithology is secondary, produced by aqueous alteration in the near-surface regions of an asteroid-sized object. Because most, if not all, CM chondrites are breccias, these two views could coexist harmoniously, were it not for the fact that some of the coarse-grained lithologies surrounded by 'accretion dust mantles' are themselves of apparently secondary origin. Such an observation must clearly force a reassessment of one or both of the present schools of thought. Our objective here is to stimulate such a reassessment. Four possible resolutions of this conflict may be postulated. First, perhaps nature found a way of permitting such secondary alteration to take place in the nebula. Second, maybe dust mantles could form in a regolith, rather than a nebular, environment. Third, it is possible that dust mantles around secondary lithologies are different from those around primary lithologies. Finally, perhaps formation of CM chondrites involved a more complex sequence of events than visualized so far, so that some apparently 'primary' processes postdated certain 'secondary' processes.

Al-Mg isotopic evidence for episodic alteration of Ca-Al-rich inclusions from Allende

NASA Astrophysics Data System (ADS)

Fagan, T. J.; Guan, Y.; MacPherson, G. J.

2007-08-01

Textures, mineral assemblages, and Al-Mg isotope systematics indicate a protracted, episodic secondary mineralization history for Allende Ca-Al-rich inclusions (CAIs). Detailed observations from one type B1 CAI, one B2, one compact type A (CTA), and one fluffy type A (FTA) indicate that these diverse types of CAIs are characterized by two distinct textural and mineralogic types of secondary mineralization: (1) grossular-rich domains, concentrated along melilite grain boundaries in CAI interiors, and (2) feldspathoid-bearing domains, confined mostly to CAI margins just interior to the Wark-Lovering rim sequence. The Al-Mg isotopic compositions of most secondary minerals in the type B1 CAI, and some secondary minerals in the other CAIs, show no resolvable excesses of 26Mg, whereas the primary CAI phases mostly yield correlated excesses of 26Mg with increasing Al/Mg corresponding to "canonical" initial 26Al/27Al ˜ 4.5-5 × 10-5. These secondary minerals formed at least 3 Ma after the primary CAI minerals. All but two analyses of secondary minerals from the fluffy type-A CAI define a correlated increase in 26Mg/24Mg with increasing Al/Mg, yielding (26Al/27Al)0 = (4.9 ± 2.8) × 10-6. The secondary minerals in this CAI formed 1.8-3.2 Ma after the primary CAI minerals. In both cases, the timing of secondary alteration is consistent with, but does not necessarily require, alteration in an asteroidal setting. One grossular from the type B2 CAI, and several grossular and secondary feldspar analyses from the compact type A CAI, have excesses of 26Mg consistent with initial 26Al/27Al ˜ 4.5 × 10-5. Especially in the compact type A CAI, where 26Mg/24Mg in grossular correlates with increasing Al/Mg, these 26Mg excesses are almost certainly due to in situ decay of 26Al. They indicate a nebular setting for formation of the grossular. The preservation of these diverse isotopic patterns indicates that heating on the Allende parent body was not pervasive enough to reset isotopic systematics of fine-grained secondary minerals. Secondary mineralization clearly was not restricted to a short time interval, and at least some alteration occurred coincident with CAI formation and melting events (chondrule formation) in the nebula. This observation supports the possibility that alteration followed by melting affected the compositional evolution of CAIs.

Alignment Test Results of the JWST Pathfinder Telescope Mirrors in the Cryogenic Environment

NASA Technical Reports Server (NTRS)

Whitman, Tony L.; Wells, Conrad; Hadaway, James; Knight, J. Scott; Lunt, Sharon

2016-01-01

After integration of the Optical Telescope Element (OTE) to the Integrated Science Instrument Module (ISIM) to become the OTIS, the James Webb Space Telescope OTIS is tested at NASAs Johnson Space Center (JSC) in the cryogenic vacuum Chamber A for alignment and optical performance. The alignment of the mirrors comprises a sequence of steps as follows: The mirrors are coarsely aligned using photogrammetry cameras with reflective targets attached to the sides of the mirrors. Then a multi-wavelength interferometer is aligned to the 18-segment primary mirror using cameras at the center of curvature to align reflected light from the segments and using fiducials at the edge of the primary mirror. Once the interferometer is aligned, the 18 primary mirror segments are then adjusted to optimize wavefront error of the aggregate mirror. This process phases the piston and tilt positions of all the mirror segments. An optical fiber placed at the Cassegrain focus of the telescope then emits light towards the secondary mirror to create a collimated beam emitting from the primary mirror. Portions of the collimated beam are retro-reflected from flat mirrors at the top of the chamber to pass through the telescope to the SI detector. The image on the detector is used for fine alignment of the secondary mirror and a check of the primary mirror alignment using many of the same analysis techniques used in the on-orbit alignment. The entire process was practiced and evaluated in 2015 at cryogenic temperature with the Pathfinder telescope.

A comparative study of primary and secondary stereotypies.

PubMed

Ghosh, Debabrata; Rajan, Prashant V; Erenberg, Gerald

2013-12-01

This study compares primary stereotypies (repetitive, self-stimulating, and seemingly nonsensical movements that can occur within typically developing children) and secondary stereotypies (those occurring within autistic or mentally retarded children). Utilizing a retrospective chart review from 1995 to 2010, the current study compares primary and secondary stereotypies by the application of a classification system that organizes the movement by its type (motor only, phonic only, mixed) and complexity. In addition, it investigates other parameters associated with the movements such as duration, frequency, age, functional impairment, and progression. The sample group consisted of 28 primary and 28 secondary cases. Primary stereotypies were predominantly motor, simple, of shorter duration, and of less frequency, whereas secondary stereotypies had more vocalization, complexity, longer durations, and higher frequencies. Moreover, functional impairment due to stereotypies was noted in 3 primary and 7 secondary cases, and worsening of stereotypies was noted in 70% of primary versus 44% of secondary cases.

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2010 CFR

2010-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2011 CFR

2011-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2014 CFR

2014-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2012 CFR

2012-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

40 CFR 421.180 - Applicability: Description of the primary and secondary germanium and gallium subcategory.

Code of Federal Regulations, 2013 CFR

2013-07-01

... primary and secondary germanium and gallium subcategory. 421.180 Section 421.180 Protection of Environment... POINT SOURCE CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.180 Applicability: Description of the primary and secondary germanium and gallium subcategory. The provisions of this subpart are...

Variation in bacterial endosymbionts associated with the date palm hopper, Ommatissus lybicus populations.

PubMed

Karimi, S; Izadi, H; Askari Seyahooei, M; Bagheri, A; Khodaygan, P

2018-04-01

The date palm hopper, Ommatissus lybicus, is a key pest of the date palm, which is expected to be comprised of many allopatric populations. The current study was carried out to determine bacterial endosymbiont diversity in the different populations of this pest. Ten date palm hopper populations were collected from the main date palm growing regions in Iran and an additional four samples from Pakistan, Oman, Egypt and Tunisia for detection of primary and secondary endosymbionts using polymerase chain reaction (PCR) assay with their specific primers. The PCR products were directly sequenced and edited using SeqMan software. The consensus sequences were subjected to a BLAST similarity search. The results revealed the presence of 'Candidatus Sulcia muelleri' (primary endosymbiont) and Wolbachia, Arsenophonus and Enterobacter (secondary endosymbionts) in all populations. This assay failed to detect 'Candidatus Nasuia deltocephalinicola' and Serratia in these populations. 'Ca. S. muelleri' exhibited a 100% infection frequency in populations and Wolbachia, Arsenophonus and Enterobacter demonstrated 100, 93.04 and 97.39% infection frequencies, respectively. The infection rate of Arsenophonus and Enterobacter ranged from 75 to 100% and 62.5 to 100%, respectively, in different populations of the insect. The results demonstrated multiple infections by 'Ca. Sulcia muelleri', Wolbachia, Arsenophonus and Enterobacter in the populations and may suggest significant roles for these endosymbionts on date palm hopper population fitness. This study provides an insight to endosymbiont variation in the date palm hopper populations; however, further investigation is needed to examine how these endosymbionts may affect host fitness.

Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences.

PubMed

Koopman, W J; Guetta, E; van de Wiel, C C; Vosman, B; van den Berg, R G

1998-11-01

Internal transcribed spacer (ITS-1) sequences from 97 accessions representing 23 species of Lactuca and related genera were determined and used to evaluate species relationships of Lactuca sensu lato (s.l.). The ITS-1 phylogenies, calculated using PAUP and PHYLIP, correspond better to the classification of Feráková than to other classifications evaluated, although the inclusion of sect. Lactuca subsect. Cyanicae is not supported. Therefore, exclusion of subsect. Cyanicae from Lactuca sensu Feráková is proposed. The amended genus contains the entire gene pool (sensu Harlan and De Wet) of cultivated lettuce (Lactuca sativa). The position of the species in the amended classification corresponds to their position in the lettuce gene pool. In the ITS-1 phylogenies, a clade with L. sativa, L. serriola, L. dregeana, L. altaica, and L. aculeata represents the primary gene pool. L. virosa and L. saligna, branching off closest to this clade, encompass the secondary gene pool. L. virosa is possibly of hybrid origin. The primary and secondary gene pool species are classified in sect. Lactuca subsect. Lactuca. The species L. quercina, L. viminea, L. sibirica, and L. tatarica, branching off next, represent the tertiary gene pool. They are classified in Lactuca sect. Lactucopsis, sect. Phaenixopus, and sect. Mulgedium, respectively. L. perennis and L. tenerrima, classified in sect. Lactuca subsect. Cyanicae, form clades with species from related genera and are not part of the lettuce gene pool.

Variation in Inflammatory/Regulatory Cytokines in Secondary, Tertiary, and Quaternary Challenges with Dengue Virus

PubMed Central

Sierra, Beatriz; Pérez, Ana B.; Alvarez, Mayling; García, Gissel; Vogt, Katrin; Aguirre, Eglys; Schmolke, Kathrin; Volk, Hans-Dieter; Guzmán, María G.

2012-01-01

Secondary heterologous dengue infection is a risk factor for severe disease manifestations because of the immune-enhancement phenomenon. Succeeding clinical infections are seldom reported, and the clinical course of tertiary and quaternary dengue infections is not clear. Cuba represents a unique environment to study tertiary/quaternary dengue infections in a population with known clinical and serologic dengue markers and no dengue endemicity. We took advantage of this exceptional epidemiologic condition to study the effect of primary, secondary, tertiary, and quaternary dengue infection exposure on the expression of pro-inflammatory and regulatory cytokines, critical in dengue infection pathogenesis, by using a dengue infection ex vivo model. Whereas secondary exposure induced a high cytokine response, we found a significantly lower expression of tumor necrosis factor-α, interferon-γ, interleukin-10, and tumor growth factor-β after tertiary and quaternary infectious challenge. Significant differences in expression of the cytokines were seen between the dengue immune profiles, suggesting that the sequence in which the immune system encounters serotypes may be important in determining the nature of the immune response to subsequent infections. PMID:22802438

Neural differentiation of caudal cell mass (secondary neurulation) in chick embryos: Hamburger and Hamilton Stages 16-45.

PubMed

Yang, Hee-Jin; Wang, Kyu-Chang; Chi, Je G; Lee, Myung-Sook; Lee, Yun-Jin; Kim, Seung-Ki; Cho, Byung-Kyu

2003-04-14

In an attempt to understand the events in the secondary neurulation in embryonic stage, we investigated morphological changes in the tail bud of normal developing chick embryos. Hamburger and Hamilton stage 16-45 embryos were harvested and processed for light microscopic studies. The secondary neural tube is formed by aggregation of the caudal cell mass. Cells are arranged into a cord-like mass (medullary cord), which is continuous with the primary neural tube. Multiple small cavities develop in the medullary cord, and these cavities coalesce into one single lumen. The process of coalescence is completed by stage 35, and the whole neural tube is transformed into one tube with a single continuous lumen. At this stage, the terminal portion of the neural tube is bulged dorsally. Thereafter, the caudal portion of the neural tube regresses, and the proximal portion develops into normal spinal cord. Transient occlusion of the central canal was observed at stage 40 in one sample. The sequence of events elucidated in this study can be used as base-line data for experiments concerning congenital malformations involving secondary neurulation.

40 CFR 50.6 - National primary and secondary ambient air quality standards for PM10.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 2 2010-07-01 2010-07-01 false National primary and secondary ambient... AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.6 National primary and secondary ambient air quality standards for PM10. (a) The level of the national...

A Study on Primary and Secondary School Students' Misconceptions about Greenhouse Effect (Erzurum Sampling)

ERIC Educational Resources Information Center

Gul, Seyda; Yesilyurt, Selami

2011-01-01

The aim of this study is to determine what level of primary and secondary school students' misconceptions related to greenhouse effect is. Study group consists of totally 280 students attended to totally 8 primary and secondary schools (4 primary school, 4 secondary school) which were determined with convenient sampling method from center of…

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

PubMed

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

BRAF/NRAS mutation frequencies among primary tumors and metastases in patients with melanoma.

PubMed

Colombino, Maria; Capone, Mariaelena; Lissia, Amelia; Cossu, Antonio; Rubino, Corrado; De Giorgi, Vincenzo; Massi, Daniela; Fonsatti, Ester; Staibano, Stefania; Nappi, Oscar; Pagani, Elena; Casula, Milena; Manca, Antonella; Sini, Mariacristina; Franco, Renato; Botti, Gerardo; Caracò, Corrado; Mozzillo, Nicola; Ascierto, Paolo A; Palmieri, Giuseppe

2012-07-10

The prevalence of BRAF, NRAS, and p16CDKN2A mutations during melanoma progression remains inconclusive. We investigated the prevalence and distribution of mutations in these genes in different melanoma tissues. In all, 291 tumor tissues from 132 patients with melanoma were screened. Paired samples of primary melanomas (n = 102) and synchronous or asynchronous metastases from the same patients (n = 165) were included. Tissue samples underwent mutation analysis (automated DNA sequencing). Secondary lesions included lymph nodes (n = 84), and skin (n = 36), visceral (n = 25), and brain (n = 44) sites. BRAF/NRAS mutations were identified in 58% of primary melanomas (43% BRAF; 15% NRAS); 62% in lymph nodes, 61% subcutaneous, 56% visceral, and 70% in brain sites. Mutations were observed in 63% of metastases (48% BRAF; 15% NRAS), a nonsignificant increase in mutation frequency after progression from primary melanoma. Of the paired samples, lymph nodes (93% consistency) and visceral metastases (96% consistency) presented a highly similar distribution of BRAF/NRAS mutations versus primary melanomas, with a significantly less consistent pattern in brain (80%) and skin metastases (75%). This suggests that independent subclones are generated in some patients. p16CDKN2A mutations were identified in 7% and 14% of primary melanomas and metastases, with a low consistency (31%) between secondary and primary tumor samples. In the era of targeted therapies, assessment of the spectrum and distribution of alterations in molecular targets among patients with melanoma is needed. Our findings about the prevalence of BRAF/NRAS/p16CDKN2A mutations in paired tumor lesions from patients with melanoma may be useful in the management of this disease.

Secondary Science Teachers' and Students' Involvement in a Primary School Community of Science Practice: How It Changed Their Practices and Interest in Science

NASA Astrophysics Data System (ADS)

Forbes, Anne; Skamp, Keith

2016-02-01

MyScience is a primary science education initiative in which being in a community of practice is integral to the learning process. In this initiative, stakeholder groups—primary teachers, primary students and mentors—interact around the `domain' of `investigating scientifically'. This paper builds on three earlier publications and interprets the findings of the views of four secondary science teachers and five year 9 secondary science students who were first-timer participants—as mentors—in MyScience. Perceptions of these mentors' interactions with primary students were analysed using attributes associated with both `communities of practice' and the `nature of science'. Findings reveal that participation in MyScience changed secondary science teachers' views and practices about how to approach the teaching of science in secondary school and fostered primary-secondary links. Year 9 students positively changed their views about secondary school science and confidence in science through participation as mentors. Implications for secondary science teaching and learning through participation in primary school community of science practice settings are discussed.

Structural Analysis of HMGD-DNA Complexes Reveal Influence of Intercalation on Sequence Selectivity and DNA Bending

PubMed Central

Churchill, Mair E.A.; Klass, Janet; Zoetewey, David L.

2010-01-01

The ubiquitous eukaryotic High-Mobility-Group-Box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 Å. The six proteins and fifty base pairs of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1-boxA-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending. PMID:20800069

Parental education, children's performance and the transition to higher secondary education: trends in primary and secondary effects over five Dutch school cohorts (1965-99).

PubMed

Kloosterman, Rianne; Ruiter, Stijn; de Graaf, Paul M; Kraaykamp, Gerbert

2009-06-01

According to Boudon, social background affects educational transitions as a result of differences in children's academic performance (primary effects) and differences in transition probabilities given children's level of academic performance (secondary effects). This study addresses historical changes in both primary and secondary effects on the educational transition from primary school to higher secondary education in The Netherlands. In addition, it considers changes over time in the relative importance of these effects. The study compares five cohorts of Dutch pupils, specifically those enrolling in secondary education in 1965, 1977, 1989, 1993 and 1999, and it employs counterfactual analyses. The main findings are that secondary effects have been stable and primary effects have fluctuated to some extent. As a result, the proportion of the total effect of social background accounted for by primary effects has increased somewhat, from 53 per cent to 58 per cent.

Using multifield measurements to eliminate alignment degeneracies in the JWST testbed telescope

NASA Astrophysics Data System (ADS)

Sabatke, Erin; Acton, Scott; Schwenker, John; Towell, Tim; Carey, Larkin; Shields, Duncan; Contos, Adam; Leviton, Doug

2007-09-01

The primary mirror of the James Webb Space Telescope (JWST) consists of 18 segments and is 6.6 meters in diameter. A sequence of commissioning steps is carried out at a single field point to align the segments. At that single field point, though, the segmented primary mirror can compensate for aberrations caused by misalignments of the remaining mirrors. The misalignments can be detected in the wavefronts of off-axis field points. The Multifield (MF) step in the commissioning process surveys five field points and uses a simple matrix multiplication to calculate corrected positions for the secondary and primary mirrors. A demonstration of the Multifield process was carried out on the JWST Testbed Telescope (TBT). The results show that the Multifield algorithm is capable of reducing the field dependency of the TBT to about 20 nm RMS, relative to the TBT design nominal field dependency.

Hyperparasitism in a Generalist Ectoparasitic Pupal Parasitoid, Pachycrepoideus vindemmiae (Hymenoptera: Pteromalidae), on Its Own Conspecifics: When the Lack of Resource Lead to Cannibalism.

PubMed

Chen, Wei; He, Zhang; Ji, Xiao-Li; Tang, Si-Ting; Hu, Hao-Yuan

2015-01-01

Hyperparasitism is a normal behavior of parasitoids, which often happens among species. Conspecific hyperparasitism, such as some kinds of heteronomous hyperparasitic behaviors, has been only reported in some species belonging to Aphelinidae. In this article, the conspecific hyperparasitism of Pachycrepoideus vindemmiae (Pteromalidae) is reported, with Drosophila puparia as hosts. Hosts were exposed to P. vindemmiae females twice to parasitism with nine, twelve, and fifteen day intervals between the two exposures. None of the infested hosts emerged more than one offspring, and emergence of parasitoid offspring occurred in two obvious events, synchronously with the exposure time intervals, which suggested that offspring emerging during the first and second events would come from the primary and secondary parasitoids, respectively, and the inference with the developmental duration of offspring also indicated this. With two P. vindemmiae strains that could be identified by a simple sequence repeat marker, the above speculation of the origin of those offspring emerging during the two events was confirmed. Dissection of hosts exposed twice revealed a cannibalism behavior of larvae from the secondary foundresses on the primary conspecific pupae. Our results suggested a conspecific hyperparasitism behavior of the secondary parasitoids on the primary conspecifics. Measures showed a reduced body size for the adults from the conspecific hyperparasitism. Foundresses from the conspecific hyperparasitism had less fitness variables than those from primary parasitism, with shorter longevity, less life time fecundity, lower values of infestation degree, and lower success rate of parasitism. However, when the parasitoids from the conspecific hyperparasitism met healthy Drosophila puparia, their offspring would recover to normal size. Frequency of the conspecific hyperparasitism behavior enhanced with the decreasing of proportion of healthy hosts in the oviposition patch. The conspecific hyperparasitism of P. vindemmiae on the primary conspecifics would be helpful to last the population when healthy hosts are absent in the oviposition patch.

Hyperparasitism in a Generalist Ectoparasitic Pupal Parasitoid, Pachycrepoideus vindemmiae (Hymenoptera: Pteromalidae), on Its Own Conspecifics: When the Lack of Resource Lead to Cannibalism

PubMed Central

Chen, Wei; He, Zhang; Ji, Xiao-Li; Tang, Si-Ting; Hu, Hao-Yuan

2015-01-01

Hyperparasitism is a normal behavior of parasitoids, which often happens among species. Conspecific hyperparasitism, such as some kinds of heteronomous hyperparasitic behaviors, has been only reported in some species belonging to Aphelinidae. In this article, the conspecific hyperparasitism of Pachycrepoideus vindemmiae (Pteromalidae) is reported, with Drosophila puparia as hosts. Hosts were exposed to P. vindemmiae females twice to parasitism with nine, twelve, and fifteen day intervals between the two exposures. None of the infested hosts emerged more than one offspring, and emergence of parasitoid offspring occurred in two obvious events, synchronously with the exposure time intervals, which suggested that offspring emerging during the first and second events would come from the primary and secondary parasitoids, respectively, and the inference with the developmental duration of offspring also indicated this. With two P. vindemmiae strains that could be identified by a simple sequence repeat marker, the above speculation of the origin of those offspring emerging during the two events was confirmed. Dissection of hosts exposed twice revealed a cannibalism behavior of larvae from the secondary foundresses on the primary conspecific pupae. Our results suggested a conspecific hyperparasitism behavior of the secondary parasitoids on the primary conspecifics. Measures showed a reduced body size for the adults from the conspecific hyperparasitism. Foundresses from the conspecific hyperparasitism had less fitness variables than those from primary parasitism, with shorter longevity, less life time fecundity, lower values of infestation degree, and lower success rate of parasitism. However, when the parasitoids from the conspecific hyperparasitism met healthy Drosophila puparia, their offspring would recover to normal size. Frequency of the conspecific hyperparasitism behavior enhanced with the decreasing of proportion of healthy hosts in the oviposition patch. The conspecific hyperparasitism of P. vindemmiae on the primary conspecifics would be helpful to last the population when healthy hosts are absent in the oviposition patch. PMID:25909476

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

PubMed Central

Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver

2007-01-01

We propose a new model for predicting the retention time of oligonucleotides. The model is based on ν support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619

The carbohydrate-binding module (CBM)-like sequence is crucial for rice CWA1/BC1 function in proper assembly of secondary cell wall materials.

PubMed

Sato, Kanna; Ito, Sachiko; Fujii, Takeo; Suzuki, Ryu; Takenouchi, Sachi; Nakaba, Satoshi; Funada, Ryo; Sano, Yuzou; Kajita, Shinya; Kitano, Hidemi; Katayama, Yoshihiro

2010-11-01

We recently reported that the cwa1 mutation disturbed the deposition and assembly of secondary cell wall materials in the cortical fiber of rice internodes. Genetic analysis revealed that cwa1 is allelic to bc1, which encodes glycosylphosphatidylinositol (GPI)-anchored COBRA-like protein with the highest homology to Arabidopsis COBRA-like 4 (COBL4) and maize Brittle Stalk 2 (Bk2). Our results suggested that CWA1/BC1 plays a role in assembling secondary cell wall materials at appropriate sites, enabling synthesis of highly ordered secondary cell wall structure with solid and flexible internodes in rice. The N-terminal amino acid sequence of CWA1/BC1, as well as its orthologs (COBL4, Bk2) and other BC1-like proteins in rice, shows weak similarity to a family II carbohydrate-binding module (CBM2) of several bacterial cellulases. To investigate the importance of the CBM-like sequence of CWA1/BC1 in the assembly of secondary cell wall materials, Trp residues in the CBM-like sequence, which is important for carbohydrate binding, were substituted for Val residues and introduced into the cwa1 mutant. CWA1/BC1 with the mutated sequence did not complement the abnormal secondary cell walls seen in the cwa1 mutant, indicating that the CBM-like sequence is essential for the proper function of CWA1/BC1, including assembly of secondary cell wall materials.

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling–A Feasibility Study

PubMed Central

Weißenborn, Sandra; Walther, Dirk

2017-01-01

Despite many developed experimental and computational approaches, functional gene annotation remains challenging. With the rapidly growing number of sequenced genomes, the concept of phylogenetic profiling, which predicts functional links between genes that share a common co-occurrence pattern across different genomes, has gained renewed attention as it promises to annotate gene functions based on presence/absence calls alone. We applied phylogenetic profiling to the problem of metabolic pathway assignments of plant genes with a particular focus on secondary metabolism pathways. We determined phylogenetic profiles for 40,960 metabolic pathway enzyme genes with assigned EC numbers from 24 plant species based on sequence and pathway annotation data from KEGG and Ensembl Plants. For gene sequence family assignments, needed to determine the presence or absence of particular gene functions in the given plant species, we included data of all 39 species available at the Ensembl Plants database and established gene families based on pairwise sequence identities and annotation information. Aside from performing profiling comparisons, we used machine learning approaches to predict pathway associations from phylogenetic profiles alone. Selected metabolic pathways were indeed found to be composed of gene families of greater than expected phylogenetic profile similarity. This was particularly evident for primary metabolism pathways, whereas for secondary pathways, both the available annotation in different species as well as the abstraction of functional association via distinct pathways proved limiting. While phylogenetic profile similarity was generally not found to correlate with gene co-expression, direct physical interactions of proteins were reflected by a significantly increased profile similarity suggesting an application of phylogenetic profiling methods as a filtering step in the identification of protein-protein interactions. This feasibility study highlights the potential and challenges associated with phylogenetic profiling methods for the detection of functional relationships between genes as well as the need to enlarge the set of plant genes with proven secondary metabolism involvement as well as the limitations of distinct pathways as abstractions of relationships between genes. PMID:29163570

Evolutionary optimization of biopolymers and sequence structure maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reidys, C.M.; Kopp, S.; Schuster, P.

1996-06-01

Searching for biopolymers having a predefined function is a core problem of biotechnology, biochemistry and pharmacy. On the level of RNA sequences and their corresponding secondary structures we show that this problem can be analyzed mathematically. The strategy will be to study the properties of the RNA sequence to secondary structure mapping that is essential for the understanding of the search process. We show that to each secondary structure s there exists a neutral network consisting of all sequences folding into s. This network can be modeled as a random graph and has the following generic properties: it is densemore » and has a giant component within the graph of compatible sequences. The neutral network percolates sequence space and any two neutral nets come close in terms of Hamming distance. We investigate the distribution of the orders of neutral nets and show that above a certain threshold the topology of neutral nets allows to find practically all frequent secondary structures.« less

V380 Dra: New short-period totally eclipsing active binary

NASA Astrophysics Data System (ADS)

Özdarcan, O.

2014-02-01

In this study, first complete and standard BVR light curves and photometric analysis of the eclipsing binary system V380 Dra are presented. Photometric analysis result indicates that the system has components which are cool main sequence stars. In light and color curves, remarkable asymmetry is observed, especially after secondary minimum, which is believed to be a result of chromospheric activity in one or both components. O-C diagram of available small number of eclipse times, together with new eclipse timings in this work, exhibits no significant variation. Preliminary light curve solution shows that the secondary minimum is total eclipse. By using the advantage of total eclipse and mass-luminosity relation, it is found that the system has a possible mass ratio of q = 0.81. First estimation of masses and radii of primary and secondary components are M1 = 0.77 M⊙,M2 = 0.62 M⊙ and R1 = 0.93 R⊙,R2 = 0.77 R⊙, respectively.

The Design and Usage of the New Data Management Features in NASTRAN

NASA Technical Reports Server (NTRS)

Pamidi, P. R.; Brown, W. K.

1984-01-01

Two new data management features are installed in the April 1984 release of NASTRAN. These two features are the Rigid Format Data Base and the READFILE capability. The Rigid Format Data Base is stored on external files in card image format and can be easily maintained and expanded by the use of standard text editors. This data base provides the user and the NASTRAN maintenance contractor with an easy means for making changes to a Rigid Format or for generating new Rigid Formats without unnecessary compilations and link editing of NASTRAN. Each Rigid Format entry in the data base contains the Direct Matrix Abstraction Program (DMAP), along with the associated restart, DMAP sequence subset and substructure control flags. The READFILE capability allows an user to reference an external secondary file from the NASTRAN primary input file and to read data from this secondary file. There is no limit to the number of external secondary files that may be referenced and read.

Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM.

PubMed

Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

2015-01-01

Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM). Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS), segmented PsePSSM, and segmented autocovariance transformation (ACT) based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640) are adopted in this paper. Then a 700-dimensional (700D) feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA). To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

The Influence of Primary and Secondary DNA Structure in Deletion and Duplication between Direct Repeats in Escherichia Coli

PubMed Central

Trinh, T. Q.; Sinden, R. R.

1993-01-01

We describe a system to measure the frequency of both deletions and duplications between direct repeats. Short 17- and 18-bp palindromic and nonpalindromic DNA sequences were cloned into the EcoRI site within the chloramphenicol acetyltransferase gene of plasmids pBR325 and pJT7. This creates an insert between direct repeated EcoRI sites and results in a chloramphenicol-sensitive phenotype. Selection for chloramphenicol resistance was utilized to select chloramphenicol resistant revertants that included those with precise deletion of the insert from plasmid pBR325 and duplication of the insert in plasmid pJT7. The frequency of deletion or duplication varied more than 500-fold depending on the sequence of the short sequence inserted into the EcoRI site. For the nonpalindromic inserts, multiple internal direct repeats and the length of the direct repeats appear to influence the frequency of deletion. Certain palindromic DNA sequences with the potential to form DNA hairpin structures that might stabilize the misalignment of direct repeats had a high frequency of deletion. Other DNA sequences with the potential to form structures that might destabilize misalignment of direct repeats had a very low frequency of deletion. Duplication mutations occurred at the highest frequency when the DNA between the direct repeats contained no direct or inverted repeats. The presence of inverted repeats dramatically reduced the frequency of duplications. The results support the slippage-misalignment model, suggesting that misalignment occurring during DNA replication leads to deletion and duplication mutations. The results also support the idea that the formation of DNA secondary structures during DNA replication can facilitate and direct specific mutagenic events. PMID:8325478

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Retention Load of Telescopic Crowns with Different Taper Angles between Cobalt-Chromium and Polyetheretherketone Made with Three Different Manufacturing Processes Examined by Pull-Off Test.

PubMed

Wagner, Christina; Stock, Veronika; Merk, Susanne; Schmidlin, Patrick R; Roos, Malgorzata; Eichberger, Marlis; Stawarczyk, Bogna

2018-02-01

To investigate the retention loads of differently fabricated secondary telescopic polyetheretherketone (PEEK) crowns on cobalt-chromium primary crowns with different tapers. Cobalt-chromium primary crowns with 0°, 1°, and 2° tapers were constructed, milled, and sintered. Corresponding secondary crowns were fabricated by milling, pressing from pellets, and pressing from granules. For these nine test groups, the pull-off tests of each crown combination were performed 20 times, and the retention loads were measured (Zwick 1445, 50 mm/min). Data were analyzed using linear regression, covariance analysis, mixed models, Kruskal-Wallis, and Mann-Whitney U-test, together with the Benferroni-Holm correction. The mixed models covariance analysis reinforced stable retention load values (p = 0.162) for each single test sequence. There was no interaction between the groups and the separation cycles (p = 0.179). Milled secondary crowns with 0° showed the lowest mean retention load values compared to all tested groups (p = 0.003) followed by those pressed form pellets with 1°. Regarding the different tapers, no effect of manufacturing method on the results was observed within 1° and 2° groups (p = 0.540; p = 0.052); however, among the 0° groups, the milled ones showed significantly the lowest retention load values (p = 0.002). Among the manufacturing methods, both pressed groups showed no impact of taper on the retention load values (p > 0.324 and p > 0.123, respectively), whereas among the milled secondary crowns, the 0° taper showed significantly lower retention load values than the 1° and 2° taper (p < 0.002). Based on these results, telescopic crowns made of PEEK seem to show stable retention load values for each test sequence; however, data with thermo-mechanical aging are still required. In addition, further developments in CAD/CAM manufacturing of PEEK materials for telescopic crowns are warranted, especially for 0°. © 2016 by the American College of Prosthodontists.

Government Funding on Access to Secondary Education in Kenya: Challenges and Prospects

ERIC Educational Resources Information Center

Ndiku, J. Mualuko; Muhavi, S. Lucy

2013-01-01

One of the major challenges facing secondary education sub-sector in Kenya over the years is low transition rate from primary to secondary level of education. This has contributed to low enrolment at secondary schools with a wide gap existing between primary and secondary enrolment. With the introduction of Free Primary Education in 2003, the gap…

Hepatitis Delta Antigen Requires a Flexible Quasi-Double-Stranded RNA Structure To Bind and Condense Hepatitis Delta Virus RNA in a Ribonucleoprotein Complex

PubMed Central

Griffin, Brittany L.; Chasovskikh, Sergey; Dritschilo, Anatoly

2014-01-01

ABSTRACT The circular genome and antigenome RNAs of hepatitis delta virus (HDV) form characteristic unbranched, quasi-double-stranded RNA secondary structures in which short double-stranded helical segments are interspersed with internal loops and bulges. The ribonucleoprotein complexes (RNPs) formed by these RNAs with the virus-encoded protein hepatitis delta antigen (HDAg) perform essential roles in the viral life cycle, including viral replication and virion formation. Little is understood about the formation and structure of these complexes and how they function in these key processes. Here, the specific RNA features required for HDAg binding and the topology of the complexes formed were investigated. Selective 2′OH acylation analyzed by primer extension (SHAPE) applied to free and HDAg-bound HDV RNAs indicated that the characteristic secondary structure of the RNA is preserved when bound to HDAg. Notably, the analysis indicated that predicted unpaired positions in the RNA remained dynamic in the RNP. Analysis of the in vitro binding activity of RNAs in which internal loops and bulges were mutated and of synthetically designed RNAs demonstrated that the distinctive secondary structure, not the primary RNA sequence, is the major determinant of HDAg RNA binding specificity. Atomic force microscopy analysis of RNPs formed in vitro revealed complexes in which the HDV RNA is substantially condensed by bending or wrapping. Our results support a model in which the internal loops and bulges in HDV RNA contribute flexibility to the quasi-double-stranded structure that allows RNA bending and condensing by HDAg. IMPORTANCE RNA-protein complexes (RNPs) formed by the hepatitis delta virus RNAs and protein, HDAg, perform critical roles in virus replication. Neither the structures of these RNPs nor the RNA features required to form them have been characterized. HDV RNA is unusual in that it forms an unbranched quasi-double-stranded structure in which short base-paired segments are interspersed with internal loops and bulges. We analyzed the role of the HDV RNA sequence and secondary structure in the formation of a minimal RNP and visualized the structure of this RNP using atomic force microscopy. Our results indicate that HDAg does not recognize the primary sequence of the RNA; rather, the principle contribution of unpaired bases in HDV RNA to HDAg binding is to allow flexibility in the unbranched quasi-double-stranded RNA structure. Visualization of RNPs by atomic force microscopy indicated that the RNA is significantly bent or condensed in the complex. PMID:24741096

Petrologic evolution of CM chondrites: The difficulty of discriminating between nebular and parent-body effects. [Abstract only

NASA Technical Reports Server (NTRS)

Kerridge, J. F.; Mcsween, H. Y., Jr.; Bunch, T. E.

1994-01-01

We wish to draw attention to a major controversy that has arisen in the area of CM-chondrite petrology. The problem is important because its resolution will have profound implications for ideas concerning nebular dynamics, gas-solid interactions in the nebula, and accretionary processes in the nebula, among other issues. On the one hand, cogent arguments have been presented that 'accretionary dust mantles,' were formed in the solar nebula prior to accretion of the CM parent asteroid(s). On the other hand, no-less-powerful arguments have been advanced that a significant fraction of the CM lithology is secondary, produced by aqueous alteration in the near-surface regions of an asteroid-sized object. Because most, if not all, CM chondrites are breccias, these two views could coexist harmoniously, were it not for the fact that some of the coarse-grained lithologies surrounded by 'accretion dust mantles' are themselves of apparently secondary origin. Such an observation must clearly force a reassessment of one or both of the present schools of thought. Our objective here is to stimulate such a reassessment. Four possible resolutions of this conflict may be postulated. First, perhaps nature found a way of permitting such secondary alteration to take place in the nebula. Second, maybe dust mantles could form in a regolith, rather than a nebular, environment. Third, it is possible that dust mantles around secondary lithologies are different from those around primary lithologies. Finally, perhaps formation of CM chondrites involved a more complex sequence of events than visualized so far, so that some apparently 'primary' processes postdated certain 'secondary' processes.

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

PubMed Central

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

Gratitude, protective buffering, and cognitive dissonance: How families respond to pediatric whole exome sequencing in the absence of actionable results.

PubMed

Werner-Lin, Allison; Zaspel, Lori; Carlson, Mae; Mueller, Rebecca; Walser, Sarah A; Desai, Ria; Bernhardt, Barbara A

2018-03-01

Clinical genome and exome sequencing (CGES) may identify variants leading to targeted management of existing conditions. Yet, CGES often fails to identify pathogenic diagnostic variants and introduces uncertainties by detecting variants of uncertain significance (VUS) and secondary findings. This study investigated how families understand findings and adjust their perspectives on CGES. As part of NIH's Clinical Sequencing Exploratory Research Consortium, children were recruited from clinics at the Children's Hospital of Pennsylvania (CHOP) and offered exome sequencing. Primary pathogenic and possibly pathogenic, and some secondary findings were returned. Investigators digitally recorded results disclosure sessions and conducted 3-month follow up interviews with 10 adolescents and a parent. An interdisciplinary team coded all transcripts. Participants were initially disappointed with findings, yet reactions evolved within disclosure sessions and at 3-month interviews toward acceptance and satisfaction. Families erroneously expected, and prepared extensively, to learn about risk for common conditions. During disclosure sessions, parents and adolescents varied in how they monitored and responded to each others reactions. Several misinterpreted, or overestimated, the utility of findings to attribute meaning and achieve closure for the CGES experience. Participants perceived testing as an opportunity to improve disease management despite results that did not introduce new treatments or diagnoses. Future research may examine whether families experience cognitive dissonance regarding discrepancies between expectations and findings, and how protective buffering minimizes the burden of disappointment on loved ones. As CGES is increasingly integrated into clinical care providers must contend with tempering family expectations and interpretations of findings while managing complex medical care. © 2018 Wiley Periodicals, Inc.

Discovery and characterization of 3000+ main-sequence binaries from APOGEE spectra

NASA Astrophysics Data System (ADS)

El-Badry, Kareem; Ting, Yuan-Sen; Rix, Hans-Walter; Quataert, Eliot; Weisz, Daniel R.; Cargile, Phillip; Conroy, Charlie; Hogg, David W.; Bergemann, Maria; Liu, Chao

2018-05-01

We develop a data-driven spectral model for identifying and characterizing spatially unresolved multiple-star systems and apply it to APOGEE DR13 spectra of main-sequence stars. Binaries and triples are identified as targets whose spectra can be significantly better fit by a superposition of two or three model spectra, drawn from the same isochrone, than any single-star model. From an initial sample of ˜20 000 main-sequence targets, we identify ˜2500 binaries in which both the primary and secondary stars contribute detectably to the spectrum, simultaneously fitting for the velocities and stellar parameters of both components. We additionally identify and fit ˜200 triple systems, as well as ˜700 velocity-variable systems in which the secondary does not contribute detectably to the spectrum. Our model simplifies the process of simultaneously fitting single- or multi-epoch spectra with composite models and does not depend on a velocity offset between the two components of a binary, making it sensitive to traditionally undetectable systems with periods of hundreds or thousands of years. In agreement with conventional expectations, almost all the spectrally identified binaries with measured parallaxes fall above the main sequence in the colour-magnitude diagram. We find excellent agreement between spectrally and dynamically inferred mass ratios for the ˜600 binaries in which a dynamical mass ratio can be measured from multi-epoch radial velocities. We obtain full orbital solutions for 64 systems, including 14 close binaries within hierarchical triples. We make available catalogues of stellar parameters, abundances, mass ratios, and orbital parameters.

Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

PubMed

Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F; Feldmann, Heinz

2013-01-01

Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

Alignment test results of the JWST Pathfinder Telescope mirrors in the cryogenic environment

NASA Astrophysics Data System (ADS)

Whitman, Tony L.; Wells, Conrad; Hadaway, James B.; Knight, J. Scott; Lunt, Sharon

2016-07-01

After integration of the Optical Telescope Element (OTE) to the Integrated Science Instrument Module (ISIM) to become the OTIS, the James Webb Space Telescope OTIS is tested at NASA's Johnson Space Center (JSC) in the cryogenic vacuum Chamber A for alignment and optical performance. The alignment of the mirrors comprises a sequence of steps as follows: The mirrors are coarsely aligned using photogrammetry cameras with reflective targets attached to the sides of the mirrors. Then a multi-wavelength interferometer is aligned to the 18-segment primary mirror using cameras at the center of curvature to align reflected light from the segments and using fiducials at the edge of the primary mirror. Once the interferometer is aligned, the 18 primary mirror segments are then adjusted to optimize wavefront error of the aggregate mirror. This process phases the piston and tilt positions of all the mirror segments. An optical fiber placed at the Cassegrain focus of the telescope then emits light towards the secondary mirror to create a collimated beam emitting from the primary mirror. Portions of the collimated beam are retro-reflected from flat mirrors at the top of the chamber to pass through the telescope to the Science Instrument (SI) detector. The image on the detector is used for fine alignment of the secondary mirror and a check of the primary mirror alignment using many of the same analysis techniques used in the on-orbit alignment. The entire process was practiced and evaluated in 2015 at cryogenic temperature with the Pathfinder telescope.

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology

PubMed Central

Durrant, Jacob D.; Amaro, Rommie E.; Xie, Lei; Urbaniak, Michael D.; Ferguson, Michael A. J.; Haapalainen, Antti; Chen, Zhijun; Di Guilmi, Anne Marie; Wunder, Frank; Bourne, Philip E.; McCammon, J. Andrew

2010-01-01

Conventional drug design embraces the “one gene, one drug, one disease” philosophy. Polypharmacology, which focuses on multi-target drugs, has emerged as a new paradigm in drug discovery. The rational design of drugs that act via polypharmacological mechanisms can produce compounds that exhibit increased therapeutic potency and against which resistance is less likely to develop. Additionally, identifying multiple protein targets is also critical for side-effect prediction. One third of potential therapeutic compounds fail in clinical trials or are later removed from the market due to unacceptable side effects often caused by off-target binding. In the current work, we introduce a multidimensional strategy for the identification of secondary targets of known small-molecule inhibitors in the absence of global structural and sequence homology with the primary target protein. To demonstrate the utility of the strategy, we identify several targets of 4,5-dihydroxy-3-(1-naphthyldiazenyl)-2,7-naphthalenedisulfonic acid, a known micromolar inhibitor of Trypanosoma brucei RNA editing ligase 1. As it is capable of identifying potential secondary targets, the strategy described here may play a useful role in future efforts to reduce drug side effects and/or to increase polypharmacology. PMID:20098496

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

PubMed

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-06

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology.

PubMed

Durrant, Jacob D; Amaro, Rommie E; Xie, Lei; Urbaniak, Michael D; Ferguson, Michael A J; Haapalainen, Antti; Chen, Zhijun; Di Guilmi, Anne Marie; Wunder, Frank; Bourne, Philip E; McCammon, J Andrew

2010-01-22

Conventional drug design embraces the "one gene, one drug, one disease" philosophy. Polypharmacology, which focuses on multi-target drugs, has emerged as a new paradigm in drug discovery. The rational design of drugs that act via polypharmacological mechanisms can produce compounds that exhibit increased therapeutic potency and against which resistance is less likely to develop. Additionally, identifying multiple protein targets is also critical for side-effect prediction. One third of potential therapeutic compounds fail in clinical trials or are later removed from the market due to unacceptable side effects often caused by off-target binding. In the current work, we introduce a multidimensional strategy for the identification of secondary targets of known small-molecule inhibitors in the absence of global structural and sequence homology with the primary target protein. To demonstrate the utility of the strategy, we identify several targets of 4,5-dihydroxy-3-(1-naphthyldiazenyl)-2,7-naphthalenedisulfonic acid, a known micromolar inhibitor of Trypanosoma brucei RNA editing ligase 1. As it is capable of identifying potential secondary targets, the strategy described here may play a useful role in future efforts to reduce drug side effects and/or to increase polypharmacology.

Use of antihypertensive medications and diagnostic tests among privately insured adolescents and young adults with primary versus secondary hypertension.

PubMed

Yoon, Esther Y; Cohn, Lisa; Freed, Gary; Rocchini, Albert; Kershaw, David; Ascione, Frank; Clark, Sarah

2014-07-01

To compare the use of antihypertensive medications and diagnostic tests among adolescents and young adults with primary versus secondary hypertension. We conducted retrospective cohort analysis of claims data for adolescents and young adults (12-21 years of age) with ≥3 years of insurance coverage (≥11 months/year) in a large private managed care plan during 2003-2009 with diagnosis of primary hypertension or secondary hypertension. We examined their use of antihypertensive medications and identified demographic characteristics and the presence of obesity-related comorbidities. For the subset receiving antihypertensive medications, we examined their diagnostic test use (echocardiograms, renal ultrasounds, and electrocardiograms). The study sample included 1,232 adolescents and young adults; 84% had primary hypertension and 16% had secondary hypertension. The overall prevalence rate of hypertension was 2.6%. One quarter (28%) with primary hypertension had one or more antihypertensive medications, whereas 65% with secondary hypertension had one or more antihypertensive medications. Leading prescribers of antihypertensives for subjects with primary hypertension were primary care physicians (80%), whereas antihypertensive medications were equally prescribed by primary care physicians (43%) and sub-specialists (37%) for subjects with secondary hypertension. The predominant hypertension diagnosis among adolescents and young adults is primary hypertension. Antihypertensive medication use was higher among those with secondary hypertension compared with those with primary hypertension. Further study is needed to determine treatment effectiveness and patient outcomes associated with differential treatment patterns used for adolescents and young adults with primary versus secondary hypertension. Copyright © 2014 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Pulse detonation engines and components thereof

NASA Technical Reports Server (NTRS)

Tangirala, Venkat Eswarlu (Inventor); Rasheed, Adam (Inventor); Vandervort, Christian Lee (Inventor); Dean, Anthony John (Inventor)

2009-01-01

A pulse detonation engine comprises a primary air inlet; a primary air plenum located in fluid communication with the primary air inlet; a secondary air inlet; a secondary air plenum located in fluid communication with the secondary air inlet, wherein the secondary air plenum is substantially isolated from the primary air plenum; a pulse detonation combustor comprising a pulse detonation chamber, wherein the pulse detonation chamber is located downstream of and in fluid communication with the primary air plenum; a coaxial liner surrounding the pulse detonation combustor defining a cooling plenum, wherein the cooling plenum is in fluid communication with the secondary air plenum; an axial turbine assembly located downstream of and in fluid communication with the pulse detonation combustor and the cooling plenum; and a housing encasing the primary air plenum, the secondary air plenum, the pulse detonation combustor, the coaxial liner, and the axial turbine assembly.

Evaluation of Peripheral Blood Circulation Disorder in Scleroderma Patients Using an Optical Sensor with a Pressurization Mechanism

PubMed Central

Yamakoshi, Yoshiki

2016-01-01

Blood circulation function of peripheral blood vessels in skin dermis was evaluated employing an optical sensor with a pressurization mechanism using the blood outflow and reflow characteristics. The device contains a light source and an optical sensor. When applied to the skin surface, it first exerts the primary pressure (higher than the systolic blood pressure), causing an outflow of blood from the dermal peripheral blood vessels. After two heartbeats, the pressure is lowered (secondary pressure) and blood reflows into the peripheral blood vessels. Hemoglobin concentration, which changes during blood outflow and reflow, is derived from the received light intensity using the Beer–Lambert law. This method was evaluated in 26 healthy female volunteers and 26 female scleroderma patients. In order to evaluate the blood circulation function of the peripheral blood vessels of scleroderma patients, pressurization sequence which consists of primary pressure followed by secondary pressure was adopted. Blood reflow during the first heartbeat period after applying the secondary pressure of 40mmHg was (mean±SD) 0.059±0.05%mm for scleroderma patients and 0.173±0.104%mm for healthy volunteers. Blood reflow was significantly lower in scleroderma patients than in healthy volunteers (p<0.05). This result indicates that the information necessary for assessing blood circulation disorder of peripheral blood vessels in scleroderma patients is objectively obtained by the proposed method. PMID:27479094

Evaluation of Peripheral Blood Circulation Disorder in Scleroderma Patients Using an Optical Sensor with a Pressurization Mechanism.

PubMed

Yamakoshi, Yoshiki; Motegi, Sei-Ichiro; Ishikawa, Osamu

2016-01-01

Blood circulation function of peripheral blood vessels in skin dermis was evaluated employing an optical sensor with a pressurization mechanism using the blood outflow and reflow characteristics. The device contains a light source and an optical sensor. When applied to the skin surface, it first exerts the primary pressure (higher than the systolic blood pressure), causing an outflow of blood from the dermal peripheral blood vessels. After two heartbeats, the pressure is lowered (secondary pressure) and blood reflows into the peripheral blood vessels. Hemoglobin concentration, which changes during blood outflow and reflow, is derived from the received light intensity using the Beer-Lambert law. This method was evaluated in 26 healthy female volunteers and 26 female scleroderma patients. In order to evaluate the blood circulation function of the peripheral blood vessels of scleroderma patients, pressurization sequence which consists of primary pressure followed by secondary pressure was adopted. Blood reflow during the first heartbeat period after applying the secondary pressure of 40mmHg was (mean±SD) 0.059±0.05%mm for scleroderma patients and 0.173±0.104%mm for healthy volunteers. Blood reflow was significantly lower in scleroderma patients than in healthy volunteers (p<0.05). This result indicates that the information necessary for assessing blood circulation disorder of peripheral blood vessels in scleroderma patients is objectively obtained by the proposed method.

Secondary reinforcement and number of primary reinforcements1

PubMed Central

Fantino, Edmund; Herrnstein, R. J.

1968-01-01

Pigeons' pecks on either of two concurrently available response keys produced secondary reinforcers according to independent one-minute variable-interval schedules. Different secondary reinforcers, in the presence of which the rates of primary reinforcement were equal, were associated with each key. The rate of pecking maintained by each secondary reinforcer varied directly, but nonproportionally, with the number of primary reinforcements given in the presence of the secondary reinforcer. PMID:5636860

Clonal evolution in therapy-related neoplasms.

PubMed

Fabiani, Emiliano; Falconi, Giulia; Fianchi, Luana; Criscuolo, Marianna; Ottone, Tiziana; Cicconi, Laura; Hohaus, Stefan; Sica, Simona; Postorino, Massimiliano; Neri, Antonino; Lionetti, Marta; Leone, Giuseppe; Lo-Coco, Francesco; Voso, Maria Teresa

2017-02-14

Therapy-related myeloid neoplasms (t-MN) may occur as a late effect of cytotoxic therapy for a primary malignancy or autoimmune diseases in susceptible individuals. We studied the development of somatic mutations in t-MN, using a collection of follow-up samples from 14 patients with a primary hematologic malignancy, who developed a secondary leukemia (13 t-MN and 1 t-acute lymphoblastic leukemia), at a median latency of 73 months (range 18-108) from primary cancer diagnosis.Using Sanger and next generation sequencing (NGS) approaches we identified 8 mutations (IDH1 R132H, ASXL1 Y591*, ASXL1 S689*, ASXL1 R693*, SRSF2 P95H, SF3B1 K700E, SETBP1 G870R and TP53 Y220C) in seven of thirteen t-MN patients (54%), whereas the t-ALL patient had a t(4,11) translocation, resulting in the KMT2A/AFF1 fusion gene. These mutations were then tracked backwards in marrow samples preceding secondary leukemia occurrence, using pyrosequencing and a NGS protocol that allows the detection of low variant allele frequencies (≥0.1%).Somatic mutations were detectable in the BM harvested at the primary diagnosis, prior to any cytotoxic treatment in three patients, while they were not detectable and apparently acquired by the t-MN clone in five patients.These data show that clonal evolution in t-MN is heterogeneous, with some somatic mutations preceding cytotoxic treatment and possibly favoring leukemic development.

Competition H(D) Kinetic Isotope Effects in the Autoxidation of Hydrocarbons

PubMed Central

Muchalski, Hubert; Levonyak, Alexander J.; Xu, Libin; Ingold, Keith U.; Porter, Ned A.

2016-01-01

Hydrogen atom transfer is central to many important radical chain sequences. We report here a method for determination of both the primary and secondary isotope effects for symmetrical substrates by the use of NMR. Intramolecular competition reactions were carried out on substrates having an increasing number of deuterium atoms at symmetry-related sites. Products that arise from peroxyl radical abstraction at each position of the various substrates reflect the competition rates for H(D) abstraction. The primary KIE for autoxidation of tetralin was determined to be 15.9 ± 1.4, a value that exceeds the maximum predicted by differences in H(D) zero-point energies (~7) and strongly suggests that H atom abstraction by the peroxyl radical occurs with substantial quantum mechanical tunneling. PMID:25533605

Neutrinos from the primary proton-proton fusion process in the Sun

NASA Astrophysics Data System (ADS)

BOREXINO Collaboration; Bellini, G.; Benziger, J.; Bick, D.; Bonfini, G.; Bravo, D.; Caccianiga, B.; Cadonati, L.; Calaprice, F.; Caminata, A.; Cavalcante, P.; Chavarria, A.; Chepurnov, A.; D'Angelo, D.; Davini, S.; Derbin, A.; Empl, A.; Etenko, A.; Fomenko, K.; Franco, D.; Gabriele, F.; Galbiati, C.; Gazzana, S.; Ghiano, C.; Giammarchi, M.; Göger-Neff, M.; Goretti, A.; Gromov, M.; Hagner, C.; Hungerford, E.; Ianni, Aldo; Ianni, Andrea; Kobychev, V.; Korablev, D.; Korga, G.; Kryn, D.; Laubenstein, M.; Lehnert, B.; Lewke, T.; Litvinovich, E.; Lombardi, F.; Lombardi, P.; Ludhova, L.; Lukyanchenko, G.; Machulin, I.; Manecki, S.; Maneschg, W.; Marcocci, S.; Meindl, Q.; Meroni, E.; Meyer, M.; Miramonti, L.; Misiaszek, M.; Montuschi, M.; Mosteiro, P.; Muratova, V.; Oberauer, L.; Obolensky, M.; Ortica, F.; Otis, K.; Pallavicini, M.; Papp, L.; Perasso, L.; Pocar, A.; Ranucci, G.; Razeto, A.; Re, A.; Romani, A.; Rossi, N.; Saldanha, R.; Salvo, C.; Schönert, S.; Simgen, H.; Skorokhvatov, M.; Smirnov, O.; Sotnikov, A.; Sukhotin, S.; Suvorov, Y.; Tartaglia, R.; Testera, G.; Vignaud, D.; Vogelaar, R. B.; von Feilitzsch, F.; Wang, H.; Winter, J.; Wojcik, M.; Wright, A.; Wurm, M.; Zaimidoroga, O.; Zavatarelli, S.; Zuber, K.; Zuzel, G.

2014-08-01

In the core of the Sun, energy is released through sequences of nuclear reactions that convert hydrogen into helium. The primary reaction is thought to be the fusion of two protons with the emission of a low-energy neutrino. These so-called pp neutrinos constitute nearly the entirety of the solar neutrino flux, vastly outnumbering those emitted in the reactions that follow. Although solar neutrinos from secondary processes have been observed, proving the nuclear origin of the Sun's energy and contributing to the discovery of neutrino oscillations, those from proton-proton fusion have hitherto eluded direct detection. Here we report spectral observations of pp neutrinos, demonstrating that about 99 per cent of the power of the Sun, 3.84 × 1033 ergs per second, is generated by the proton-proton fusion process.

Competition H(D) kinetic isotope effects in the autoxidation of hydrocarbons.

PubMed

Muchalski, Hubert; Levonyak, Alexander J; Xu, Libin; Ingold, Keith U; Porter, Ned A

2015-01-14

Hydrogen atom transfer is central to many important radical chain sequences. We report here a method for determination of both the primary and secondary isotope effects for symmetrical substrates by the use of NMR. Intramolecular competition reactions were carried out on substrates having an increasing number of deuterium atoms at symmetry-related sites. Products that arise from peroxyl radical abstraction at each position of the various substrates reflect the competition rates for H(D) abstraction. The primary KIE for autoxidation of tetralin was determined to be 15.9 ± 1.4, a value that exceeds the maximum predicted by differences in H(D) zero-point energies (∼7) and strongly suggests that H atom abstraction by the peroxyl radical occurs with substantial quantum mechanical tunneling.

Space ten-meter telescope (STMT) - Structural and thermal feasibility study of the primary mirror

NASA Technical Reports Server (NTRS)

Bely, Pierre Y.; Bolton, John F.; Neeck, Steven P.; Tulkoff, Philip J.

1987-01-01

The structural and thermal behavior of a ten-meter primary mirror for a space optical/near-IR telescope in geosynchronous orbit is studied. The glass-type lightweighted mirror is monolithic, of the double arch type, and is supported at only three points. The computer programs SSPTA (thermal), NASTRAN (finite element), and ACCOS V (optical) are used in sequence to determine the temperature, deformation, and optical performance of the mirror. A mirror temperature of 130 K or less appears to be obtainable by purely passive means. With a fused silica or standard Zerodur blank, thermally-induced deformation is unacceptable and cannot be fully corrected by an active secondary mirror over the desired field. Either active thermal control or a blank of lower thermal expansion coefficient would be required.

Quantitative analysis of RNA-protein interactions on a massively parallel array for mapping biophysical and evolutionary landscapes

PubMed Central

Buenrostro, Jason D.; Chircus, Lauren M.; Araya, Carlos L.; Layton, Curtis J.; Chang, Howard Y.; Snyder, Michael P.; Greenleaf, William J.

2015-01-01

RNA-protein interactions drive fundamental biological processes and are targets for molecular engineering, yet quantitative and comprehensive understanding of the sequence determinants of affinity remains limited. Here we repurpose a high-throughput sequencing instrument to quantitatively measure binding and dissociation of MS2 coat protein to >107 RNA targets generated on a flow-cell surface by in situ transcription and inter-molecular tethering of RNA to DNA. We decompose the binding energy contributions from primary and secondary RNA structure, finding that differences in affinity are often driven by sequence-specific changes in association rates. By analyzing the biophysical constraints and modeling mutational paths describing the molecular evolution of MS2 from low- to high-affinity hairpins, we quantify widespread molecular epistasis, and a long-hypothesized structure-dependent preference for G:U base pairs over C:A intermediates in evolutionary trajectories. Our results suggest that quantitative analysis of RNA on a massively parallel array (RNAMaP) relationships across molecular variants. PMID:24727714

Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities.

PubMed

Xing, Wei; Li, Jinlong; Li, Peng; Wang, Chong; Cao, Yanan; Li, Desheng; Yang, Yunfeng; Zhou, Jizhong; Zuo, Jiane

2018-03-01

Hydrogenotrophic denitrification is promising for tertiary nitrogen removal from municipal wastewater. To reveal the influence of residual organics in municipal wastewater on hydrogenotrophic denitrifiers, we adopted high-throughput 16S rRNA gene amplicon sequencing to examine microbial communities in hydrogenotrophic denitrification enrichments. Using effluent from a municipal wastewater treatment plant as water source, COD, nitrate and pH were controlled the same except for a gradient of biodegradable carbon (i.e., primary effluent (PE), secondary effluent (SE), or combined primary and secondary effluent (CE)). Inorganic synthetic water (IW) was used as a control. Hydrogenophaga, a major facultative autotroph, accounted for 17.1%, 5.3%, 32.7% and 12.9% of the sequences in PE, CE, SE and IW, respectively, implicating that Hydrogenophaga grew well with or without organics. Thauera, which contains likely obligate autotrophic denitrifiers, appeared to be the most dominant genera (23.6%) in IW and accounted for 2.5%, 4.6% and 8.9% in PE, CE and SE, respectively. Thermomonas, which is related to heterotrophic denitrification, accounted for 4.2% and 7.9% in PE and CE fed with a higher content of labile organics, respectively. In contrast, Thermomonas was not detected in IW and accounted for only 0.6% in SE. Our results suggest that Thermomonas are more competitive than Thauera in hydrogenotrophic denitrification with biodegradable organics. Moreover, facultative autotrophic denitrifiers, Hydrogenophaga, are accommodating to residual organic in effluent wastewater, thus we propose that hydrogenotrophic denitrification is amenable for tertiary nitrogen removal. Copyright © 2017. Published by Elsevier B.V.

[Analysis of the primary and secondary structure of the mitochondrial serine transfer RNA in seven species of Lutzomyia].

PubMed

Vivero, Rafael José; Contreras-Gutiérrez, Maria Angélica; Bejarano, Eduar Elías

2007-09-01

Lutzomyia sand flies are involved in the transmission of the parasite Leishmania spp. in America. The taxonomy of these vectors is traditionally based on morphological features of the adult stage, particularly the paired structures of the head and genitalia. Although these characters are useful to distinguish most species of Lutzomyia, morphological identification may be complicated by the similarities within subgenera and species group. To evaluate the utility of mitochondrial serine transfer RNA tRNA Ser for taxonomic identification of Lutzomyia. Seven sand fly species, each representing one of the 27 taxonomic subdivisions in genus Lutzomyia, were analyzed including L. trinidadensis (Oswaldoi group), L. (Psychodopygus) panamensis, L.(Micropygomyia) cayennensis cayennensis, L. dubitans (Migonei group), L. (Lutzomyia) gomezi, L. rangeliana (ungrouped) and L. evansi (Verrucarum group). The mitochondrial tRNA Ser gene, flanked by the cytochrome b and NAD dehydrogenase subunit one genes, was extracted, amplified and sequenced from each specimen. Secondary structure of the tRNA Ser was predicted by comparisons with previously described homologous structures from other dipteran species. The tRNA Ser gene ranged in size from 66 base pairs in L. gomezi to 69 base pairs in L. trinidadensis. Fourteen polymorphic sites, including four insertion-deletion events, were observed in the aligned 70 nucleotide positions. The majority of the substitutions were located in the dihydrouridine, ribothymidine-pseudouridine-cytosine and variable loops, as well as in the basal extreme of the anticodon arm. Changes of primary sequence of the tRNASer provided useful molecular characters for taxonomic identification of the sand fly species under consideration.

Compound mutations in BCR-ABL1 are not major drivers of primary or secondary resistance to ponatinib in CP-CML patients

PubMed Central

Hodgson, J. Graeme; Shah, Neil P.; Cortes, Jorge E.; Kim, Dong-Wook; Nicolini, Franck E.; Talpaz, Moshe; Baccarani, Michele; Müller, Martin C.; Li, Jin; Parker, Wendy T.; Lustgarten, Stephanie; Clackson, Tim; Haluska, Frank G.; Guilhot, Francois; Kantarjian, Hagop M.; Soverini, Simona; Hochhaus, Andreas; Hughes, Timothy P.; Rivera, Victor M.; Branford, Susan

2016-01-01

BCR-ABL1 kinase domain mutations can confer resistance to first- and second-generation tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML). In preclinical studies, clinically achievable concentrations of the third-generation BCR-ABL1 TKI ponatinib inhibit T315I and all other single BCR-ABL1 mutants except T315M, which generates a single amino acid exchange, but requires 2 sequential nucleotide exchanges. In addition, certain compound mutants (containing ≥2 mutations in cis) confer resistance. Initial analyses based largely on conventional Sanger sequencing (SS) have suggested that the preclinical relationship between BCR-ABL1 mutation status and ponatinib efficacy is generally recapitulated in patients receiving therapy. Thus far, however, such analyses have been limited by the inability of SS to definitively identify compound mutations or mutations representing less than ∼20% of total alleles (referred to as “low-level mutations”), as well as limited patient follow-up. Here we used next-generation sequencing (NGS) to define the baseline BCR-ABL1 mutation status of 267 heavily pretreated chronic phase (CP)-CML patients from the PACE trial, and used SS to identify clonally dominant mutants that may have developed on ponatinib therapy (30.1 months median follow-up). Durable cytogenetic and molecular responses were observed irrespective of baseline mutation status and included patients with compound mutations. No single or compound mutation was identified that consistently conferred primary and/or secondary resistance to ponatinib in CP-CML patients. Ponatinib is effective in CP-CML irrespective of baseline mutation status. PMID:26603839

RNA-SSPT: RNA Secondary Structure Prediction Tools.

PubMed

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

RNA-SSPT: RNA Secondary Structure Prediction Tools

PubMed Central

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

Prediction of primary vs secondary hypertension in children.

PubMed

Baracco, Rossana; Kapur, Gaurav; Mattoo, Tej; Jain, Amrish; Valentini, Rudolph; Ahmed, Maheen; Thomas, Ronald

2012-05-01

Despite current guidelines, variability exists in the workup of hypertensive children due to physician preferences. The study evaluates primary vs secondary hypertension diagnosis from investigations routinely performed in hypertensive children. This retrospective study included children 5 to 19 years with primary and secondary hypertension. The proportions of abnormal laboratory and imaging tests were compared between primary and secondary hypertension groups. Risk factors for primary vs secondary hypertension were evaluated by logistic regression and likelihood function analysis. Patients with secondary hypertension were younger (5-12 years) and had a higher proportion of abnormal creatinine, renal ultrasound, and echocardiogram findings. There was no significant difference in abnormal results of thyroid function, urine catecholamines, plasma renin, and aldosterone. Abnormal renal ultrasound findings and age were predictors of secondary hypertension by regression and likelihood function analysis. Children aged 5 to 12 years with abnormal renal ultrasound findings and high diastolic blood pressures are at higher risk for secondary hypertension that requires detailed evaluation. © 2012 Wiley Periodicals, Inc.

A comparison of demographic and psychosexual characteristics of women with primary versus secondary provoked vestibulodynia.

PubMed

Brotto, Lori A; Sadownik, Leslie A; Thomson, Sydney; Dayan, Marcy; Smith, Kelly B; Seal, Brooke N; Moses, Melissa; Zhang, Areiyu

2014-05-01

Provoked vestibulodynia (PVD) is a distressing genital pain condition affecting approximately 12% of premenopausal women. It has been speculated that primary (ie, lifelong) and secondary (ie, acquired) PVD may represent 2 distinct conditions with different etiologies. There is also evidence that primary and secondary PVD subtypes may respond differently to conventional treatments. The goal of this study was to compare the demographic, clinical, and psychosexual characteristics of a large sample of premenopausal women with primary and secondary PVD. A total of 132 premenopausal women (n=42 primary; n=90 secondary) with PVD who sought treatment in a Multidisciplinary Vulvodynia Program completed demographic questions and a battery of validated self-report measures before treatment. Women with primary PVD had a longer duration of PVD as well as more time before diagnosis. Women with secondary PVD reported significantly more clitoral hood pain, higher overall vestibular pain levels, more overall sexual dysfunction and sex-related distress, and proportionately more intercourse occasions that were painful. Women with primary pain stated they had significantly more dysmenorrhea and were more likely to report that their partners were unaware of their PVD symptoms. There were no significant subtype differences on any psychological measure but a trend towards higher magnification of symptoms in women with secondary PVD. Overall the findings suggest some important differences in the characteristics of women with primary versus secondary PVD which may have management-related implications.

GeneSilico protein structure prediction meta-server.

PubMed

Kurowski, Michal A; Bujnicki, Janusz M

2003-07-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.

GeneSilico protein structure prediction meta-server

PubMed Central

Kurowski, Michal A.; Bujnicki, Janusz M.

2003-01-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta. PMID:12824313

Cellulose synthase complexes display distinct dynamic behaviors during xylem transdifferentiation.

PubMed

Watanabe, Yoichiro; Schneider, Rene; Barkwill, Sarah; Gonzales-Vigil, Eliana; Hill, Joseph L; Samuels, A Lacey; Persson, Staffan; Mansfield, Shawn D

2018-06-05

In plants, plasma membrane-embedded CELLULOSE SYNTHASE (CESA) enzyme complexes deposit cellulose polymers into the developing cell wall. Cellulose synthesis requires two different sets of CESA complexes that are active during cell expansion and secondary cell wall thickening, respectively. Hence, developing xylem cells, which first undergo cell expansion and subsequently deposit thick secondary walls, need to completely reorganize their CESA complexes from primary wall- to secondary wall-specific CESAs. Using live-cell imaging, we analyzed the principles underlying this remodeling. At the onset of secondary wall synthesis, the primary wall CESAs ceased to be delivered to the plasma membrane and were gradually removed from both the plasma membrane and the Golgi. For a brief transition period, both primary wall- and secondary wall-specific CESAs coexisted in banded domains of the plasma membrane where secondary wall synthesis is concentrated. During this transition, primary and secondary wall CESAs displayed discrete dynamic behaviors and sensitivities to the inhibitor isoxaben. As secondary wall-specific CESAs were delivered and inserted into the plasma membrane, the primary wall CESAs became concentrated in prevacuolar compartments and lytic vacuoles. This adjustment in localization between the two CESAs was accompanied by concurrent decreased primary wall CESA and increased secondary wall CESA protein abundance. Our data reveal distinct and dynamic subcellular trafficking patterns that underpin the remodeling of the cellulose biosynthetic machinery, resulting in the removal and degradation of the primary wall CESA complex with concurrent production and recycling of the secondary wall CESAs. Copyright © 2018 the Author(s). Published by PNAS.

Multiplex Real-Time PCR for Detection of Staphylococcus aureus, mecA and Panton-Valentine Leukocidin (PVL) Genes from Selective Enrichments from Animals and Retail Meat

PubMed Central

Velasco, Valeria; Sherwood, Julie S.; Rojas-García, Pedro P.; Logue, Catherine M.

2014-01-01

The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL) genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat). The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus), mecA (associated with methicillin resistance) and PVL (virulence factor), and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68–0.88 (from substantial to almost perfect agreement) and 0.29–0.77 (from fair to substantial agreement) for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0–0.49 (from no agreement beyond that expected by chance to moderate agreement) for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA) using the standard culture method. PMID:24849624

Multiplex real-time PCR for detection of Staphylococcus aureus, mecA and Panton-Valentine Leukocidin (PVL) genes from selective enrichments from animals and retail meat.

PubMed

Velasco, Valeria; Sherwood, Julie S; Rojas-García, Pedro P; Logue, Catherine M

2014-01-01

The aim of this study was to compare a real-time PCR assay, with a conventional culture/PCR method, to detect S. aureus, mecA and Panton-Valentine Leukocidin (PVL) genes in animals and retail meat, using a two-step selective enrichment protocol. A total of 234 samples were examined (77 animal nasal swabs, 112 retail raw meat, and 45 deli meat). The multiplex real-time PCR targeted the genes: nuc (identification of S. aureus), mecA (associated with methicillin resistance) and PVL (virulence factor), and the primary and secondary enrichment samples were assessed. The conventional culture/PCR method included the two-step selective enrichment, selective plating, biochemical testing, and multiplex PCR for confirmation. The conventional culture/PCR method recovered 95/234 positive S. aureus samples. Application of real-time PCR on samples following primary and secondary enrichment detected S. aureus in 111/234 and 120/234 samples respectively. For detection of S. aureus, the kappa statistic was 0.68-0.88 (from substantial to almost perfect agreement) and 0.29-0.77 (from fair to substantial agreement) for primary and secondary enrichments, using real-time PCR. For detection of mecA gene, the kappa statistic was 0-0.49 (from no agreement beyond that expected by chance to moderate agreement) for primary and secondary enrichment samples. Two pork samples were mecA gene positive by all methods. The real-time PCR assay detected the mecA gene in samples that were negative for S. aureus, but positive for Staphylococcus spp. The PVL gene was not detected in any sample by the conventional culture/PCR method or the real-time PCR assay. Among S. aureus isolated by conventional culture/PCR method, the sequence type ST398, and multi-drug resistant strains were found in animals and raw meat samples. The real-time PCR assay may be recommended as a rapid method for detection of S. aureus and the mecA gene, with further confirmation of methicillin-resistant S. aureus (MRSA) using the standard culture method.

Recommendation on transition from primary/secondary radar to secondary-only radar capability

DOT National Transportation Integrated Search

1994-10-01

This recommendation has been prepared to support the FAA decision to deactivate primary Long-range radars and presents a : transition strategy and implementation plan for the transformation of the existing primary/secondary en route radar : system to...

Prediction of protein secondary structure content for the twilight zone sequences.

PubMed

Homaeian, Leila; Kurgan, Lukasz A; Ruan, Jishou; Cios, Krzysztof J; Chen, Ke

2007-11-15

Secondary protein structure carries information about local structural arrangements, which include three major conformations: alpha-helices, beta-strands, and coils. Significant majority of successful methods for prediction of the secondary structure is based on multiple sequence alignment. However, multiple alignment fails to provide accurate results when a sequence comes from the twilight zone, that is, it is characterized by low (<30%) homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation, called PSSC-core. The method uses a multiple linear regression model and introduces a comprehensive feature-based sequence representation to predict amount of helices and strands for sequences from the twilight zone. The PSSC-core method was tested and compared with two other state-of-the-art prediction methods on a set of 2187 twilight zone sequences. The results indicate that our method provides better predictions for both helix and strand content. The PSSC-core is shown to provide statistically significantly better results when compared with the competing methods, reducing the prediction error by 5-7% for helix and 7-9% for strand content predictions. The proposed feature-based sequence representation uses a comprehensive set of physicochemical properties that are custom-designed for each of the helix and strand content predictions. It includes composition and composition moment vectors, frequency of tetra-peptides associated with helical and strand conformations, various property-based groups like exchange groups, chemical groups of the side chains and hydrophobic group, auto-correlations based on hydrophobicity, side-chain masses, hydropathy, and conformational patterns for beta-sheets. The PSSC-core method provides an alternative for predicting the secondary structure content that can be used to validate and constrain results of other structure prediction methods. At the same time, it also provides useful insight into design of successful protein sequence representations that can be used in developing new methods related to prediction of different aspects of the secondary protein structure. (c) 2007 Wiley-Liss, Inc.

From Primary to Secondary Science: Keeping the Threads Intact

ERIC Educational Resources Information Center

Mould, Kirsten

2015-01-01

There are many transition points in the school life of a child, but the move from primary to secondary school is a particularly significant one. How can both the social and academic threads remain intact? In this article, Kristen Mould discusses the main issues relating to transition from primary to secondary science. She cites the primary factors…

Primary Versus Secondary Diagnosis of Generalized Anxiety Disorder in Youth: Is the Distinction an Important One?

PubMed

Ollendick, Thomas H; Jarrett, Matthew A; White, Bradley A; White, Susan W; Grills, Amie E

2016-08-01

Examine whether children with a primary diagnosis of generalized anxiety disorder (GAD) differ from children with a secondary diagnosis of GAD on clinician, parent, teacher, and youth-report measures. Based on consensus diagnoses, 64 youth referred to a general outpatient assessment clinic were categorized as having either a primary or secondary diagnosis of GAD. A semi-structured diagnostic interview was used to guide diagnostic decisions and assign primary versus secondary diagnostic status. We predicted that youth with a primary GAD diagnosis would present with greater anxiety symptomatology and symptom impairment on a variety of anxiety-related measures than youth with a secondary GAD diagnosis. Contrary to our hypotheses, no differences were found between those with primary versus secondary GAD diagnoses on measures of symptom severity and clinical impairment, comorbid diagnoses, or youth and teacher-report measures. Our findings have potential implications for the current practice of requiring primary anxiety diagnostic status as an inclusion criterion in clinical research and treatment outcome studies. Assuming our findings are confirmed in larger samples and with other anxiety disorders, future clinical trials and basic psychopathology research might not exclude youth based on absence of a particular anxiety disorder as the primary disorder but rather include individuals for whom that anxiety disorder is secondary as well.

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

PubMed

Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

2017-09-01

Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production.

PubMed

Robertsen, Helene Lunde; Weber, Tilmann; Kim, Hyun Uk; Lee, Sang Yup

2018-01-01

Streptomycetes are known for their inherent ability to produce pharmaceutically relevant secondary metabolites. Discovery of medically useful, yet novel compounds has become a great challenge due to frequent rediscovery of known compounds and a consequent decline in the number of relevant clinical trials in the last decades. A paradigm shift took place when the first whole genome sequences of streptomycetes became available, from which silent or "cryptic" biosynthetic gene clusters (BGCs) were discovered. Cryptic BGCs reveal a so far untapped potential of the microorganisms for the production of novel compounds, which has spurred new efforts in understanding the complex regulation between primary and secondary metabolism. This new trend has been accompanied with development of new computational resources (genome and compound mining tools), generation of various high-quality omics data, establishment of molecular tools, and other strain engineering strategies. They all come together to enable systems metabolic engineering of streptomycetes, allowing more systematic and efficient strain development. In this review, the authors present recent progresses within systems metabolic engineering of streptomycetes for uncovering their hidden potential to produce novel compounds and for the improved production of secondary metabolites. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase.

PubMed

Tobias, Nicholas J; Ahrendt, Tilman; Schell, Ursula; Miltenberger, Melissa; Hilbi, Hubert; Bode, Helge B

2016-01-01

Several members of the genus Legionella cause Legionnaires' disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella . Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella , we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict some novel compounds that are probably involved in cell-cell communication, differing to known communication systems. We identify several gene clusters, which may represent novel signaling mechanisms and demonstrate the natural product potential of Legionella .

Primary and Secondary Variants of Psychopathy in a Volunteer Sample Are Associated With Different Neurocognitive Mechanisms.

PubMed

Sethi, Arjun; McCrory, Eamon; Puetz, Vanessa; Hoffmann, Ferdinand; Knodt, Annchen R; Radtke, Spenser R; Brigidi, Bartholomew D; Hariri, Ahmad R; Viding, Essi

2018-04-12

Recent work has indicated that there at least two distinct subtypes of psychopathy. Primary psychopathy is characterized by low anxiety and thought to result from a genetic predisposition, whereas secondary psychopathy is characterized by high anxiety and thought to develop in response to environmental adversity. Primary psychopathy is robustly associated with reduced neural activation to others' emotions and, in particular, distress. However, it has been proposed that the secondary presentation has different neurocognitive correlates. Primary (n = 50), secondary (n = 100), and comparison (n = 82) groups were drawn from a large volunteer sample (N = 1444) using a quartile-split approach across psychopathic trait (affective-interpersonal) and anxiety measures. Participants performed a widely utilized emotional face processing task during functional magnetic resonance imaging. The primary group showed reduced amygdala and insula activity in response to fear. The secondary group did not differ from the comparison group in these regions. Instead, the secondary group showed reduced activity compared with the comparison group in other areas, including the superior temporal sulcus/inferior parietal lobe, thalamus, pallidum, and substantia nigra. Both psychopathy groups also showed reduced activity in response to fear in the anterior cingulate cortex. During anger processing, the secondary group exhibited reduced activity in the anterior cingulate cortex compared with the primary group. Distinct neural correlates of fear processing characterize individuals with primary and secondary psychopathy. The reduced neural response to fear that characterizes individuals with the primary variant of psychopathic traits is not observed in individuals with the secondary presentation. The neurocognitive mechanisms underpinning secondary psychopathy warrant further systematic investigation. Copyright © 2018 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

TIME-SERIES SPECTROSCOPY OF THE ECLIPSING BINARY Y CAM WITH A PULSATING COMPONENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Kyeongsoo; Lee, Jae Woo; Kim, Seung-Lee

We present the physical properties of the semi-detached Algol-type eclipsing binary Y Cam based on high resolution spectra obtained using the Bohyunsan Optical Echelle Spectrograph. This is the first spectroscopic monitoring data obtained for this interesting binary system, which has a δ Sct-type pulsating component. We obtained a total of 59 spectra over 14 nights from 2009 December to 2011 March. Double-lined spectral features from the hot primary and cool secondary components were well identified. We determined the effective temperatures of the two stars to be T{sub eff,1} = 8000 ± 250 K and T{sub eff,2} = 4629 ± 150more » K. The projected rotational velocities are v{sub 1}sin i{sub 1} = 51 ± 4 km s{sup −1} and v{sub 2}sin i{sub 2} = 50 ± 10 km s{sup −1}, which are very similar to a synchronous rotation with the orbital motion. Physical parameters of each component were derived by analyzing our radial velocity data together with previous photometric light curves from the literature. The masses and radii are M{sub 1} = 2.08 ± 0.09 M{sub ⊙}, M{sub 2} = 0.48 ± 0.03 M{sub ⊙}, R{sub 1} = 3.14 ± 0.05 R{sub ⊙}, and R{sub 2} = 3.33 ± 0.05 R{sub ⊙}, respectively. A comparison of these parameters with the theoretical evolution tracks showed that the primary component is located between the zero-age main sequence and the terminal-age main sequence, while the low-mass secondary is noticeably evolved. This indicates that the two components have experienced mass exchange with each other and the primary has undergone an evolution process different from that of single δ Sct-type pulsators.« less

Influence of genome-scale RNA structure disruption on the replication of murine norovirus—similar replication kinetics in cell culture but attenuation of viral fitness in vivo

PubMed Central

McFadden, Nora; Arias, Armando; Dry, Inga; Bailey, Dalan; Witteveldt, Jeroen; Evans, David J.; Goodfellow, Ian; Simmonds, Peter

2013-01-01

Mechanisms by which certain RNA viruses, such as hepatitis C virus, establish persistent infections and cause chronic disease are of fundamental importance in viral pathogenesis. Mammalian positive-stranded RNA viruses establishing persistence typically possess genome-scale ordered RNA secondary structure (GORS) in their genomes. Murine norovirus (MNV) persists in immunocompetent mice and provides an experimental model to functionally characterize GORS. Substitution mutants were constructed with coding sequences in NS3/4- and NS6/7-coding regions replaced with sequences with identical coding and (di-)nucleotide composition but disrupted RNA secondary structure (F1, F2, F1/F2 mutants). Mutants replicated with similar kinetics to wild-type (WT) MNV3 in RAW264.7 cells and primary macrophages, exhibited similar (highly restricted) induction and susceptibility to interferon-coupled cellular responses and equal replication fitness by serial passaging of co-cultures. In vivo, both WT and F1/F2 mutant viruses persistently infected mice, although F1, F2 and F1/F2 mutant viruses were rapidly eliminated 1–7 days post-inoculation in competition experiments with WT. F1/F2 mutants recovered from tissues at 9 months showed higher synonymous substitution rates than WT and nucleotide substitutions that potentially restored of RNA secondary structure. GORS plays no role in basic replication of MNV but potentially contributes to viral fitness and persistence in vivo. PMID:23630317

[Colonization of Porphyromonas endodontalis in primary and secondary endodontic infections].

PubMed

Hong, Li; Hai, Ji; Yan-Yan, He; Shenghui, Yang; Benxiang, Hou

2015-02-01

This study aims to assess and compare the prevalence of Porphyromonas endodontalis (P. endodontalis) in root canals associated with primary and secondary endodontic infections by using 16s rDNA PCR and real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR). A total of 120 adult patients with one radiographically documented periapical lesion were included. Sixty teeth presented with primary endodontic infections and 60 with secondary endodontic infections requiring retreatment. P. endodontalis was identified by using 16s rDNA PCR techniques. The positive DNA expression of P. endodontalis in two types of infected root canals were quantitatively compared by using SYBR GREEN I RTFQ-PCR. The prevalence of P. endodontalis in the root canals with primary endodontic infections was significantly higher than that in root canals with secondary endodontic infections (P = 0.001). However, RTFQ-PCR results showed no significant difference in DNA expression quantities between the primary and secondary endodontic infections root canals (P = 0.303). P. endodontalis is more highly associated with root canals having primary endodontic infections, although P. endodontalis colonize in both root canals with primary and secondary chronic apical periodontitis.

High-Speed Numeric Function Generator Using Piecewise Quadratic Approximations

DTIC Science & Technology

2007-09-01

application; User specifies the fuction to approxiamte. % % This programs turns the function provided into an inline function... PRIMARY = < primary file 1> < primary file 2> #SECONDARY = <secondary file 1> <secondary file 2> #CHIP2 = <file to compile to user chip

AN M DWARF COMPANION TO AN F-TYPE STAR IN A YOUNG MAIN-SEQUENCE BINARY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eigmüller, Ph.; Csizmadia, Sz.; Erikson, A.

2016-03-15

Only a few well characterized very low-mass M dwarfs are known today. Our understanding of M dwarfs is vital as these are the most common stars in our solar neighborhood. We aim to characterize the properties of a rare F+dM stellar system for a better understanding of the low-mass end of the Hertzsprung–Russel diagram. We used photometric light curves and radial velocity follow-up measurements to study the binary. Spectroscopic analysis was used in combination with isochrone fitting to characterize the primary star. The primary star is an early F-type main-sequence star with a mass of (1.493 ± 0.073) M{sub ⊙}more » and a radius of (1.474 ± 0.040) R{sub ⊙}. The companion is an M dwarf with a mass of (0.188 ± 0.014) M{sub ⊙} and a radius of (0.234 ± 0.009) R{sub ⊙}. The orbital period is (1.35121 ± 0.00001) days. The secondary star is among the lowest-mass M dwarfs known to date. The binary has not reached a 1:1 spin–orbit synchronization. This indicates a young main-sequence binary with an age below ∼250 Myr. The mass–radius relation of both components are in agreement with this finding.« less

Primary and Secondary Yield Losses Caused by Pests and Diseases: Assessment and Modeling in Coffee

PubMed Central

Gary, Christian; Tixier, Philippe; Lechevallier, Esther

2017-01-01

The assessment of crop yield losses is needed for the improvement of production systems that contribute to the incomes of rural families and food security worldwide. However, efforts to quantify yield losses and identify their causes are still limited, especially for perennial crops. Our objectives were to quantify primary yield losses (incurred in the current year of production) and secondary yield losses (resulting from negative impacts of the previous year) of coffee due to pests and diseases, and to identify the most important predictors of coffee yields and yield losses. We established an experimental coffee parcel with full-sun exposure that consisted of six treatments, which were defined as different sequences of pesticide applications. The trial lasted three years (2013–2015) and yield components, dead productive branches, and foliar pests and diseases were assessed as predictors of yield. First, we calculated yield losses by comparing actual yields of specific treatments with the estimated attainable yield obtained in plots which always had chemical protection. Second, we used structural equation modeling to identify the most important predictors. Results showed that pests and diseases led to high primary yield losses (26%) and even higher secondary yield losses (38%). We identified the fruiting nodes and the dead productive branches as the most important and useful predictors of yields and yield losses. These predictors could be added in existing mechanistic models of coffee, or can be used to develop new linear mixed models to estimate yield losses. Estimated yield losses can then be related to production factors to identify corrective actions that farmers can implement to reduce losses. The experimental and modeling approaches of this study could also be applied in other perennial crops to assess yield losses. PMID:28046054

Primary and Secondary Yield Losses Caused by Pests and Diseases: Assessment and Modeling in Coffee.

PubMed

Cerda, Rolando; Avelino, Jacques; Gary, Christian; Tixier, Philippe; Lechevallier, Esther; Allinne, Clémentine

2017-01-01

The assessment of crop yield losses is needed for the improvement of production systems that contribute to the incomes of rural families and food security worldwide. However, efforts to quantify yield losses and identify their causes are still limited, especially for perennial crops. Our objectives were to quantify primary yield losses (incurred in the current year of production) and secondary yield losses (resulting from negative impacts of the previous year) of coffee due to pests and diseases, and to identify the most important predictors of coffee yields and yield losses. We established an experimental coffee parcel with full-sun exposure that consisted of six treatments, which were defined as different sequences of pesticide applications. The trial lasted three years (2013-2015) and yield components, dead productive branches, and foliar pests and diseases were assessed as predictors of yield. First, we calculated yield losses by comparing actual yields of specific treatments with the estimated attainable yield obtained in plots which always had chemical protection. Second, we used structural equation modeling to identify the most important predictors. Results showed that pests and diseases led to high primary yield losses (26%) and even higher secondary yield losses (38%). We identified the fruiting nodes and the dead productive branches as the most important and useful predictors of yields and yield losses. These predictors could be added in existing mechanistic models of coffee, or can be used to develop new linear mixed models to estimate yield losses. Estimated yield losses can then be related to production factors to identify corrective actions that farmers can implement to reduce losses. The experimental and modeling approaches of this study could also be applied in other perennial crops to assess yield losses.

Effect of Mass Flow on Stack Eductor Performance.

DTIC Science & Technology

1984-06-01

absolute viscosity, lbf-sec/ft2 - density, Ibm/ft 3 "function of" ENGLISH LETTER SYMBOLS 2 A - area, in , ft B - atmospheric pressure, in Hg c - sonic... absolute temperature ratio T* - tertiary flow to primary flow absolute temperature t ratio - secondary -o primary mass flow rate ratio W* - tertiary to...secondary to primary absolute Tp temperature ratio TiL tertiary to primary absolute -TE temperature ratio secondary to primary flow density ratio

A SUBSTELLAR COMPANION TO THE DUSTY PLEIADES STAR HD 23514

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez, David R.; Zuckerman, B.; Marois, Christian

2012-03-20

With adaptive optics imaging at Keck observatory, we have discovered a substellar companion to the F6 Pleiades star HD 23514, one of the dustiest main-sequence stars known to date (L{sub IR}/L{sub *} {approx} 2%). This is one of the first brown dwarfs discovered as a companion to a star in the Pleiades. The 0.06 M{sub Sun} late-M secondary has a projected separation of {approx}360 AU. The scarcity of substellar companions to stellar primaries in the Pleiades combined with the extremely dusty environment make this a unique system to study.

Cullen's sign and massive ovarian enlargement secondary to primary hypothyroidism in a patient with a normal FSH receptor

PubMed Central

Sultan, A; Velaga, M R; Fleet, M; Cheetham, T

2006-01-01

Ovarian hyperstimulation is a recognised complication of longstanding hypothyroidism. A 12 year old girl with atrophic thyroiditis who presented with abdominal pain and distension is reported. She was noted to have bruising in the vicinity of the umbilicus (Cullen's sign). She had pronounced ovarian enlargement on ultrasonography and it was hypothesised that this profound phenotype might reflect an abnormal FSH receptor. However sequencing of the FSH receptor was normal. The ovarian enlargement resolved with thyroxine replacement. Physicians and surgeons should consider longstanding hypothyroidism in patients presenting with Cullen's sign. PMID:16714722

Age and Diet Affect Genetically Separable Secondary Injuries that Cause Acute Mortality Following Traumatic Brain Injury in Drosophila

PubMed Central

Katzenberger, Rebeccah J.; Ganetzky, Barry; Wassarman, David A.

2016-01-01

Outcomes of traumatic brain injury (TBI) vary because of differences in primary and secondary injuries. Primary injuries occur at the time of a traumatic event, whereas secondary injuries occur later as a result of cellular and molecular events activated in the brain and other tissues by primary injuries. We used a Drosophila melanogaster TBI model to investigate secondary injuries that cause acute mortality. By analyzing mortality percentage within 24 hr of primary injuries, we previously found that age at the time of primary injuries and diet afterward affect the severity of secondary injuries. Here, we show that secondary injuries peaked in activity 1–8 hr after primary injuries. Additionally, we demonstrate that age and diet activated distinct secondary injuries in a genotype-specific manner, and that concurrent activation of age- and diet-regulated secondary injuries synergistically increased mortality. To identify genes involved in secondary injuries that cause mortality, we compared genome-wide mRNA expression profiles of uninjured and injured flies under age and diet conditions that had different mortalities. During the peak period of secondary injuries, innate immune response genes were the predominant class of genes that changed expression. Furthermore, age and diet affected the magnitude of the change in expression of some innate immune response genes, suggesting roles for these genes in inhibiting secondary injuries that cause mortality. Our results indicate that the complexity of TBI outcomes is due in part to distinct, genetically controlled, age- and diet-regulated mechanisms that promote secondary injuries and that involve a subset of innate immune response genes. PMID:27754853

Introduction to Semiconductor Physics in Secondary Education: Evaluation of a Teaching Sequence

ERIC Educational Resources Information Center

Garcia-Carmona, Antonio; Criado, Ana Maria

2009-01-01

The present article presents a didactic proposal oriented to teaching notions of semiconductor physics in secondary education. The methods and the results of a pilot study designed to analyse the effectiveness of a teaching sequence on the topic are also described. The subjects were 60 students, aged 14-15 years, of a secondary school in Seville,…

Transcriptome-wide identification of Rauvolfia serpentina microRNAs and prediction of their potential targets.

PubMed

Prakash, Pravin; Rajakani, Raja; Gupta, Vikrant

2016-04-01

MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 19-24 nucleotides (nt) in length and considered as potent regulators of gene expression at transcriptional and post-transcriptional levels. Here we report the identification and characterization of 15 conserved miRNAs belonging to 13 families from Rauvolfia serpentina through in silico analysis of available nucleotide dataset. The identified mature R. serpentina miRNAs (rse-miRNAs) ranged between 20 and 22nt in length, and the average minimal folding free energy index (MFEI) value of rse-miRNA precursor sequences was found to be -0.815 kcal/mol. Using the identified rse-miRNAs as query, their potential targets were predicted in R. serpentina and other plant species. Gene Ontology (GO) annotation showed that predicted targets of rse-miRNAs include transcription factors as well as genes involved in diverse biological processes such as primary and secondary metabolism, stress response, disease resistance, growth, and development. Few rse-miRNAs were predicted to target genes of pharmaceutically important secondary metabolic pathways such as alkaloids and anthocyanin biosynthesis. Phylogenetic analysis showed the evolutionary relationship of rse-miRNAs and their precursor sequences to homologous pre-miRNA sequences from other plant species. The findings under present study besides giving first hand information about R. serpentina miRNAs and their targets, also contributes towards the better understanding of miRNA-mediated gene regulatory processes in plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Wireless power transfer system

DOEpatents

Wu, Hunter; Sealy, Kylee; Gilchrist, Aaron

2016-02-23

A system includes a first stage of an inductive power transfer system with an LCL load resonant converter with a switching section, an LCL tuning circuit, and a primary receiver pad. The IPT system includes a second stage with a secondary receiver pad, a secondary resonant circuit, a secondary rectification circuit, and a secondary decoupling converter. The secondary receiver pad connects to the secondary resonant circuit. The secondary resonant circuit connects to the secondary rectification circuit. The secondary rectification circuit connects to the secondary decoupling converter. The second stage connects to a load. The load includes an energy storage element. The second stage and load are located on a vehicle and the first stage is located at a fixed location. The primary receiver pad wirelessly transfers power to the secondary receiver pad across a gap when the vehicle positions the secondary receiver pad with respect to the primary receiver pad.

Dual Tank Fuel System

DOEpatents

Wagner, Richard William; Burkhard, James Frank; Dauer, Kenneth John

1999-11-16

A dual tank fuel system has primary and secondary fuel tanks, with the primary tank including a filler pipe to receive fuel and a discharge line to deliver fuel to an engine, and with a balance pipe interconnecting the primary tank and the secondary tank. The balance pipe opens close to the bottom of each tank to direct fuel from the primary tank to the secondary tank as the primary tank is filled, and to direct fuel from the secondary tank to the primary tank as fuel is discharged from the primary tank through the discharge line. A vent line has branches connected to each tank to direct fuel vapor from the tanks as the tanks are filled, and to admit air to the tanks as fuel is delivered to the engine.

Comparison of depression symptoms between primary depression and secondary-to-schizophrenia depression.

PubMed

Rahim, Twana; Rashid, Roshe

2017-11-01

This study exclusively aimed to clinically assess which symptom pattern discriminates primary depression from depression-secondary to-schizophrenia. A total of 98 patients with primary depression and 71 patients with secondary-to-schizophrenia depression were assessed for identifying the clinical phenomena of depression. Diagnosis of schizophrenia was confirmed by Mini International Neuropsychiatric Interview. Each participant was, however, assessed by Patient Health Questionnaire-9 as well as Calgary Depression Scale for Schizophrenia (CDSS) for possible concurrent depressive symptoms. Depressed mood, loss of interest, reduced energy and pathological guilt were more common in primary depression, whereas sleep disturbance and guilty ideas of reference were more amounting towards the diagnosis of depression secondary-to-schizophrenia. It is clinically hard to differentiate primary from secondary-to-schizophrenia depression, especially in the absence of obvious psychotic symptoms. However, the classical symptoms of depression like subjective depressed mood, anhedonia, reduced energy and pathological guilt are more prominent in the primary depression.

Bridging the Transition from Primary to Secondary School

ERIC Educational Resources Information Center

Howe, Alan, Ed.; Richards, Val, Ed.

2011-01-01

The transition from primary to secondary school can often be a difficult time for children, and managing the transition smoothly has posed a problem for teachers at both upper primary and lower secondary level. At a time when "childhood" recedes and "adulthood" beckons, the inequalities between individual children can widen,…

Transcervical embryoscopic and cytogenetic findings reveal distinctive differences in primary and secondary recurrent pregnancy loss.

PubMed

Feichtinger, Michael; Wallner, Elisabeth; Hartmann, Beda; Reiner, Angelika; Philipp, Thomas

2017-01-01

To assess the cytogenetic and embryoscopic characteristics of primary and secondary recurrent pregnancy loss. Clinical prospective descriptive study. Tertiary care center. Nine hundred and eighty-four women affected by first-trimester pregnancy loss; 145 patients with recurrent pregnancy loss (RPL) and 839 patients with nonrecurrent pregnancy loss as controls. Transcervical embryoscopic examination of the embryo before uterine evacuation, and cytogenetic analysis of the chorionic villi by standard G-banding cytogenetic techniques. Aneuploidy frequency in the primary and secondary RPL group and the nonrecurrent pregnancy loss (non-RPL) control group. Patients with RPL showed statistically significantly fewer aneuploid pregnancy losses (odds ratio [OR] 0.596; 95% confidence interval [CI], 0.40-0.88). Primary RPL was associated with lower aneuploidy rates compared with the non-RPL group (OR 0.423; 95% CI, 0.27-0.66) while secondary RPL was not (OR 1.414; 95% CI, 0.67-2.99). Patients with primary RPL had statistically significantly more morphologically normal embryos compared with non-RPL and secondary RPL. Patients' embryos after primary and secondary RPL show distinctive differences in aneuploidy and morphologic defect rates. These findings suggest different treatment approaches for the patients with primary and secondary RPL. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Basic Education from Early Childhood: Impacts of Free Primary Education and Subsidized Secondary Education on Public ECDE Centers in Nyahururu District, Kenya

ERIC Educational Resources Information Center

Mwangi, Peter Murage; Serem, T. D. K.

2013-01-01

Kenya must invest more in education to realize her vision 2030. The government commitment to Education for All's goal has been expressed through provision of basic education in pre-primary, primary and secondary school levels. To this end, the government introduced two kitties; Free Primary Education in 2003 and Subsidized Secondary Education in…

Primary vs. Secondary Antibody Deficiency: Clinical Features and Infection Outcomes of Immunoglobulin Replacement

PubMed Central

Duraisingham, Sai S.; Buckland, Matthew; Dempster, John; Lorenzo, Lorena; Grigoriadou, Sofia; Longhurst, Hilary J.

2014-01-01

Secondary antibody deficiency can occur as a result of haematological malignancies or certain medications, but not much is known about the clinical and immunological features of this group of patients as a whole. Here we describe a cohort of 167 patients with primary or secondary antibody deficiencies on immunoglobulin (Ig)-replacement treatment. The demographics, causes of immunodeficiency, diagnostic delay, clinical and laboratory features, and infection frequency were analysed retrospectively. Chemotherapy for B cell lymphoma and the use of Rituximab, corticosteroids or immunosuppressive medications were the most common causes of secondary antibody deficiency in this cohort. There was no difference in diagnostic delay or bronchiectasis between primary and secondary antibody deficiency patients, and both groups experienced disorders associated with immune dysregulation. Secondary antibody deficiency patients had similar baseline levels of serum IgG, but higher IgM and IgA, and a higher frequency of switched memory B cells than primary antibody deficiency patients. Serious and non-serious infections before and after Ig-replacement were also compared in both groups. Although secondary antibody deficiency patients had more serious infections before initiation of Ig-replacement, treatment resulted in a significant reduction of serious and non-serious infections in both primary and secondary antibody deficiency patients. Patients with secondary antibody deficiency experience similar delays in diagnosis as primary antibody deficiency patients and can also benefit from immunoglobulin-replacement treatment. PMID:24971644

Changes in hemp secondary fiber production related to technical fiber variability revealed by light microscopy and attenuated total reflectance Fourier transform infrared spectroscopy

PubMed Central

Fernandez-Tendero, Eva; Day, Arnaud; Legros, Sandrine; Habrant, Anouck; Hawkins, Simon

2017-01-01

Interest in hemp (Cannabis sativa L.) is increasing due to the development of a new range of industrial applications based on bast fibers. However the variability of bast fiber yield and quality represents an important barrier to further exploitation. Primary and secondary fiber content was examined in two commercial hemp varieties (Fedora 17, Santhica 27) grown under contrasted sowing density and irrigation conditions. Both growing conditions and hemp varieties impact stem tissue architecture with a large effect on the proportion of secondary fibers but not primary fibers. Attenuated total reflectance infrared spectroscopy allowed the discrimination of manually-isolated native primary fibers and secondary fibers but did not reveal any clustering according to growing conditions and variety. Infrared data were confirmed by wet chemistry analyses that revealed slight but significant differences between primary and secondary fiber cell wall composition. Infrared spectroscopy of technical fibers obtained after mechanical defibering revealed differences with native primary, but not secondary fibers and also discriminated samples obtained from plants grown under different conditions. Altogether the results suggested that the observed variability of hemp technical fibers could be partially explained by i) differences in secondary fiber production and ii) differential behavior during mechanical defibering resulting in unequal separation of primary and secondary fibers. PMID:28640922

Changes in hemp secondary fiber production related to technical fiber variability revealed by light microscopy and attenuated total reflectance Fourier transform infrared spectroscopy.

PubMed

Fernandez-Tendero, Eva; Day, Arnaud; Legros, Sandrine; Habrant, Anouck; Hawkins, Simon; Chabbert, Brigitte

2017-01-01

Interest in hemp (Cannabis sativa L.) is increasing due to the development of a new range of industrial applications based on bast fibers. However the variability of bast fiber yield and quality represents an important barrier to further exploitation. Primary and secondary fiber content was examined in two commercial hemp varieties (Fedora 17, Santhica 27) grown under contrasted sowing density and irrigation conditions. Both growing conditions and hemp varieties impact stem tissue architecture with a large effect on the proportion of secondary fibers but not primary fibers. Attenuated total reflectance infrared spectroscopy allowed the discrimination of manually-isolated native primary fibers and secondary fibers but did not reveal any clustering according to growing conditions and variety. Infrared data were confirmed by wet chemistry analyses that revealed slight but significant differences between primary and secondary fiber cell wall composition. Infrared spectroscopy of technical fibers obtained after mechanical defibering revealed differences with native primary, but not secondary fibers and also discriminated samples obtained from plants grown under different conditions. Altogether the results suggested that the observed variability of hemp technical fibers could be partially explained by i) differences in secondary fiber production and ii) differential behavior during mechanical defibering resulting in unequal separation of primary and secondary fibers.

A modeling analysis of alternative primary and secondary US ozone standards in urban and rural areas

NASA Astrophysics Data System (ADS)

Nopmongcol, Uarporn; Emery, Chris; Sakulyanontvittaya, Tanarit; Jung, Jaegun; Knipping, Eladio; Yarwood, Greg

2014-12-01

This study employed the High-Order Decoupled Direct Method (HDDM) of sensitivity analysis in a photochemical grid model to determine US anthropogenic emissions reductions required from 2006 levels to meet alternative US primary (health-based) and secondary (welfare-based) ozone (O3) standards. Applying the modeling techniques developed by Yarwood et al. (2013), we specifically evaluated sector-wide emission reductions needed to meet primary standards in the range of 60-75 ppb, and secondary standards in the range of 7-15 ppm-h, in 22 cities and at 20 rural sites across the US for NOx-only, combined NOx and VOC, and VOC-only scenarios. Site-specific model biases were taken into account by applying adjustment factors separately for the primary and secondary standard metrics, analogous to the US Environmental Protection Agency's (EPA) relative response factor technique. Both bias-adjusted and unadjusted results are presented and analyzed. We found that the secondary metric does not necessarily respond to emission reductions the same way the primary metric does, indicating sensitivity to their different forms. Combined NOx and VOC reductions are most effective for cities, whereas NOx-only reductions are sufficient at rural sites. Most cities we examined require more than 50% US anthropogenic emission reductions from 2006 levels to meet the current primary 75 ppb US standard and secondary 15 ppm-h target. Most rural sites require less than 20% reductions to meet the primary 75 ppb standard and less than 40% reductions to meet the secondary 15 ppm-h target. Whether the primary standard is protective of the secondary standard depends on the combination of alternative standard levels. Our modeling suggests that the current 75 ppb standard achieves a 15 ppm-h secondary target in most (17 of 22) cities, but only half of the rural sites; the inability for several western cities and rural areas to achieve the seasonally-summed secondary 15 ppm-h target while meeting the 75 ppb primary target is likely driven by higher background O3 that is commonly reported in the western US. However, a 70 ppb primary standard is protective of a 15 ppm-h secondary standard in all cities and 18 of 20 rural sites we examined, and a 60 ppb primary standard is protective of a 7 ppm-h secondary standard in all cities and 19 of 20 rural sites. If EPA promulgates separate primary and secondary standards, exceedance areas will need to develop and demonstrate control strategies to achieve both. This HDDM analysis provides an illustrative screening assessment by which to estimate emissions reductions necessary to satisfy both standards.

Does charging different user fees for primary and secondary care affect first-contacts with primary healthcare? A systematic review

PubMed Central

Hone, Thomas; Lee, John Tayu; Majeed, Azeem; Conteh, Lesong; Millett, Christopher

2017-01-01

Abstract Policy-makers are increasingly considering charging users different fees between primary and secondary care (differential user charges) to encourage utilisation of primary health care in health systems with limited gate keeping. A systematic review was conducted to evaluate the impact of introducing differential user charges on service utilisation. We reviewed studies published in MEDLINE, EMBASE, the Cochrane library, EconLIT, HMIC, and WHO library databases from January 1990 until June 2015. We extracted data from the studies meeting defined eligibility criteria and assessed study quality using an established checklist. We synthesized evidence narratively. Eight studies from six countries met our eligibility criteria. The overall study quality was low, with diversity in populations, interventions, settings, and methods. Five studies examined the introduction of or increase in user charges for secondary care, with four showing decreased secondary care utilisation, and three showing increased primary care utilisation. One study identified an increase in primary care utilisation after primary care user charges were reduced. The introduction of a non-referral charge in secondary care was associated with lower primary care utilisation in one study. One study compared user charges across insurance plans, associating higher charges in secondary care with higher utilisation in both primary and secondary care. Overall, the impact of introducing differential user-charges on primary care utilisation remains uncertain. Further research is required to understand their impact as a demand side intervention, including implications for health system costs and on utilisation among low-income patients. PMID:28453713

Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine

PubMed Central

Stavropoulos, Dimitri J; Merico, Daniele; Jobling, Rebekah; Bowdin, Sarah; Monfared, Nasim; Thiruvahindrapuram, Bhooma; Nalpathamkalam, Thomas; Pellecchia, Giovanna; Yuen, Ryan K C; Szego, Michael J; Hayeems, Robin Z; Shaul, Randi Zlotnik; Brudno, Michael; Girdea, Marta; Frey, Brendan; Alipanahi, Babak; Ahmed, Sohnee; Babul-Hirji, Riyana; Porras, Ramses Badilla; Carter, Melissa T; Chad, Lauren; Chaudhry, Ayeshah; Chitayat, David; Doust, Soghra Jougheh; Cytrynbaum, Cheryl; Dupuis, Lucie; Ejaz, Resham; Fishman, Leona; Guerin, Andrea; Hashemi, Bita; Helal, Mayada; Hewson, Stacy; Inbar-Feigenberg, Michal; Kannu, Peter; Karp, Natalya; Kim, Raymond H; Kronick, Jonathan; Liston, Eriskay; MacDonald, Heather; Mercimek-Mahmutoglu, Saadet; Mendoza-Londono, Roberto; Nasr, Enas; Nimmo, Graeme; Parkinson, Nicole; Quercia, Nada; Raiman, Julian; Roifman, Maian; Schulze, Andreas; Shugar, Andrea; Shuman, Cheryl; Sinajon, Pierre; Siriwardena, Komudi; Weksberg, Rosanna; Yoon, Grace; Carew, Chris; Erickson, Raith; Leach, Richard A; Klein, Robert; Ray, Peter N; Meyn, M Stephen; Scherer, Stephen W; Cohn, Ronald D; Marshall, Christian R

2016-01-01

The standard of care for first-tier clinical investigation of the aetiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy-number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion–deletions (indels) and single-nucleotide variant (SNV) mutations. Whole-genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilised WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a fourfold increase in diagnostic rate over CMA (8%; P value=1.42E−05) alone and more than twofold increase in CMA plus targeted gene sequencing (13%; P value=0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harbouring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counselling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis. PMID:28567303

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.

PubMed

Stavropoulos, Dimitri J; Merico, Daniele; Jobling, Rebekah; Bowdin, Sarah; Monfared, Nasim; Thiruvahindrapuram, Bhooma; Nalpathamkalam, Thomas; Pellecchia, Giovanna; Yuen, Ryan K C; Szego, Michael J; Hayeems, Robin Z; Shaul, Randi Zlotnik; Brudno, Michael; Girdea, Marta; Frey, Brendan; Alipanahi, Babak; Ahmed, Sohnee; Babul-Hirji, Riyana; Porras, Ramses Badilla; Carter, Melissa T; Chad, Lauren; Chaudhry, Ayeshah; Chitayat, David; Doust, Soghra Jougheh; Cytrynbaum, Cheryl; Dupuis, Lucie; Ejaz, Resham; Fishman, Leona; Guerin, Andrea; Hashemi, Bita; Helal, Mayada; Hewson, Stacy; Inbar-Feigenberg, Michal; Kannu, Peter; Karp, Natalya; Kim, Raymond; Kronick, Jonathan; Liston, Eriskay; MacDonald, Heather; Mercimek-Mahmutoglu, Saadet; Mendoza-Londono, Roberto; Nasr, Enas; Nimmo, Graeme; Parkinson, Nicole; Quercia, Nada; Raiman, Julian; Roifman, Maian; Schulze, Andreas; Shugar, Andrea; Shuman, Cheryl; Sinajon, Pierre; Siriwardena, Komudi; Weksberg, Rosanna; Yoon, Grace; Carew, Chris; Erickson, Raith; Leach, Richard A; Klein, Robert; Ray, Peter N; Meyn, M Stephen; Scherer, Stephen W; Cohn, Ronald D; Marshall, Christian R

2016-01-13

The standard of care for first-tier clinical investigation of the etiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion-deletions (indels) and single nucleotide variant (SNV) mutations. Whole genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilized WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a 4-fold increase in diagnostic rate over CMA (8%) (p-value = 1.42e-05) alone and >2-fold increase in CMA plus targeted gene sequencing (13%) (p-value = 0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counseling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.

Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations.

PubMed

Hu, Xihao; Wu, Yang; Lu, Zhi John; Yip, Kevin Y

2016-11-01

High-throughput sequencing has been used to study posttranscriptional regulations, where the identification of protein-RNA binding is a major and fast-developing sub-area, which is in turn benefited by the sequencing methods for whole-transcriptome probing of RNA secondary structures. In the study of RNA secondary structures using high-throughput sequencing, bases are modified or cleaved according to their structural features, which alter the resulting composition of sequencing reads. In the study of protein-RNA binding, methods have been proposed to immuno-precipitate (IP) protein-bound RNA transcripts in vitro or in vivo By sequencing these transcripts, the protein-RNA interactions and the binding locations can be identified. For both types of data, read counts are affected by a combination of confounding factors, including expression levels of transcripts, sequence biases, mapping errors and the probing or IP efficiency of the experimental protocols. Careful processing of the sequencing data and proper extraction of important features are fundamentally important to a successful analysis. Here we review and compare different experimental methods for probing RNA secondary structures and binding sites of RNA-binding proteins (RBPs), and the computational methods proposed for analyzing the corresponding sequencing data. We suggest how these two types of data should be integrated to study the structural properties of RBP binding sites as a systematic way to better understand posttranscriptional regulations. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

A Field Trial to Assess a Blood-Stage Malaria Vaccine

PubMed Central

Thera, Mahamadou A.; Doumbo, Ogobara K.; Coulibaly, Drissa; Laurens, Matthew B.; Ouattara, Amed; Kone, Abdoulaye K.; Guindo, Ando B.; Traore, Karim; Traore, Idrissa; Kouriba, Bourema; Diallo, Dapa A.; Diarra, Issa; Daou, Modibo; Dolo, Amagana; Tolo, Youssouf; Sissoko, Mahamadou S.; Niangaly, Amadou; Sissoko, Mady; Takala-Harrison, Shannon; Lyke, Kirsten E.; Wu, Yukun; Blackwelder, William C.; Godeaux, Olivier; Vekemans, Johan; Dubois, Marie-Claude; Ballou, W. Ripley; Cohen, Joe; Thompson, Darby; Dube, Tina; Soisson, Lorraine; Diggs, Carter L.; House, Brent; Lanar, David E.; Dutta, Sheetij; Heppner, D. Gray; Plowe, Christopher V.

2011-01-01

BACKGROUND Blood-stage malaria vaccines are intended to prevent clinical disease. The malaria vaccine FMP2.1/AS02A, a recombinant protein based on apical membrane antigen 1 (AMA1) from the 3D7 strain of Plasmodium falciparum, has previously been shown to have immunogenicity and acceptable safety in Malian adults and children. METHODS In a double-blind, randomized trial, we immunized 400 Malian children with either the malaria vaccine or a control (rabies) vaccine and followed them for 6 months. The primary end point was clinical malaria, defined as fever and at least 2500 parasites per cubic millimeter of blood. A secondary end point was clinical malaria caused by parasites with the AMA1 DNA sequence found in the vaccine strain. RESULTS The cumulative incidence of the primary end point was 48.4% in the malaria-vaccine group and 54.4% in the control group; efficacy against the primary end point was 17.4% (hazard ratio for the primary end point, 0.83; 95% confidence interval [CI], 0.63 to 1.09; P = 0.18). Efficacy against the first and subsequent episodes of clinical malaria, as defined on the basis of various parasite-density thresholds, was approximately 20%. Efficacy against clinical malaria caused by parasites with AMA1 corresponding to that of the vaccine strain was 64.3% (hazard ratio, 0.36; 95% CI, 0.08 to 0.86; P = 0.03). Local reactions and fever after vaccination were more frequent with the malaria vaccine. CONCLUSIONS On the basis of the primary end point, the malaria vaccine did not provide significant protection against clinical malaria, but on the basis of secondary results, it may have strain-specific efficacy. If this finding is confirmed, AMA1 might be useful in a multicomponent malaria vaccine. PMID:21916638

Primary versus secondary closure of cutaneous abscesses in the emergency department: a randomized controlled trial.

PubMed

Singer, Adam J; Taira, Breena R; Chale, Stuart; Bhat, Rahul; Kennedy, David; Schmitz, Gillian

2013-01-01

Cutaneous abscesses have traditionally been treated with incision and drainage (I&D) and left to heal by secondary closure. The objective was to compare the healing rates of cutaneous abscesses following I&D after primary or secondary closure. This was a randomized, controlled, trial, balanced by center, with blocked randomization created by a random-number generator. One urban and one suburban academic emergency department (ED) participated. Subjects were randomized to primary or secondary wound closure following I&D of the abscess. Main outcome measures were the percentage of healed wounds (wound was completely closed by visual inspection; a 40% difference in wound healing was sought) and overall failure rate (need for additional intervention including suture removal, additional drainage, antibiotics, or admission within 7 days after drainage). Fifty-six adult patients with simple localized cutaneous abscesses were included; 29 were randomized to primary closure, and 27 were randomized to secondary closure. Healing rates at 7 days were similar between the primary and secondary closure groups (69.6%, 95% confidence interval [CI] = 49.1% to 84.4% vs. 59.3%, 95% CI = 40.7% to 75.5%; difference 10.3%, 95% CI = -15.8% to 34.1%). Overall failure rates at 7 days were also similar between the primary and secondary closure groups (30.4%, 95% CI = 15.6% to 50.9% vs. 28.6%, 95% CI = 15.2% to 47.1%; difference 1.8%, 95% CI = -24.2% to 28.8%). The rates of wound healing and treatment failure following I&D of simple abscesses in the ED are similar after primary or secondary closure. The authors did not detect a difference of at least 40% in healing rates between primary and secondary closure. © 2013 by the Society for Academic Emergency Medicine.

Mapping the Geometric Evolution of Protein Folding Motor.

PubMed

Jerath, Gaurav; Hazam, Prakash Kishore; Shekhar, Shashi; Ramakrishnan, Vibin

2016-01-01

Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ1, and χ2 of side chain. In this work, protein molecule is metaphorically modelled as a machine with 4 rotors ϕ, ψ, χ1 and χ2, with its evolution to the functional fold is directed by combinations of its rotor directions. We observe that differential rotor motions lead to different secondary structure formations and the combinatorial pattern is unique and consistent for particular secondary structure type. Further, we found that combination of rotor geometries of each amino acid is unique which partly explains how different amino acid sequence combinations have unique structural evolution and functional adaptation. Quantification of these amino acid rotor preferences, resulted in the generation of 3 substitution matrices, which later on plugged in the BLAST tool, for evaluating their efficiency in aligning sequences. We have employed BLOSUM62 and PAM30 as standard for primary evaluation. Generation of substitution matrices is a logical extension of the conceptual framework we attempted to build during the development of this work. Optimization of matrices following the conventional routines and possible application with biologically relevant data sets are beyond the scope of this manuscript, though it is a part of the larger project design.

Sequential Metabolism of Secondary Alkyl Amines to Metabolic-Intermediate Complexes: Opposing Roles for the Secondary Hydroxylamine and Primary Amine Metabolites of Desipramine, (S)-Fluoxetine, and N-Desmethyldiltiazem

PubMed Central

Hanson, Kelsey L.; VandenBrink, Brooke M.; Babu, Kantipudi N.; Allen, Kyle E.; Nelson, Wendel L.

2010-01-01

Three secondary amines desipramine (DES), (S)-fluoxetine [(S)-FLX], and N-desmethyldiltiazem (MA) undergo N-hydroxylation to the corresponding secondary hydroxylamines [N-hydroxydesipramine, (S)-N-hydroxyfluoxetine, and N-hydroxy-N-desmethyldiltiazem] by cytochromes P450 2C11, 2C19, and 3A4, respectively. The expected primary amine products, N-desmethyldesipramine, (S)-norfluoxetine, and N,N-didesmethyldiltiazem, are also observed. The formation of metabolic-intermediate (MI) complexes from these substrates and metabolites was examined. In each example, the initial rates of MI complex accumulation followed the order secondary hydroxylamine > secondary amine ≫ primary amine, suggesting that the primary amine metabolites do not contribute to formation of MI complexes from these secondary amines. Furthermore, the primary amine metabolites, which accumulate in incubations of the secondary amines, inhibit MI complex formation. Mass balance studies provided estimates of the product ratios of N-dealkylation to N-hydroxylation. The ratios were 2.9 (DES-CYP2C11), 3.6 [(S)-FLX-CYP2C19], and 0.8 (MA-CYP3A4), indicating that secondary hydroxylamines are significant metabolites of the P450-mediated metabolism of secondary alkyl amines. Parallel studies with N-methyl-d3-desipramine and CYP2C11 demonstrated significant isotopically sensitive switching from N-demethylation to N-hydroxylation. These findings demonstrate that the major pathway to MI complex formation from these secondary amines arises from N-hydroxylation rather than N-dealkylation and that the primary amines are significant competitive inhibitors of MI complex formation. PMID:20200233

Sequential metabolism of secondary alkyl amines to metabolic-intermediate complexes: opposing roles for the secondary hydroxylamine and primary amine metabolites of desipramine, (s)-fluoxetine, and N-desmethyldiltiazem.

PubMed

Hanson, Kelsey L; VandenBrink, Brooke M; Babu, Kantipudi N; Allen, Kyle E; Nelson, Wendel L; Kunze, Kent L

2010-06-01

Three secondary amines desipramine (DES), (S)-fluoxetine [(S)-FLX], and N-desmethyldiltiazem (MA) undergo N-hydroxylation to the corresponding secondary hydroxylamines [N-hydroxydesipramine, (S)-N-hydroxyfluoxetine, and N-hydroxy-N-desmethyldiltiazem] by cytochromes P450 2C11, 2C19, and 3A4, respectively. The expected primary amine products, N-desmethyldesipramine, (S)-norfluoxetine, and N,N-didesmethyldiltiazem, are also observed. The formation of metabolic-intermediate (MI) complexes from these substrates and metabolites was examined. In each example, the initial rates of MI complex accumulation followed the order secondary hydroxylamine > secondary amine > primary amine, suggesting that the primary amine metabolites do not contribute to formation of MI complexes from these secondary amines. Furthermore, the primary amine metabolites, which accumulate in incubations of the secondary amines, inhibit MI complex formation. Mass balance studies provided estimates of the product ratios of N-dealkylation to N-hydroxylation. The ratios were 2.9 (DES-CYP2C11), 3.6 [(S)-FLX-CYP2C19], and 0.8 (MA-CYP3A4), indicating that secondary hydroxylamines are significant metabolites of the P450-mediated metabolism of secondary alkyl amines. Parallel studies with N-methyl-d(3)-desipramine and CYP2C11 demonstrated significant isotopically sensitive switching from N-demethylation to N-hydroxylation. These findings demonstrate that the major pathway to MI complex formation from these secondary amines arises from N-hydroxylation rather than N-dealkylation and that the primary amines are significant competitive inhibitors of MI complex formation.

Is Primary-Process Cognition a Feature of Hypnosis?

PubMed

Finn, Michael T; Goldman, Jared I; Lyon, Gyrid B; Nash, Michael R

2017-01-01

The division of cognition into primary and secondary processes is an important part of contemporary psychoanalytic metapsychology. Whereas primary processes are most characteristic of unconscious thought and loose associations, secondary processes generally govern conscious thought and logical reasoning. It has been theorized that an induction into hypnosis is accompanied by a predomination of primary-process cognition over secondary-process cognition. The authors hypothesized that highly hypnotizable individuals would demonstrate more primary-process cognition as measured by a recently developed cognitive-perceptual task. This hypothesis was not supported. In fact, low hypnotizable participants demonstrated higher levels of primary-process cognition. Exploratory analyses suggested a more specific effect: felt connectedness to the hypnotist seemed to promote secondary-process cognition among low hypnotizable participants.

Characterization of xylan in the early stages of secondary cell wall formation in tobacco bright yellow-2 cells.

PubMed

Ishii, Tadashi; Matsuoka, Keita; Ono, Hiroshi; Ohnishi-Kameyama, Mayumi; Yaoi, Katsuro; Nakano, Yoshimi; Ohtani, Misato; Demura, Taku; Iwai, Hiroaki; Satoh, Shinobu

2017-11-15

The major polysaccharides present in the primary and secondary walls surrounding plant cells have been well characterized. However, our knowledge of the early stages of secondary wall formation is limited. To address this, cell walls were isolated from differentiating xylem vessel elements of tobacco bright yellow-2 (BY-2) cells induced by VASCULAR-RELATED NAC-DOMAIN7 (VND7). The walls of induced VND7-VP16-GR BY-2 cells consisted of cellulose, pectic polysaccharides, hemicelluloses, and lignin, and contained more xylan and cellulose compared with non-transformed BY-2 and uninduced VND7-VP16-GR BY-2 cells. A reducing end sequence of xylan containing rhamnose and galaturonic acid- residues is present in the walls of induced, uninduced, and non-transformed BY-2 cells. Glucuronic acid residues in xylan from walls of induced cells are O-methylated, while those of xylan in non-transformed BY-2 and uninduced cells are not. Our results show that xylan changes in chemical structure and amounts during the early stages of xylem differentiation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

Associations Between Secondary Caregivers' Supportive Behavior and Psychological Distress of Primary Spousal Caregivers of Cognitively Intact and Impaired Elders.

PubMed

Lou, Vivian W Q; Kwan, Chi Wai; Chong, Ming Lin Alice; Chi, Iris

2015-08-01

This study examined associations between the availability and types of supportive behavior provided by secondary caregivers and the psychological distress of primary spousal caregivers of cognitively intact and impaired elders. A sample of 8,087 assessments using the validated Chinese version of the Minimum Data Set-Home Care of individuals applying for government-subsidized long-term care services from 2006 to 2009 in Hong Kong were selected based on inclusion criteria. More than 70% of primary caregivers had secondary caregivers; the rate was slightly lower for those caring for moderately or severely cognitively impaired spouses. More than half of the primary spousal caregivers had secondary caregivers who provided both emotional and instrumental support. Emotional support provided by secondary caregivers had a negative association with primary caregivers' psychological distress when their care recipients were cognitively intact. When secondary caregivers provided both instrumental and emotional support, primary caregivers had a higher likelihood of psychological distress when care recipients had greater negative mood symptoms as compared to those who had less negative mood symptoms. This is the first study that examined the association between availability and types of supportive behavior provided by secondary caregivers and the psychological distress of primary spousal caregivers of cognitively intact and impaired elders. The findings suggest a need to provide services that enhance the provision of emotional support from both secondary and primary caregivers to cognitively intact elders and support primary spousal caregivers to seek appropriate help according to the mood of care recipients. © The Author 2013. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Variation among cleft centres in the use of secondary surgery for children with cleft palate: a retrospective cohort study

PubMed Central

Sitzman, Thomas J; Hossain, Monir; Carle, Adam C; Heaton, Pamela C; Britto, Maria T

2017-01-01

Objectives To test whether cleft centres vary in their use of secondary cleft palate surgery, also known as revision palate surgery, and if so to identify modifiable hospital factors and surgeon factors that are associated with use of secondary surgery. Design Retrospective cohort study. Setting Forty-three paediatric hospitals across the USA. Patients Children with cleft lip and palate who underwent primary cleft palate repair from 1999 to 2013. Main outcome measures Time from primary cleft palate repair to secondary palate surgery. Results We identified 4939 children who underwent primary cleft palate repair. At 10 years after primary palate repair, 44% of children had undergone secondary palate surgery. Significant variation existed among hospitals (p<0.001); the proportion of children undergoing secondary surgery by 10 years ranged from 9% to 77% across hospitals. After adjusting for patient demographics, primary palate repair before 9 months of age was associated with an increased hazard of secondary palate surgery (initial HR 6.74, 95% CI 5.30 to 8.73). Postoperative antibiotics, surgeon procedure volume and hospital procedure volume were not associated with time to secondary surgery (p>0.05). Of the outcome variation attributable to hospitals and surgeons, between-hospital differences accounted for 59% (p<0.001), while between-surgeon differences accounted for 41% (p<0.001). Conclusions Substantial variation in the hazard of secondary palate surgery exists depending on a child’s age at primary palate repair and the hospital and surgeon performing their repair. Performing primary palate repair before 9 months of age substantially increases the hazard of secondary surgery. Further research is needed to identify other factors contributing to variation in palate surgery outcomes among hospitals and surgeons. PMID:29479567

Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.

PubMed

Ikeda, Shun; Abe, Takashi; Nakamura, Yukiko; Kibinge, Nelson; Hirai Morita, Aki; Nakatani, Atsushi; Ono, Naoaki; Ikemura, Toshimichi; Nakamura, Kensuke; Altaf-Ul-Amin, Md; Kanaya, Shigehiko

2013-05-01

Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.

Facial growth and development in unilateral cleft lip and palate: comparison between secondary alveolar bone grafting and primary periosteoplasty.

PubMed

Cagáňová, Veronika; Borský, Jiří; Smahel, Zbyněk; Velemínská, Jana

2014-01-01

To describe the effect of secondary alveolar bone grafting in patients with unilateral cleft lip and palate by comparison with a sample of patients who have undergone primary periosteoplasty. Cephalometric analysis of lateral x-ray films in a retrospective semilongitudinal study. Lateral x-ray films of 18 secondary alveolar bone grafting patients and 48 primary periosteoplasty patients at 10 years of age and again at 15 years of age. The treatment of secondary alveolar bone grafting patients included lip repair according to Tennison, palatoplasty including retropositioning, pharyngeal flap surgery, and secondary alveolar bone grafting. The lips of primary periosteoplasty patient were repaired using the methods of Tennison and Veau, followed by primary periosteoplasty, palatoplasty including retropositioning, and pharyngeal flap surgery. Lateral radiographs were assessed using classical morphometry. There were few significant differences at 10 years of age between the secondary alveolar bone grafting and primary periosteoplasty patients. At 15 years of age, there were several significant differences. Compared with primary periosteoplasty patients, subsequent development in patients who had undergone secondary alveolar bone grafting was characterized by a significantly better position of the upper and lower dentoalveolar components in relation to the facial plane, a higher increase in the global convexity of the soft profile, a significantly better maxillary inclination, and a more favorable development of vertical intermaxillary relationships. Craniofacial development in secondary alveolar bone grafting patients was better than that in primary periosteoplasty patients due to the more marked facial convexity, the increased prominence of the nose, and better vertical intermaxillary relationships.

Poliovirus removal from primary and secondary sewage effluent by soil filtration.

PubMed Central

Gerba, C P; Lance, J C

1978-01-01

Adsorption of poliovirus from primary sewage effluent was similar to that from secondary sewage effluent in both batch soil studies and experiments with soil columns 240 cm long. Virus desorption by distilled water was also similar in a soil column that had been flooded with either primary or secondary effluent seeded with virus. These results indicated that absorption of poliovirus from primary effluent and virus movement through the soil were not affected by the higher organic content of primary sewage effluent. PMID:211936

A variant of Leber hereditary optic neuropathy characterized by recovery of vision and by an unusual mitochondrial genetic etiology.

PubMed Central

Mackey, D; Howell, N

1992-01-01

The Tas2 and Vic2 Australian families are affected with a variant of Leber hereditary optic neuropathy (LHON). The risk of developing the optic neuropathy shows strict maternal inheritance, and the ophthalmological changes in affected family members are characteristic of LHON. However, in contrast to the common form of the disease, members of these two families show a high frequency of vision recovery. To ascertain the mitochondrial genetic etiology of the LHON in these families, both (a) the the nucleotide sequences of the seven mitochondrial genes encoding subunits of respiratory-chain complex I and (b) the mitochondrial cytochrome b gene were determined for representatives of both families. Neither family carries any of the previously identified primary mitochondrial LHON mutations: ND4/11778, ND1/3460, or ND1/4160. Instead, both LHON families carry multiple nucleotide changes in the mitochondrial complex I genes, which produce conservative amino acid changes. From the available sequence data, it is inferred that the Vic2 and Tas2 LHON families are phylogenetically related to each other and to a cluster of LHON families in which mutations in the mitochondrial cytochrome b gene have been hypothesized to play a primary etiological role. However, sequencing analysis establishes that the Vic2 and Tas2 LHON families do not carry these cytochrome b mutations. There are two hypotheses to account for the unusual mitochondrial genetic etiology of the LHON in the Tas2 and Vic2 LHON families. One possibility is that there is a primary LHON mutation within the mitochondrial genome but that it is at a site that was not included in the sequencing analyses. Alternatively, the disease in these families may result from the cumulative effects of multiple secondary LHON mutations that have less severe phenotypic consequences. PMID:1463007

A variant of Leber hereditary optic neuropathy characterized by recovery of vision and by an unusual mitochondrial genetic etiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mackey, D.; Howell, N.

1992-12-01

The Tas2 and Vic2 Australian families are affected with a variant of Leber hereditary optic neuropathy (LHON). The risk of developing the optic neuropathy shows strict maternal inheritance, and the opthalmological changes in affected family members are characteristic of LHON. However, in contrast to the common form of the disease, members of these two families show a high frequency of vision recovery. To ascertain the mitochondrial genetic etiology of the LHON in these families, both (a) the nucleotide sequences of the seven mitochondrial genes encoding subunits of respiratory-chain complex I and (b) the mitochondrial cytochrome b gene were determined formore » representatives of both families. Neither family carries any of the previously identified primary mitochondrial LHON mutations: ND4/11778, ND1/3460, or ND1/4160. Instead, both LHON families carry multiple nucleotide changes in the mitochondrial complex I genes, which produce conservative amino acid changes. From the available sequence data, it is inferred that the Vic2 and Tas2 LHON families are phylogenetically related to each other and to a cluster of LHON families in which mutations in the mitochondrial cytochrome b gene have been hypothesized to play a primary etiological role. However, sequencing analysis establishes that the Vic2 and Tas2 LHON families do not carry these cytochrome b mutations. There are two hypotheses to account for the unusual mitochondrial genetic etiology of the LHON in the Tas2 and Vic2 LHON families. One possibility is that there is a primary LHON mutation within the mitochondrial genome but that it is at a site that was not included in the sequencing analyses. Alternatively, the disease in these families may result from the cumulative effects of multiple secondary LHON mutations that have less severe phenotypic consequences. 29 refs., 3 figs., 3 tabs.« less

An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

PubMed Central

Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

2016-01-01

Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2011 CFR

2011-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.15 - National primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... air quality standards for ozone. 50.15 Section 50.15 Protection of Environment ENVIRONMENTAL....15 National primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone (O3) is 0.075 parts per...

40 CFR 50.16 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2011 CFR

2011-07-01

... air quality standards for lead. 50.16 Section 50.16 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) The national primary and secondary ambient air quality standards for lead (Pb) and its compounds are 0.15 micrograms per cubic meter...

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2013 CFR

2013-07-01

... air quality standards for lead. 50.12 Section 50.12 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) National primary and secondary ambient air quality standards for lead and its compounds, measured as elemental lead by a reference method...

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2012 CFR

2012-07-01

... air quality standards for lead. 50.12 Section 50.12 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) National primary and secondary ambient air quality standards for lead and its compounds, measured as elemental lead by a reference method...

40 CFR 50.12 - National primary and secondary ambient air quality standards for lead.

Code of Federal Regulations, 2011 CFR

2011-07-01

... air quality standards for lead. 50.12 Section 50.12 Protection of Environment ENVIRONMENTAL PROTECTION... National primary and secondary ambient air quality standards for lead. (a) National primary and secondary ambient air quality standards for lead and its compounds, measured as elemental lead by a reference method...

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms

PubMed Central

Kameshwar, Ayyappa kumar Sista; Qin, Wensheng

2016-01-01

Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation. PMID:26884714

Isolation and in silico analysis of a novel H+-pyrophosphatase gene orthologue from the halophytic grass Leptochloa fusca

NASA Astrophysics Data System (ADS)

Rauf, Muhammad; Saeed, Nasir A.; Habib, Imran; Ahmed, Moddassir; Shahzad, Khurram; Mansoor, Shahid; Ali, Rashid

2017-02-01

Structure prediction can provide information about function and active sites of protein which helps to design new functional proteins. H+-pyrophosphatase is transmembrane protein involved in establishing proton motive force for active transport of Na+ across membrane by Na+/H+ antiporters. A full length novel H+-pyrophosphatase gene was isolated from halophytic grass Leptochloa fusca using RT-PCR and RACE method. Full length LfVP1 gene sequence of 2292 nucleotides encodes protein of 764 amino acids. DNA and protein sequences were used for characterization using bioinformatics tools. Various important potential sites were predicted by PROSITE webserver. Primary structural analysis showed LfVP1 as stable protein and Grand average hydropathy (GRAVY) indicated that LfVP1 protein has good hydrosolubility. Secondary structure analysis showed that LfVP1 protein sequence contains significant proportion of alpha helix and random coil. Protein membrane topology suggested the presence of 14 transmembrane domains and presence of catalytic domain in TM3. Three dimensional structure from LfVP1 protein sequence also indicated the presence of 14 transmembrane domains and hydrophobicity surface model showed amino acid hydrophobicity. Ramachandran plot showed that 98% amino acid residues were predicted in the favored region.

The Global Contribution of Secondary Craters on the Icy Satellites

NASA Astrophysics Data System (ADS)

Hoogenboom, T.; Johnson, K. E.; Schenk, P.

2014-12-01

At present, surface ages of bodies in the Outer Solar System are determined only from crater size-frequency distributions (a method dependent on an understanding of the projectile populations responsible for impact craters in these planetary systems). To derive accurate ages using impact craters, the impactor population must be understood. Impact craters in the Outer Solar System can be primary, secondary or sesquinary. The contribution of secondary craters to the overall population has recently become a "topic of interest." Our objective is to better understand the contribution of dispersed secondary craters to the small crater populations, and ultimately that of small comets to the projectile flux on icy satellites in general. We measure the diameters of obvious secondary craters (determined by e.g. irregular crater shape, small size, clustering) formed by all primary craters on Ganymede for which we have sufficiently high resolution data to map secondary craters. Primary craters mapped range from approximately 40 km to 210 km. Image resolution ranges from 45 to 440 m/pixel. Bright terrain on Ganymede is our primary focus. These resurfaced terrains have relatively low crater densities and serve as a basis for characterizing secondary populations as a function of primary size on an icy body for the first time. Although focusing on Ganymede, we also investigate secondary crater size, frequency, distribution, and formation, as well as secondary crater chain formation on icy satellites throughout the Saturnian and Jovian systems principally Rhea. We compare our results to similar studies of secondary cratering on the Moon and Mercury. Using Galileo and Voyager data, we have identified approximately 3,400 secondary craters on Ganymede. In some cases, we measured crater density as a function of distance from a primary crater. Because of the limitations of the Galileo data, it is necessary to extrapolate from small data sets to the global population of secondary craters. Nonetheless, we confirm that secondary craters on Ganymede have narrow size-frequency distributions and that they correlate with primary crater diameter. From these data we will evaluate the contribution of secondary craters over a range of crater diameters.

New insights into pioneer root xylem development: evidence obtained from Populus trichocarpa plants grown under field conditions

PubMed Central

Bagniewska-Zadworna, Agnieszka; Arasimowicz-Jelonek, Magdalena; Smoliński, Dariusz J.; Stelmasik, Agnieszka

2014-01-01

Background and Aims Effective programmed xylogenesis is critical to the structural framework of the plant root system and its central role in the acquisition and long-distance transport of water and nutrients. The process of xylem differentiation in pioneer roots under field conditions is poorly understood. In this study it is hypothesized that xylogenesis, an example of developmental programmed cell death (PCD), in the roots of woody plants demonstrates a clearly defined sequence of events resulting in cell death. A comprehensive analysis was therefore undertaken to identify the stages of xylogenesis in pioneer roots from procambial cells to fully functional vessels with lignified cell walls and secondary cell wall thickenings. Methods Xylem differentiation was monitored in the pioneer roots of Populus trichocarpa at the cytological level using rhizotrons under field conditions. Detection and localization of the signalling molecule nitric oxide (NO) and hydrogen peroxide (H2O2) was undertaken and a detailed examination of nuclear changes during xylogenesis was conducted. In addition, analyses of the expression of genes involved in secondary cell wall synthesis were performed in situ. Key Results The primary event in initially differentiating tracheary elements (TEs) was a burst of NO in thin-walled cells, followed by H2O2 synthesis and the appearance of TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling)-positive nuclei. The first changes in nuclear structure were observed in the early stages of xylogenesis of pioneer roots, prior to lignification; however, the nucleus was detectable under transmission electron microscopy in differentiating cells until the stage at which vacuole integrity was maintained, indicating that their degradation was slow and prolonged. The subsequent sequence of events involved secondary cell wall formation and autophagy. Potential gene markers from the cinnamyl alcohol dehydrogenase (CAD) gene family that were related to secondary wall synthesis were associated with primary xylogenesis, showing clear expression in cells that undergo differentiation into TEs and in the thin-walled cells adjacent to the xylem pole. Conclusions The early events of TE formation during pioneer root development are described, together with the timing of xylogenesis from signalling via NO, through secondary cell wall synthesis and autophagy events that are initiated long before lignification. This is the first work describing experiments conducted in planta on roots under field conditions demonstrating that the process of xylogenesis in vivo might be gradual and complex. PMID:24812251

Ways Constituency Development Fund Promotes Secondary Education in Laikipia West District, Kenya

ERIC Educational Resources Information Center

Mwangi, Peter Murage

2013-01-01

Kenya started providing secondary school education as part of her basic education in 2008 through subsidized secondary education in 2008, but was faced by two major challenges; secondary schools are fewer than primary schools, and secondary education is more costly than primary education. This has made many students especially those from poor…

Root development and structure in seedlings of Ginkgo biloba.

PubMed

Bonacorsi, Nikole K; Seago, James L

2016-02-01

The popular, highly recognizable, well-known gymnosperm, Ginkgo biloba, was studied to document selected developmental features, which are little known in its primary root system from root tips to cotyledonary node following seed germination. Using seedlings grown in soil, vermiculite, or a mixture, we examined sections at various distances from the root cap to capture a developmental sequence of anatomical structures by using standard brightfield, epifluorescence, and confocal microscopic techniques. The vascular cylinder is usually a diarch stele, although modified diarchy and triarchy are found. Between exarch protoxylem poles, metaxylem usually develops into a complete disc, except near the transition region, which has irregularly arranged tracheary cells. The disc of primary xylem undergoes secondary growth on its metaxylem flanks with many tracheids added radially within a few weeks. Production of fibers in secondary phloem also accompanies secondary growth. In the cortex, endodermis produces Casparian bands early in development and continues into the upper transition region. Phi cells with phi-thickenings (bands of lignified walls) of a layer of inner cortex are often evident before endodermis, and then adjoining, additional layers of cortex develop phi cells; phi cells do not occur in the upper transition region or stem. An exodermis is produced early in root development and is continuous into the transition region and cotyledonary node. Seedling root axes of Ginkgo biloba are more complex than the literature suggests, and our findings contribute to our knowledge of root structure of this ancient gymnosperm. © 2016 Botanical Society of America.

Secondary transfer effect among children: The role of social dominance orientation and outgroup attitudes.

PubMed

Vezzali, Loris; Di Bernardo, Gian Antonio; Stathi, Sofia; Cadamuro, Alessia; Lášticová, Barbara; Andraščiková, Simona

2018-02-24

Research has provided evidence that the effects of intergroup contact on prejudice reduction are not limited to the outgroup one has contact with (primary outgroup). Rather, they extend to secondary outgroups uninvolved in the contact situation (secondary transfer effect; Pettigrew, 2009, Social Psychology, 40, 55). We aimed to provide the first empirical evidence for the emergence of the secondary transfer effect among children. Majority (Italian) and minority (with an immigrant background) elementary schoolchildren were administered a questionnaire including measures of contact with the primary outgroup (minority children for the majority, majority children for the minority), prejudice towards the primary outgroup and towards a dissimilar secondary outgroup (disabled children), and social dominance orientation. Results revealed that among the majority group, contact with the primary outgroup had indirect associations with reduced prejudice towards the secondary outgroup. Specifically, we found evidence for sequential mediation by social dominance orientation and prejudice towards the primary outgroup. No secondary transfer effects emerged among minority group members. We discuss theoretical and practical implications of the findings, arguing for the importance of identifying the core processes driving the secondary transfer effect. © 2018 The British Psychological Society.

Fluid channeling system

NASA Technical Reports Server (NTRS)

Davis, Donald Y. (Inventor); Hitch, Bradley D. (Inventor)

1994-01-01

A fluid channeling system includes a fluid ejector, a heat exchanger, and a fluid pump disposed in series flow communication The ejector includes a primary inlet for receiving a primary fluid, and a secondary inlet for receiving a secondary fluid which is mixed with the primary fluid and discharged therefrom as ejector discharge. Heat is removed from the ejector discharge in the heat exchanger, and the heat exchanger discharge is compressed in the fluid pump and channeled to the ejector secondary inlet as the secondary fluid In an exemplary embodiment, the temperature of the primary fluid is greater than the maximum operating temperature of a fluid motor powering the fluid pump using a portion of the ejector discharge, with the secondary fluid being mixed with the primary fluid so that the ejector discharge temperature is equal to about the maximum operating temperature of the fluid motor.

An empirical analysis of primary and secondary pharmaceutical patents in Chile.

PubMed

Abud, María José; Hall, Bronwyn; Helmers, Christian

2015-01-01

We analyze the patent filing strategies of foreign pharmaceutical companies in Chile distinguishing between "primary" (active ingredient) and "secondary" patents (patents on modified compounds, formulations, dosages, particular medical uses, etc.). There is prior evidence that secondary patents are used by pharmaceutical originator companies in the U.S. and Europe to extend patent protection on drugs in length and breadth. Using a novel dataset that comprises all drugs registered in Chile between 1991 and 2010 as well as the corresponding patents and trademarks, we find evidence that foreign originator companies pursue similar strategies in Chile. We find a primary to secondary patents ratio of 1:4 at the drug-level, which is comparable to the available evidence for Europe; most secondary patents are filed over several years following the original primary patent and after the protected active ingredient has obtained market approval in Chile. This points toward effective patent term extensions through secondary patents. Secondary patents dominate "older" therapeutic classes like anti-ulcer and anti-depressants. In contrast, newer areas like anti-virals and anti-neoplastics (anti-cancer) have a much larger share of primary patents.

PhDAHP1 is required for floral volatile benzenoid/phenylpropanoid biosynthesis in Petunia × hybrida cv 'Mitchell Diploid'.

PubMed

Langer, Kelly M; Jones, Correy R; Jaworski, Elizabeth A; Rushing, Gabrielle V; Kim, Joo Young; Clark, David G; Colquhoun, Thomas A

2014-07-01

Floral volatile benzenoid/phenylpropanoid (FVBP) biosynthesis consists of numerous enzymatic and regulatory processes. The initial enzymatic step bridging primary metabolism to secondary metabolism is the condensation of phosphoenolpyruvate (PEP) and erythrose-4-phosphate (E4P) carried out via 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE (DAHP) synthase. Here, identified, cloned, localized, and functionally characterized were two DAHP synthases from the model plant species Petunia × hybrida cv 'Mitchell Diploid' (MD). Full-length transcript sequences for PhDAHP1 and PhDAHP2 were identified and cloned using cDNA SMART libraries constructed from pooled MD corolla and leaf total RNA. Predicted amino acid sequence of PhDAHP1 and PhDAHP2 proteins were 76% and 80% identical to AtDAHP1 and AtDAHP2 from Arabidopsis, respectively. PhDAHP1 transcript accumulated to relatively highest levels in petal limb and tube tissues, while PhDAHP2 accumulated to highest levels in leaf and stem tissues. Through floral development, PhDAHP1 transcript accumulated to highest levels during open flower stages, and PhDAHP2 transcript remained constitutive throughout. Radiolabeled PhDAHP1 and PhDAHP2 proteins localized to plastids, however, PhDAHP2 localization appeared less efficient. PhDAHP1 RNAi knockdown petunia lines were reduced in total FVBP emission compared to MD, while PhDAHP2 RNAi lines emitted 'wildtype' FVBP levels. These results demonstrate that PhDAHP1 is the principal DAHP synthase protein responsible for the coupling of metabolites from primary metabolism to secondary metabolism, and the ultimate biosynthesis of FVBPs in the MD flower. Copyright © 2014 Elsevier Ltd. All rights reserved.

THE K2 M67 STUDY: AN EVOLVED BLUE STRAGGLER IN M67 FROM K2 MISSION ASTEROSEISMOLOGY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leiner, Emily; Mathieu, Robert D.; Stello, Dennis

Yellow straggler stars (YSSs) fall above the subgiant branch in optical color–magnitude diagrams (CMDs), between the blue stragglers and the red giants. YSSs may represent a population of evolved blue stragglers, but none have the direct and precise mass and radius measurements needed to determine their evolutionary states and formation histories. Here we report the first asteroseismic mass and radius measurements of such a star, the yellow straggler S1237 in the open cluster M67. We apply asteroseismic scaling relations to a frequency analysis of the Kepler K2 light curve and find a mass of 2.9 ± 0.2 M {sub ⊙}more » and a radius of 9.2 ± 0.2 R{sub ⊙}. This is more than twice the mass of the main-sequence turnoff in M67, suggesting that S1237 is indeed an evolved blue straggler. S1237 is the primary in a spectroscopic binary. We update the binary orbital solution and use spectral energy distribution fitting to constrain the CMD location of the secondary star. We find that the secondary is likely an upper main-sequence star near the turnoff, but a slightly hotter blue straggler companion is also possible. We then compare the asteroseismic mass of the primary to its mass from CMD fitting, finding that the photometry implies a mass and radius more than 2 σ below the asteroseismic measurement. Finally, we consider formation mechanisms for this star and suggest that S1237 may have formed from dynamical encounters resulting in stellar collisions or a binary merger.« less

A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters

PubMed Central

Saier, Milton H.

2000-01-01

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects. PMID:10839820

Identification and Functional Characterization of Monofunctional ent-Copalyl Diphosphate and ent-Kaurene Synthases in White Spruce Reveal Different Patterns for Diterpene Synthase Evolution for Primary and Secondary Metabolism in Gymnosperms1[W][OA

PubMed Central

Keeling, Christopher I.; Dullat, Harpreet K.; Yuen, Mack; Ralph, Steven G.; Jancsik, Sharon; Bohlmann, Jörg

2010-01-01

The biosynthesis of the tetracyclic diterpene ent-kaurene is a critical step in the general (primary) metabolism of gibberellin hormones. ent-Kaurene is formed by a two-step cyclization of geranylgeranyl diphosphate via the intermediate ent-copalyl diphosphate. In a lower land plant, the moss Physcomitrella patens, a single bifunctional diterpene synthase (diTPS) catalyzes both steps. In contrast, in angiosperms, the two consecutive cyclizations are catalyzed by two distinct monofunctional enzymes, ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS). The enzyme, or enzymes, responsible for ent-kaurene biosynthesis in gymnosperms has been elusive. However, several bifunctional diTPS of specialized (secondary) metabolism have previously been characterized in gymnosperms, and all known diTPSs for resin acid biosynthesis in conifers are bifunctional. To further understand the evolution of ent-kaurene biosynthesis as well as the evolution of general and specialized diterpenoid metabolisms in gymnosperms, we set out to determine whether conifers use a single bifunctional diTPS or two monofunctional diTPSs in the ent-kaurene pathway. Using a combination of expressed sequence tag, full-length cDNA, genomic DNA, and targeted bacterial artificial chromosome sequencing, we identified two candidate CPS and KS genes from white spruce (Picea glauca) and their orthologs in Sitka spruce (Picea sitchensis). Functional characterization of the recombinant enzymes established that ent-kaurene biosynthesis in white spruce is catalyzed by two monofunctional diTPSs, PgCPS and PgKS. Comparative analysis of gene structures and enzyme functions highlights the molecular evolution of these diTPSs as conserved between gymnosperms and angiosperms. In contrast, diTPSs for specialized metabolism have evolved differently in angiosperms and gymnosperms. PMID:20044448

Human IgG2- and IgG4-expressing memory B cells display enhanced molecular and phenotypic signs of maturity and accumulate with age.

PubMed

de Jong, Britt G; IJspeert, Hanna; Marques, Lemelinda; van der Burg, Mirjam; van Dongen, Jacques Jm; Loos, Bruno G; van Zelm, Menno C

2017-10-01

The mechanisms involved in sequential immunoglobulin G (IgG) class switching are still largely unknown. Sequential IG class switching is linked to higher levels of somatic hypermutation (SHM) in vivo, but it remains unclear if these are generated temporally during an immune response or upon activation in a secondary response. We here aimed to uncouple these processes and to distinguish memory B cells from primary and secondary immune responses. SHM levels and IgG subclasses were studied with 454 pyrosequencing on blood mononuclear cells from young children and adults as models for primary and secondary immunological memory. Additional sequencing and detailed immunophenotyping with IgG subclass-specific antibodies was performed on purified IgG + memory B-cell subsets. In both children and adults, SHM levels were higher in transcripts involving more downstream-located IGHG genes (esp. IGHG2 and IGHG4). In adults, SHM levels were significantly higher than in children, and downstream IGHG genes were more frequently utilized. This was associated with increased frequencies of CD27 + IgG + memory B cells, which contained higher levels of SHM, more IGHG2 usage, and higher expression levels of activation markers than CD27 - IgG + memory B cells. We conclude that secondary immunological memory accumulates with age and these memory B cells express CD27, high levels of activation markers, and carry high SHM levels and frequent usage of IGHG2. These new insights contribute to our understanding of sequential IgG subclass switching and show a potential relevance of using serum IgG2 levels or numbers of IgG2-expressing B cells as markers for efficient generation of memory responses.

Magnetic Inflation and Stellar Mass. I. Revised Parameters for the Component Stars of the Kepler Low-mass Eclipsing Binary T-Cyg1-12664

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Eunkyu; Muirhead, Philip S.; Swift, Jonathan J.

Several low-mass eclipsing binary stars show larger than expected radii for their measured mass, metallicity, and age. One proposed mechanism for this radius inflation involves inhibited internal convection and starspots caused by strong magnetic fields. One particular eclipsing binary, T-Cyg1-12664, has proven confounding to this scenario. Çakırlı et al. measured a radius for the secondary component that is twice as large as model predictions for stars with the same mass and age, but a primary mass that is consistent with predictions. Iglesias-Marzoa et al. independently measured the radii and masses of the component stars and found that the radius ofmore » the secondary is not in fact inflated with respect to models, but that the primary is, which is consistent with the inhibited convection scenario. However, in their mass determinations, Iglesias-Marzoa et al. lacked independent radial velocity measurements for the secondary component due to the star’s faintness at optical wavelengths. The secondary component is especially interesting, as its purported mass is near the transition from partially convective to a fully convective interior. In this article, we independently determined the masses and radii of the component stars of T-Cyg1-12664 using archival Kepler data and radial velocity measurements of both component stars obtained with IGRINS on the Discovery Channel Telescope and NIRSPEC and HIRES on the Keck Telescopes. We show that neither of the component stars is inflated with respect to models. Our results are broadly consistent with modern stellar evolutionary models for main-sequence M dwarf stars and do not require inhibited convection by magnetic fields to account for the stellar radii.« less

The CASE Programme Implemented Across the Primary and Secondary School Transition in Ireland

NASA Astrophysics Data System (ADS)

McCormack, Lorraine; Finlayson, Odilla E.; McCloughlin, Thomas J. J.

2014-11-01

In the Irish education system, there is little continuity between the primary and secondary education systems. The transfer between these systems is particularly problematic in the area of science. In order to alleviate some of these problems, as well as to enhance the cognitive development of students, the Cognitive Acceleration through Science Education programme was adapted for use and implemented across the primary-secondary school transition in Ireland. The programme was delivered in a variety of ways across the two levels, including the teacher and researcher teaching the programmes individually and team-teaching arrangements. The results on cognitive development measures showed that the students who were taught the programme in primary and secondary school made significant gains, when compared to the non-intervention group. There were also gains evident for students who only received one part of the programme (i.e. in either primary or secondary school). The greater gains, in terms of effect size, were evident at secondary school. The rationale, methodology and results are detailed in this paper.

Belongingness in Early Secondary School: Key Factors that Primary and Secondary Schools Need to Consider.

PubMed

Vaz, Sharmila; Falkmer, Marita; Ciccarelli, Marina; Passmore, Anne; Parsons, Richard; Black, Melissa; Cuomo, Belinda; Tan, Tele; Falkmer, Torbjörn

2015-01-01

It is unknown if, and how, students redefine their sense of school belongingness after negotiating the transition to secondary school. The current study used longitudinal data from 266 students with, and without, disabilities who negotiated the transition from 52 primary schools to 152 secondary schools. The study presents the 13 most significant personal student and contextual factors associated with belongingness in the first year of secondary school. Student perception of school belongingness was found to be stable across the transition. No variability in school belongingness due to gender, disability or household-socio-economic status (SES) was noted. Primary school belongingness accounted for 22% of the variability in secondary school belongingness. Several personal student factors (competence, coping skills) and school factors (low-level classroom task-goal orientation), which influenced belongingness in primary school, continued to influence belongingness in secondary school. In secondary school, effort-goal orientation of the student and perception of their school's tolerance to disability were each associated with perception of school belongingness. Family factors did not influence belongingness in secondary school. Findings of the current study highlight the need for primary schools to foster belongingness among their students at an early age, and transfer students' belongingness profiles as part of the hand-over documentation. Most of the factors that influenced school belongingness before and after the transition to secondary are amenable to change.

Belongingness in Early Secondary School: Key Factors that Primary and Secondary Schools Need to Consider

PubMed Central

Vaz, Sharmila; Falkmer, Marita; Ciccarelli, Marina; Passmore, Anne; Parsons, Richard; Black, Melissa; Cuomo, Belinda; Tan, Tele; Falkmer, Torbjörn

2015-01-01

It is unknown if, and how, students redefine their sense of school belongingness after negotiating the transition to secondary school. The current study used longitudinal data from 266 students with, and without, disabilities who negotiated the transition from 52 primary schools to 152 secondary schools. The study presents the 13 most significant personal student and contextual factors associated with belongingness in the first year of secondary school. Student perception of school belongingness was found to be stable across the transition. No variability in school belongingness due to gender, disability or household-socio-economic status (SES) was noted. Primary school belongingness accounted for 22% of the variability in secondary school belongingness. Several personal student factors (competence, coping skills) and school factors (low-level classroom task-goal orientation), which influenced belongingness in primary school, continued to influence belongingness in secondary school. In secondary school, effort-goal orientation of the student and perception of their school’s tolerance to disability were each associated with perception of school belongingness. Family factors did not influence belongingness in secondary school. Findings of the current study highlight the need for primary schools to foster belongingness among their students at an early age, and transfer students’ belongingness profiles as part of the hand-over documentation. Most of the factors that influenced school belongingness before and after the transition to secondary are amenable to change. PMID:26372554

Modeling repetitive, non‐globular proteins

PubMed Central

Basu, Koli; Campbell, Robert L.; Guo, Shuaiqi; Sun, Tianjun

2016-01-01

Abstract While ab initio modeling of protein structures is not routine, certain types of proteins are more straightforward to model than others. Proteins with short repetitive sequences typically exhibit repetitive structures. These repetitive sequences can be more amenable to modeling if some information is known about the predominant secondary structure or other key features of the protein sequence. We have successfully built models of a number of repetitive structures with novel folds using knowledge of the consensus sequence within the sequence repeat and an understanding of the likely secondary structures that these may adopt. Our methods for achieving this success are reviewed here. PMID:26914323

Does charging different user fees for primary and secondary care affect first-contacts with primary healthcare? A systematic review.

PubMed

Hone, Thomas; Lee, John Tayu; Majeed, Azeem; Conteh, Lesong; Millett, Christopher

2017-06-01

Policy-makers are increasingly considering charging users different fees between primary and secondary care (differential user charges) to encourage utilisation of primary health care in health systems with limited gate keeping. A systematic review was conducted to evaluate the impact of introducing differential user charges on service utilisation. We reviewed studies published in MEDLINE, EMBASE, the Cochrane library, EconLIT, HMIC, and WHO library databases from January 1990 until June 2015. We extracted data from the studies meeting defined eligibility criteria and assessed study quality using an established checklist. We synthesized evidence narratively. Eight studies from six countries met our eligibility criteria. The overall study quality was low, with diversity in populations, interventions, settings, and methods. Five studies examined the introduction of or increase in user charges for secondary care, with four showing decreased secondary care utilisation, and three showing increased primary care utilisation. One study identified an increase in primary care utilisation after primary care user charges were reduced. The introduction of a non-referral charge in secondary care was associated with lower primary care utilisation in one study. One study compared user charges across insurance plans, associating higher charges in secondary care with higher utilisation in both primary and secondary care. Overall, the impact of introducing differential user-charges on primary care utilisation remains uncertain. Further research is required to understand their impact as a demand side intervention, including implications for health system costs and on utilisation among low-income patients. © The Author 2017. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Rotary Transformer Seals Power In

NASA Technical Reports Server (NTRS)

Studer, P. A.; Paulkovich, J.

1982-01-01

Rotary transformer originally developed for spacecraft transfers electrical power from stationary primary winding to rotating secondary without sliding contacts and very little leakage of electromagnetic radiation. Transformer has two stationary primary windings connected in parallel. Secondary, mounted on a shaft that extends out of housing, rotates between two windings of primary. Shaft of secondary is composed of electrically conducting inner and outer parts separated by an insulator. Electrical contact is made from secondary winding, through shaft, to external leads.

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.10 - National 8-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ambient air quality standards for ozone. 50.10 Section 50.10 Protection of Environment ENVIRONMENTAL....10 National 8-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 8-hour primary and secondary ambient air quality standards for ozone, measured by a...

40 CFR 50.9 - National 1-hour primary and secondary ambient air quality standards for ozone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ambient air quality standards for ozone. 50.9 Section 50.9 Protection of Environment ENVIRONMENTAL....9 National 1-hour primary and secondary ambient air quality standards for ozone. (a) The level of the national 1-hour primary and secondary ambient air quality standards for ozone measured by a...

Self-Efficacy, School Resources, Job Stressors and Burnout among Spanish Primary and Secondary School Teachers: A Structural Equation Approach

ERIC Educational Resources Information Center

Betoret, Fernando Domenech

2009-01-01

This study examines the relationship between school resources, teacher self-efficacy, potential multi-level stressors and teacher burnout using structural equation modelling. The causal structure for primary and secondary school teachers was also examined. The sample was composed of 724 primary and secondary Spanish school teachers. The changes…

Access to Education in Bangladesh: Country Analytic Review of Primary and Secondary School

ERIC Educational Resources Information Center

Ahmed, Manzoor; Ahmed, Kazi Saleh; Khan, Nurul Islam; Ahmed, Romij

2007-01-01

This country analytical review examines the key issues in access to and participation in primary and secondary education in Bangladesh, with a special focus on areas and dimensions of exclusion. Against a background of overall progress, particularly in closing the gender gap in primary and secondary enrollment, the research applies a conceptual…

Tests as Boundary Signifiers: Level 6 Tests and the Primary Secondary Divide

ERIC Educational Resources Information Center

Coldwell, Mike; Willis, Ben

2017-01-01

This paper addresses the question: How do teachers and school leaders respond to high stakes testing of pupils transitioning from primary to secondary school? It explores how a new test, the Level 6 test, operated with regard to primary/secondary school relationships in England. It draws on an analysis of qualitative interviews with teachers and…

Architecture and reservoir quality of low-permeable Eocene lacustrine turbidite sandstone from the Dongying Depression, East China

NASA Astrophysics Data System (ADS)

Munawar, Muhammad Jawad; Lin, Chengyan; Chunmei, Dong; Zhang, Xianguo; Zhao, Haiyan; Xiao, Shuming; Azeem, Tahir; Zahid, Muhammad Aleem; Ma, Cunfei

2018-05-01

The architecture and quality of lacustrine turbidites that act as petroleum reservoirs are less well documented. Reservoir architecture and multiscale heterogeneity in turbidites represent serious challenges to production performance. Additionally, establishing a hierarchy profile to delineate heterogeneity is a challenging task in lacustrine turbidite deposits. Here, we report on the turbidites in the middle third member of the Eocene Shahejie Formation (Es3), which was deposited during extensive Middle to Late Eocene rifting in the Dongying Depression. Seismic records, wireline log responses, and core observations were integrated to describe the reservoir heterogeneity by delineating the architectural elements, sequence stratigraphic framework and lithofacies assemblage. A petrographic approach was adopted to constrain microscopic heterogeneity using an optical microscope, routine core analyses and X-ray diffraction (XRD) analyses. The Es3m member is interpreted as a sequence set composed of four composite sequences: CS1, CS2, CS3 and CS4. A total of forty-five sequences were identified within these four composite sequences. Sand bodies were mainly deposited as channels, levees, overbank splays, lobes and lobe fringes. The combination of fining-upward and coarsening-upward lithofacies patterns in the architectural elements produces highly complex composite flow units. Microscopic heterogeneity is produced by diagenetic alteration processes (i.e., feldspar dissolution, authigenic clay formation and quartz cementation). The widespread kaolinization of feldspar and mobilization of materials enhanced the quality of the reservoir by producing secondary enlarged pores. In contrast, the formation of pore-filling authigenic illite and illite/smectite clays reduced its permeability. Recovery rates are higher in the axial areas and smaller in the marginal areas of architectural elements. This study represents a significant insight into the reservoir architecture and heterogeneity of lacustrine turbidites, and the understanding of compartmentalization and distribution of high-quality sand reservoirs can be applied to improve primary and secondary production in these fields.

The influence of timing, radiation and reconstruction on complications and speech outcomes with tracheoesophageal puncture

PubMed Central

Gitomer, Sarah A.; Hutcheson, Kate A.; Christianson, Brandon L.; Samuelson, Madeleine B.; Barringer, Denise A.; Roberts, Dianna B.; Hessel, Amy C.; Weber, Randal S.; Lewin, Jan S.; Zafereo, Mark E.

2016-01-01

Background We evaluated impact of radiation, reconstruction and timing of tracheoesophageal puncture (TEP) on complications and speech outcomes. Methods Retrospective review identified 145 TEP patients between 2003–2007. Results Ninety-nine patients (68%) had primary and 46 (32%) secondary TEP, with complications occurring in 65% and 61% respectively (p=0.96). Twenty-nine patients (20%) had major complications (18 primary; 11 secondary, p=0.42). Ninety-four patients (65%) had pre-TEP radiation, 39 (27%) post-TEP radiation, and 12 (8%) no radiation. With patients grouped by TEP timing and radiation history, there was no difference in complications, fluency, or TEP use. With mean 4.7-year follow up, 82% primary and 85% secondary used TEP for primary communication (p=0.66). Free-flap patients used TEP more commonly for primary communication after secondary versus primary TEP (90% v 50%, p=0.02). Conclusions Primary and secondary tracheoesophageal speakers experience similar high rates of complications. Extent of pharyngeal reconstruction, rather than radiation, may be more important in selection of TEP timing. PMID:27394060

Function of identified motoneurones and co-ordination of primary and secondary motor systems during zebra fish swimming.

PubMed Central

Liu, D W; Westerfield, M

1988-01-01

1. The activity of the two classes of motoneurones, primary and secondary, which innervate myotomal muscle fibres in the zebra fish, was monitored with electromyographic and intracellular techniques. 2. Simultaneous EMG and intracellular recordings from muscle fibres showed that the activity of the two motor systems and of individual primary motoneurones can be distinguished by recording EMG spikes during swimming. 3. Measurements of EMG spikes demonstrated that primary and secondary motoneurones are co-ordinately activated over a wide range of conditions during normal swimming. 4. During swimming the primary motoneurones within a given segment are usually co-activated although they sometimes fire independently. 5. When different primary motoneurones within a given segment are co-activated, they fire nearly synchronously. 6. We conclude that the primary motoneurones are used principally, although not exclusively, during fast swimming, struggling and the startle response, whereas secondary motoneurones function primarily during slower swimming. PMID:3253426

46 CFR 111.50-5 - Location of overcurrent protective devices.

Code of Federal Regulations, 2014 CFR

2014-10-01

... primary side of a single phase transformer (two wire with single-voltage secondary) also protects the... secondary conductor by the secondary to primary transformer voltage ratio, and this protection meets § 111...

46 CFR 111.50-5 - Location of overcurrent protective devices.

Code of Federal Regulations, 2011 CFR

2011-10-01

... primary side of a single phase transformer (two wire with single-voltage secondary) also protects the... secondary conductor by the secondary to primary transformer voltage ratio, and this protection meets § 111...

46 CFR 111.50-5 - Location of overcurrent protective devices.

Code of Federal Regulations, 2010 CFR

2010-10-01

... primary side of a single phase transformer (two wire with single-voltage secondary) also protects the... secondary conductor by the secondary to primary transformer voltage ratio, and this protection meets § 111...

46 CFR 111.50-5 - Location of overcurrent protective devices.

Code of Federal Regulations, 2013 CFR

2013-10-01

... primary side of a single phase transformer (two wire with single-voltage secondary) also protects the... secondary conductor by the secondary to primary transformer voltage ratio, and this protection meets § 111...

46 CFR 111.50-5 - Location of overcurrent protective devices.

Code of Federal Regulations, 2012 CFR

2012-10-01

... primary side of a single phase transformer (two wire with single-voltage secondary) also protects the... secondary conductor by the secondary to primary transformer voltage ratio, and this protection meets § 111...

Cyclical period changes in cataclysmic variables: evidence of magnetic activity cycles in the mass-donor star

NASA Astrophysics Data System (ADS)

Borges, B. W.; Baptista, R.

2005-09-01

Cataclymic variables (CVs) are semi-detached binary systems in which a main sequence late-type star (the secondary) fills its Roche lobe and transfers matter to a white dwarf (the primary) through the inner Lagragian point L1. Evolutive models of CVs predicts that the orbital periods Porb of these systems would decrease on time scales of 108 - 109 years due to angular momentum losses either by magnetic braking via the secondary star's wind (Porb > 3 hr) or by emission of gravitational radiation (Porb > 3 hr). These models try to explain the observed gap of systems with Porb in the range of ~ 2 to 3 hr as the consequence of a sharp reduction of magnetic field open lines when the secondary star become fully convective (at Porb ~ 3 hr). However, up to now no well-studied CVs show evidence of period decrease. Instead, most well-observed eclipsing CVs show cyclical period changes probably associated to solar-type (quasi-periodic and/or multiperiodic) magnetic activity cycles in the secondary star. The fast spinning secondaries of CVs, covering a range of masses and rotation periods, are an important laboratory to understand magnetic activities cycles in late type stars. In the present work, we report the investigation of cyclical period changes in IP Peg: CV with orbital periods of 3.8 hr.

Primary and Secondary Stroke Prevention Using Left Atrial Appendage Closure with Watchman Devices in Atrial Fibrillation Patients: A Single Center Experience from Mainland China.

PubMed

Chen, Yanhong; Zhang, Yonghua; Huang, Weiping; Huang, Keqiang; Xu, Bei; Su, X I

2017-06-01

Atrial fibrillation (AF) is associated with increased stroke risk resulting from cardiac embolism of the left atrial appendage (LAA). Stroke tends to recur in NVAF patients. Yet safety and feasibility of secondary stroke preventions with LAA closure (LAAC) have not been assessed in detail. This retrospective study was designed to compare the feasibility and safety of LAAC in primary and secondary stroke preventions, in a real-world setting of Chinese patients. From 2014 to 2015, non-valvular AF patients with CHA2DS2-VASc ≥1 were selected for percutaneous LAAC operations. Outcome observations of primary and secondary stroke preventions with Watchman devices were analyzed and compared. Overall, 122 patients were included. LAAC with Watchman devices were attempted in 115 patients, of whom 68 were for primary stroke prevention and 47 were for secondary prevention. Both the CHA2DS2-VASc score and the HASBLED score were significantly higher in the secondary prevention group (4.09 ± 1.06 vs. 1.93 ± 1.09 for CHA2DS2-VASc and 1.83 ± 1.03 vs. 1.26 ± 0.87 for HASBLED, P < 0.01). In both groups LAAC were achieved with high successful rate (98.53% in the primary prevention group and 100% in the secondary prevention group, P > 0.05) and low complication rates. The stroke rates were at a low level in both groups (1.47% in primary prevention group vs. 2.13% in secondary prevention group, P > 0.05). In our initial single-center experience, percutaneous LAA closure was a feasible and safe procedure for both primary and secondary stroke preventions in Chinese patients with nonvalvular AF. © 2017 Wiley Periodicals, Inc.

Blood pressure variability in children with primary vs secondary hypertension.

PubMed

Leisman, Daniel; Meyers, Melissa; Schnall, Jeremy; Chorny, Nataliya; Frank, Rachel; Infante, Lulette; Sethna, Christine B

2014-06-01

Increased blood pressure variability (BPV) is correlated with adverse cardiovascular (CV) events in adults. However, there has been limited research on its effect in the pediatric population. Additionally, BPV differences between primary and secondary hypertension (HTN) are not known. Children with primary and secondary HTN underwent 24-hour ambulatory blood pressure monitoring and echocardiography studies. BPV measures of standard deviation (SD), average real variability (ARV), and range were calculated for the 24-hour, daytime, and nighttime periods. Seventy-four patients (median age, 13.5 years; 74% boys) were examined, 40 of whom had primary HTN. Body mass index z score and age were independent predictors of systolic ARV (R(2) =0.14) and SD (R(2) =0.39). There were no statistically significant differences in overall or wake period BPV measures between secondary or primary HTN groups, but sleep period diastolic SD was significantly greater in the secondary HTN group (9.26±3.8 vs 7.1±2.8, P=.039). On multiple regression analysis, secondary HTN was associated with increased sleep period diastolic SD (P=.025). No metrics of BPV in the overall, wake, and sleep periods were found to be significantly associated with left ventricular hypertrophy (LVH). The results of this study do not show a strong relationship between overall or wake BPV with primary vs secondary HTN, but the association of secondary HTN with sleep period diastolic BPV deserves further exploration. Contrary to expectation, the findings of this study failed to indicate a relationship between BPV and LVH for all patients as well for primary hypertensive and secondary hypertensive patients. ©2014 Wiley Periodicals, Inc.

Strain-Level Diversity of Secondary Metabolism in Streptomyces albus

PubMed Central

Seipke, Ryan F.

2015-01-01

Streptomyces spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental Streptomyces spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, Streptomyces albus has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by Streptomyces albus strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of Streptomyces albus strains suggests that each strain of a Streptomyces species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty. PMID:25635820

Effect of Public Deliberation on Attitudes toward Return of Secondary Results in Genomic Sequencing

PubMed Central

Gornick, Michele C.; Scherer, Aaron M.; Sutton, Erica J.; Ryan, Kerry A.; Exe, Nicole L.; Li, Ming; Uhlmann, Wendy R.; Kim, Scott Y.H.; Roberts, J. Scott; De Vries, Raymond G.

2016-01-01

The increased use of genomic sequencing in clinical diagnostics and therapeutics makes imperative the development of guidelines and policies about how to handle secondary findings. For reasons both practical and ethical, the creation of these guidelines must take into consideration the informed opinions of the lay public. As part of a larger Clinical Sequencing Exploratory Research (CSER) consortium project, we organized a deliberative democracy (DD) session that engaged 66 participants in dialogue about the benefits and risks associated with the return of secondary findings from clinical genomic sequencing. Participants were educated about the scientific and ethical aspects of the disclosure of secondary findings by experts in medical genetics and bioethics, and then engaged in facilitated discussion of policy options for the disclosure of three types of secondary findings: 1) medically actionable results; 2) adult onset disorders found in children; and 3) carrier status. Participants’ opinions were collected via surveys administered one month before, immediately following, and one month after the DD session. Post DD session, participants were significantly more willing to support policies that do not allow access to secondary findings related to adult onset conditions in children (Χ2 (2, N = 62) = 13.300, p = 0.001) or carrier status (Χ2 (2, N = 60) = 11.375, p = 0.003). After one month, the level of support for the policy denying access to secondary findings regarding adult-onset conditions remained significantly higher than the pre-DD level, although less than immediately post-DD (Χ2 (1, N = 60) = 2.465, p = 0.041). Our findings suggest that education and deliberation enhance public appreciation of the scientific and ethical complexities of genome sequencing. PMID:27307100

Effect of Public Deliberation on Attitudes toward Return of Secondary Results in Genomic Sequencing.

PubMed

Gornick, Michele C; Scherer, Aaron M; Sutton, Erica J; Ryan, Kerry A; Exe, Nicole L; Li, Ming; Uhlmann, Wendy R; Kim, Scott Y H; Roberts, J Scott; De Vries, Raymond G

2017-02-01

The increased use of genomic sequencing in clinical diagnostics and therapeutics makes imperative the development of guidelines and policies about how to handle secondary findings. For reasons both practical and ethical, the creation of these guidelines must take into consideration the informed opinions of the lay public. As part of a larger Clinical Sequencing Exploratory Research (CSER) consortium project, we organized a deliberative democracy (DD) session that engaged 66 participants in dialogue about the benefits and risks associated with the return of secondary findings from clinical genomic sequencing. Participants were educated about the scientific and ethical aspects of the disclosure of secondary findings by experts in medical genetics and bioethics, and then engaged in facilitated discussion of policy options for the disclosure of three types of secondary findings: 1) medically actionable results; 2) adult onset disorders found in children; and 3) carrier status. Participants' opinions were collected via surveys administered one month before, immediately following, and one month after the DD session. Post DD session, participants were significantly more willing to support policies that do not allow access to secondary findings related to adult onset conditions in children (Χ 2 (2, N = 62) = 13.300, p = 0.001) or carrier status (Χ 2 (2, N = 60) = 11.375, p = 0.003). After one month, the level of support for the policy denying access to secondary findings regarding adult-onset conditions remained significantly higher than the pre-DD level, although less than immediately post-DD (Χ 2 (1, N = 60) = 2.465, p = 0.041). Our findings suggest that education and deliberation enhance public appreciation of the scientific and ethical complexities of genome sequencing.

Rolled-up transformer structure for a radiofrequency integrated circuit (RFIC)

DOEpatents

Li, Xiuling; Huang, Wen

2016-05-03

A rolled-up transformer structure comprises a multilayer sheet having a rolled configuration comprising multiple turns about a longitudinal axis. The multilayer sheet comprises more than one conductive pattern layer on a strain-relieved layer, including a first conductive film and a second conductive film separated from the first conductive film in a thickness direction. The first conductive film comprises an even number of primary conductive strips, where each primary conductive strip has a length extending in the rolling direction, and the second conductive film comprises an even number of secondary conductive strips, where each secondary conductive strip has a length extending in the rolling direction. In the rolled configuration, turns of the primary conductive strips and turns of the secondary conductive strips wrap around the longitudinal axis. The primary conductive strips serve as a primary winding and the secondary conductive strips serve as a secondary winding of the rolled-up transformer structure.

Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.

PubMed

Naghdi, Mohammad Reza; Smail, Katia; Wang, Joy X; Wade, Fallou; Breaker, Ronald R; Perreault, Jonathan

2017-03-15

The discovery of noncoding RNAs (ncRNAs) and their importance for gene regulation led us to develop bioinformatics tools to pursue the discovery of novel ncRNAs. Finding ncRNAs de novo is challenging, first due to the difficulty of retrieving large numbers of sequences for given gene activities, and second due to exponential demands on calculation needed for comparative genomics on a large scale. Recently, several tools for the prediction of conserved RNA secondary structure were developed, but many of them are not designed to uncover new ncRNAs, or are too slow for conducting analyses on a large scale. Here we present various approaches using the database RiboGap as a primary tool for finding known ncRNAs and for uncovering simple sequence motifs with regulatory roles. This database also can be used to easily extract intergenic sequences of eubacteria and archaea to find conserved RNA structures upstream of given genes. We also show how to extend analysis further to choose the best candidate ncRNAs for experimental validation. Copyright © 2017 Elsevier Inc. All rights reserved.

Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus

PubMed Central

Cao, Xiaoxiao; Li, Shaohua; Chen, Liucun; Ding, Hongmei; Xu, Hua; Huang, Yanping; Li, Jie; Liu, Nongle; Cao, Weihong; Zhu, Yanjun; Shen, Beifen; Shao, Ningsheng

2009-01-01

In this article, a panel of ssDNA aptamers specific to Staphylococcus aureus was obtained by a whole bacterium-based SELEX procedure and applied to probing S. aureus. After several rounds of selection with S. aureus as the target and Streptococcus and S. epidermidis as counter targets, the highly enriched oligonucleic acid pool was sequenced and then grouped under different families on the basis of the homology of the primary sequence and the similarity of the secondary structure. Eleven sequences from different families were selected for further characterization by confocal imaging and flow cytometry analysis. Results showed that five aptamers demonstrated high specificity and affinity to S. aureus individually. The five aptamers recognize different molecular targets by competitive experiment. Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains. In addition, the combined aptamers can probe single S. aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer. PMID:19498077

Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus.

PubMed

Cao, Xiaoxiao; Li, Shaohua; Chen, Liucun; Ding, Hongmei; Xu, Hua; Huang, Yanping; Li, Jie; Liu, Nongle; Cao, Weihong; Zhu, Yanjun; Shen, Beifen; Shao, Ningsheng

2009-08-01

In this article, a panel of ssDNA aptamers specific to Staphylococcus aureus was obtained by a whole bacterium-based SELEX procedure and applied to probing S. aureus. After several rounds of selection with S. aureus as the target and Streptococcus and S. epidermidis as counter targets, the highly enriched oligonucleic acid pool was sequenced and then grouped under different families on the basis of the homology of the primary sequence and the similarity of the secondary structure. Eleven sequences from different families were selected for further characterization by confocal imaging and flow cytometry analysis. Results showed that five aptamers demonstrated high specificity and affinity to S. aureus individually. The five aptamers recognize different molecular targets by competitive experiment. Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains. In addition, the combined aptamers can probe single S. aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer.

A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification.

PubMed

Park, Jung Hun; Jang, Hyowon; Jung, Yun Kyung; Jung, Ye Lim; Shin, Inkyung; Cho, Dae-Yeon; Park, Hyun Gyu

2017-05-15

We herein describe a new mass spectrometry-based method for multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification (SDA) reaction. In this method, allele-specific ligation is first performed to discriminate base sequence variations at the SNP site within the PCR-amplified target DNA. The primary ligation probe is extended by a universal primer annealing site while the secondary ligation probe has base sequences as an overhang with a nicking enzyme recognition site and complementary mass marker sequence. The ligation probe pairs are ligated by DNA ligase only at specific allele in the target DNA and the resulting ligated product serves as a template to promote the SDA reaction using a universal primer. This process isothermally amplifies short DNA fragments, called mass markers, to be analyzed by mass spectrometry. By varying the sizes of the mass markers, we successfully demonstrated the multiplex SNP genotyping capability of this method by reliably identifying several BRCA mutations in a multiplex manner with mass spectrometry. Copyright © 2016 Elsevier B.V. All rights reserved.

Digit-color synaesthesia only enhances memory for colors in a specific context: A new method of duration thresholds to measure serial recall.

PubMed

Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N

2017-08-01

For digit-color synaesthetes, digits elicit vivid experiences of color that are highly consistent for each individual. The conscious experience of synaesthesia is typically unidirectional: Digits evoke colors but not vice versa. There is an ongoing debate about whether synaesthetes have a memory advantage over non-synaesthetes. One key question in this debate is whether synaesthetes have a general superiority or whether any benefit is specific to a certain type of material. Here, we focus on immediate serial recall and ask digit-color synaesthetes and controls to memorize digit and color sequences. We developed a sensitive staircase method manipulating presentation duration to measure participants' serial recall of both overlearned and novel sequences. Our results show that synaesthetes can activate digit information to enhance serial memory for color sequences. When color sequences corresponded to ascending or descending digit sequences, synaesthetes encoded these sequences at a faster rate than their non-synaesthetes counterparts and faster than non-structured color sequences. However, encoding color sequences is approximately 200 ms slower than encoding digit sequences directly, independent of group and condition, which shows that the translation process is time consuming. These results suggest memory advantages in synaesthesia require a modified dual-coding account, in which secondary (synaesthetically linked) information is useful only if it is more memorable than the primary information to be recalled. Our study further shows that duration thresholds are a sensitive method to measure subtle differences in serial recall performance. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Follow-up of cancer in primary care versus secondary care: systematic review

PubMed Central

Lewis, Ruth A; Neal, Richard D; Williams, Nefyn H; France, Barbara; Hendry, Maggie; Russell, Daphne; Hughes, Dyfrig A; Russell, Ian; Stuart, Nicholas SA; Weller, David; Wilkinson, Clare

2009-01-01

Background Cancer follow-up has traditionally been undertaken in secondary care, but there are increasing calls to deliver it in primary care. Aim To compare the effectiveness and cost-effectiveness of primary versus secondary care follow-up of cancer patients, determine the effectiveness of the integration of primary care in routine hospital follow-up, and evaluate the impact of patient-initiated follow-up on primary care. Design of study Systematic review. Setting Primary and secondary care settings. Method A search was carried out of 19 electronic databases, online trial registries, conference proceedings, and bibliographies of included studies. The review included comparative studies or economic evaluations of primary versus secondary care follow-up, hospital follow-up with formal primary care involvement versus conventional hospital follow-up, and hospital follow-up versus patient-initiated or minimal follow-up if the study reported the impact on primary care. Results There was no statistically significant difference for patient wellbeing, recurrence rate, survival, recurrence-related serious clinical events, diagnostic delay, or patient satisfaction. GP-led breast cancer follow-up was cheaper than hospital follow-up. Intensified primary health care resulted in increased home-care nurse contact, and improved discharge summary led to increased GP contact. Evaluation of patient-initiated or minimal follow-up found no statistically significant impact on the number of GP consultations or cancer-related referrals. Conclusion Weak evidence suggests that breast cancer follow-up in primary care is effective. Interventions improving communication between primary and secondary care could lead to greater GP involvement. Discontinuation of formal follow-up may not increase GP workload. However, the quality of the data in general was poor, and no firm conclusions can be reached. PMID:19566990

[Skeletal manifestations of primary and secondary hyperparathyroiditis. Differential radiological diagnostic problems].

PubMed

Melella, A; Basilico, L; Lupini, A; Renda, F

1978-10-31

Primary and secondary hyperparathyroidism are both marked by widespread skeletal demineralisation, subperiosteal erosion of the cortex, brown tumours, osteosclerosis, and extraosseous calcification. Differential diagnosis is guided by the different association of these findings. Brown tumours and more extensive erosion are marks of the primary form, whereas osteosclerosis and extra-osseous calcification are a prominent feature of secondary hyperparathyroidism. Radiologists, therefore, should direct their attention to features suggesting the presence of secondary forms in addition to looking for bone alterations associated with hyperparathyroidism.

Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

PubMed

Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

2003-09-01

Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

Complete genome sequence of Streptomyces venezuelae ATCC 15439, a promising cell factory for production of secondary metabolites.

PubMed

Song, Ju Yeon; Yoo, Young Ji; Lim, Si-Kyu; Cha, Sun Ho; Kim, Ji-Eun; Roe, Jung-Hye; Kim, Jihyun F; Yoon, Yeo Joon

2016-02-10

Streptomyces venezuelae ATCC 15439, which produces 12- and 14-membered ring macrolide antibiotics, is a platform strain for heterologous expression of secondary metabolites. Its 9.05-Mb genome sequence revealed an abundance of genes involved in the biosynthesis of secondary metabolites and their precursors, which should be useful for the production of bioactive compounds. Copyright © 2015 Elsevier B.V. All rights reserved.

A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package

PubMed Central

Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M.

2013-01-01

Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs. PMID:24688703

A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package.

PubMed

Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M

2013-01-01

Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs.

Why are there more arboreal ant species in primary than in secondary tropical forests?

PubMed

Klimes, Petr; Idigel, Cliffson; Rimandai, Maling; Fayle, Tom M; Janda, Milan; Weiblen, George D; Novotny, Vojtech

2012-09-01

1. Species diversity of arboreal arthropods tends to increase during rainforest succession so that primary forest communities comprise more species than those from secondary vegetation, but it is not well understood why. Primary forests differ from secondary forests in a wide array of factors whose relative impacts on arthropod diversity have not yet been quantified. 2. We assessed the effects of succession-related determinants on a keystone ecological group, arboreal ants, by conducting a complete census of 1332 ant nests from all trees with diameter at breast height ≥ 5 cm occurring within two (unreplicated) 0·32-ha plots, one in primary and one in secondary lowland forest in New Guinea. Specifically, we used a novel rarefaction-based approach to match number, size distribution and taxonomic structure of trees in primary forest communities to those in secondary forest and compared the resulting numbers of ant species. 3. In total, we recorded 80 nesting ant species from 389 trees in primary forest but only 42 species from 295 trees in secondary forest. The two habitats did not differ in the mean number of ant species per tree or in the relationship between ant diversity and tree size. However, the between-tree similarity of ant communities was higher in secondary forest than in primary forest, as was the between-tree nest site similarity, suggesting that secondary trees were more uniform in providing nesting microhabitats. 4. Using our rarefaction method, the difference in ant species richness between two forest types was partitioned according to the effects of higher tree density (22·6%), larger tree size (15·5%) and higher taxonomic diversity of trees (14·3%) in primary than in secondary forest. The remaining difference (47·6%) was because of higher beta diversity of ant communities between primary forest trees. In contrast, difference in nest density was explained solely by difference in tree density. 5. Our study shows that reduction in plant taxonomic diversity in secondary forests is not the main driver of the reduction in canopy ant species richness. We suggest that the majority of arboreal species losses in secondary tropical forests are attributable to simpler vegetation structure, combined with lower turnover of nesting microhabitats between trees. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Bangladesh: Summary Report. Financing Primary and Secondary Education in Bangladesh. Asia-South Pacific Education Watch

ERIC Educational Resources Information Center

Ahmad, Qazi Kholiquzzaman

2007-01-01

The main objective of the study is to gain an understanding on educational expenditure at primary and secondary levels in Bangladesh. In estimating educational expenditure by source, it has been sought to determine: (1) sources of financing of primary and secondary education; (2) rural-urban variation; (3) variation between boys and girls; (4)…

Improving Achievement in Science in Primary and Secondary Schools. Improving Series

ERIC Educational Resources Information Center

Her Majesty's Inspectorate of Education, 2005

2005-01-01

This report is based on inspections of science in primary and secondary schools carried out between September 2000 and March 2004. In addition to schools inspected as part of the generational cycle, HMI also visited other primary and secondary schools to observe and describe aspects of best practice. The report also draws on other major sources of…

How Do Primary and Lower Secondary Teachers Compare? Education Indicators in Focus. No. 58

ERIC Educational Resources Information Center

OECD Publishing, 2018

2018-01-01

While policy debate is often focused on the whole teaching profession, primary and secondary teachers differ in more ways than one. While all countries require teachers to have at least a bachelor degree to enter the profession in primary or lower secondary education, the structure and content of the programmes vary and are less geared towards…

Component Control System for a Vehicle

NASA Technical Reports Server (NTRS)

Lee, Chunhao J. (Inventor); Fraser-Chanpong, Nathan (Inventor); Vitale, Robert L. (Inventor); Akinyode, Akinjide Akinniyi (Inventor); Dawson, Andrew D. (Inventor); Guo, Raymond (Inventor); Waligora, Thomas M. (Inventor); Spain, Ivan (Inventor); Bluethmann, William J. (Inventor); Reed, Ryan M. (Inventor)

2016-01-01

A vehicle includes a chassis, a modular component, and a central operating system. The modular component is supported by the chassis. The central operating system includes a component control system, a primary master controller, and a secondary master controller. The component control system is configured for controlling the modular component. The primary and secondary master controllers are in operative communication with the component control system. The primary and secondary master controllers are configured to simultaneously transmit commands to the component control system. The component control system is configured to accept commands from the secondary master controller only when a fault occurs in the primary master controller.

The fate of close encounters between binary stars and binary supermassive black holes

NASA Astrophysics Data System (ADS)

Wang, Yi-Han; Leigh, Nathan; Yuan, Ye-Fei; Perna, Rosalba

2018-04-01

The evolution of main-sequence binaries that reside in the Galactic Centre can be heavily influenced by the central supermassive black hole (SMBH). Due to these perturbative effects, the stellar binaries in dense environments are likely to experience mergers, collisions, or ejections through secular and/or non-secular interactions. More direct interactions with the central SMBH are thought to produce hypervelocity stars (HVSs) and tidal disruption events (TDEs). In this paper, we use N-body simulations to study the dynamics of stellar binaries orbiting a central SMBH primary with an outer SMBH secondary orbiting this inner triple. The effects of the secondary SMBH on the event rates of HVSs, TDEs, and stellar mergers are investigated, as a function of the SMBH-SMBH binary mass ratio. Our numerical experiments reveal that, relative to the isolated SMBH case, the TDE and HVS rates are enhanced for, respectively, the smallest and largest mass ratio SMBH-SMBH binaries. This suggests that the observed event rates of TDEs and HVSs have the potential to serve as a diagnostic of the mass ratio of a central SMBH-SMBH binary. The presence of a secondary SMBH also allows for the creation of hypervelocity binaries. Observations of these systems could thus constrain the presence of a secondary SMBH in the Galactic Centre.

Patients' perspectives on the medical primary-secondary care interface: systematic review and synthesis of qualitative research.

PubMed

Sampson, Rod; Cooper, Jamie; Barbour, Rosaline; Polson, Rob; Wilson, Philip

2015-10-15

To synthesise the published literature on the patient experience of the medical primary-secondary care interface and to determine priorities for future work in this field aimed at improving clinical outcomes. Systematic review and metaethnographic synthesis of primary studies that used qualitative methods to explore patients' perspectives of the medical primary-secondary care interface. International primary-secondary care interface. EMBASE, MEDLINE, CINAHL Plus with Full text, PsycINFO, Psychology and Behavioural Sciences Collection, Health Business Elite, Biomedica Reference Collection: Comprehensive Library, Information Science & Technology Abstracts, eBook Collection, Web of Science Core Collection: Citation Indexes and Social Sciences Citation Index, and grey literature. Studies were eligible for inclusion if they were full research papers employing qualitative methodology to explore patients' perspectives of the medical primary-secondary care interface. The 7-step metaethnographic approach described by Noblit and Hare, which involves cross-interpretation between studies while preserving the context of the primary data. The search identified 690 articles, of which 39 were selected for full-text review. 20 articles were included in the systematic review that encompassed a total of 689 patients from 10 countries. 4 important areas specific to the primary-secondary care interface from the patients' perspective emerged: barriers to care, communication, coordination, and 'relationships and personal value'. Patients should be the focus of any transfer of care between primary and secondary systems. From their perspective, areas for improvement may be classified into four domains that should usefully guide future work aimed at improving quality at this important interface. PROSPERO CRD42014009486. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

A constraint logic programming approach to associate 1D and 3D structural components for large protein complexes.

PubMed

Dal Palù, Alessandro; Pontelli, Enrico; He, Jing; Lu, Yonggang

2007-01-01

The paper describes a novel framework, constructed using Constraint Logic Programming (CLP) and parallelism, to determine the association between parts of the primary sequence of a protein and alpha-helices extracted from 3D low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

Space Shuttle to deploy Magellan planetary science mission

NASA Technical Reports Server (NTRS)

1989-01-01

The objectives of Space Shuttle Mission STS-30 are described along with major flight activities, prelaunch and launch operations, trajectory sequence of events, and landing and post-landing operations. The primary objective of STS-30 is to successfully deploy the Magellan spacecraft into low earth orbit. Following deployment, Magellan will be propelled to its Venus trajectory by an Inertial Upper Stage booster. The objectives of the Magellan mission are to obtain radar images of more than 70 percent of Venus' surface, a near-global topographic map, and near-global gravity field data. Secondary STS-30 payloads include the Fluids Experiment Apparatus (FEA) and the Mesoscale Lightning Experiment (MLE).

Kidney cancer: current and novel treatment options.

PubMed

Jonasch, Eric

2015-05-01

Antiangiogenic therapies remain the standard of care in the front-line setting for renal cell carcinoma, although vascular endothelial growth factor (VEGF) blockade is not sufficient, and many patients do not respond to such treatment. With a host of approved agents, questions arise as to how best to use them in both initial and secondary treatments. Optimal sequences are currently being tested in various clinical trials. Because approximately 20% of patients exhibiting primary resistance to these anti-VEGF therapies, new therapies are needed. Novel therapies such as MET and AXL inhibitors as well as checkpoint antibodies hold promise for the future. Copyright © 2015 by the National Comprehensive Cancer Network.

NEW PRECISION ORBITS OF BRIGHT DOUBLE-LINED SPECTROSCOPIC BINARIES. V. THE AM STARS HD 434 AND 41 SEXTANTIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fekel, Francis C.; Williamson, Michael H., E-mail: fekel@evans.tsuniv.ed

We have detected the secondary component in two previously known spectroscopic binaries, HD 434 and 41 Sex, and for the first time determined double-lined orbits for them. Despite the relatively long period of 34.26 days and a moderate eccentricity of 0.32, combined with the components' rotationally broadened lines, measurement of the primary and secondary radial velocities of HD 434 has enabled us to obtain significantly improved orbital elements. While the 41 Sex system has a much shorter period of 6.167 days and a circular orbit, the estimated V mag difference of 3.2 between its components also makes this a challengingmore » system. The new orbital dimensions (a{sub 1} sin i and a{sub 2} sin i) and minimum masses (m{sub 1} sin{sup 3} i and m{sub 2} sin{sup 3} i) of HD 434 have accuracies of 0.8% or better, while the same quantities for 41 Sex are good to 0.5% or better. Both components of HD 434 are Am stars while the Am star primary of 41 Sex has a late-F or early-G companion. All four stars are on the main sequence. The two components of HD 434 are rotating much faster than their predicted pseudosynchronous velocities, while both components of 41 Sex are synchronously rotating. For the primary of 41 Sex, the spectrum line depth changes noted by Sreedhar Rao et al. were not detected.« less

Analysis of ProSEDS Test of Bare-Tether Collection

NASA Technical Reports Server (NTRS)

Sanmartin, J. R.; Lorenzini, E. C.; Estes, R. D.; Charro, M.; Cosmo, M. L.

2003-01-01

NASA's tether experiment ProSEDS will be placed in orbit on board a Delta-II rocket to test bare-tether electron collection, deorbiting of the rocket second stage, and the system dynamic stability. ProSEDS performance will vary because ambient conditions change along the orbit and tether-circuit bulk elements at the cathodic end follow the step-by-step sequence for the current cycles of operating modes (open-circuit, shunt and resistor modes for primary cycles; shunt and battery modes for secondary cycles). In this work we discuss expected ProSEDS values of the ratio L,/L*, which jointly with cathodic bulk elements determines bias and current tether profiles; L, is tether length, and L* (changing with tether temperature and ionospheric plasma density and magnetic field) is a characteristic length gauging ohmic versus baretether collection impedances. We discuss how to test bare-tether electron collection during primary cycles, using probe measurements of plasma density, measurements of cathodic current in resistor and shunt modes, and an estimate of tether temperature based on ProSEDS orbital position at the particular cycle concerned. We discuss how a temperature misestimate might occasionally affect the test of bare-tether collection, and how introducing the battery mode in some primary cycles, for an additional current measurement, could obviate the need of a temperature estimate. We also show how to test bare-tether collection by estimating orbit-decay rate from measurements of cathodic current for the shunt and battery modes of secondary cycles.

Spectrum sharing between a surveillance radar and secondary Wi-Fi networks

NASA Astrophysics Data System (ADS)

Hessar, Farzad; Roy, Sumit

2016-06-01

Co-existence between unlicensed networks that share spectrum spatio-temporally with terrestrial (e.g. Air Traffic Control) and shipborne radars in 3-GHz band is attracting significant interest. Similar to every primary-secondary coexistence scenario, interference from unlicensed devices to a primary receiver must be within acceptable bounds. In this work, we formulate the spectrum sharing problem between a pulsed, search radar (primary) and 802.11 WLAN as the secondary. We compute the protection region for such a search radar for a) a single secondary user (initially) as well as b) a random spatial distribution of multiple secondary users. Furthermore, we also analyze the interference to the WiFi devices from the radar's transmissions to estimate the impact on achievable WLAN throughput as a function of distance to the primary radar.

Endodontic 'solutions' part 1: a literature review on the use of endodontic lubricants, irrigants and medicaments.

PubMed

Good, Melissa; El, Karim Ikhlas A; Hussey, David L

2012-05-01

Endodontic lubricants, irrigants and medicaments help prepare and disinfect root canal systems (RCS) but primary and secondary cases involve different microbes and therefore it is unlikely that one protocol will be effective for both case types. Each individual 'solution' or sequence of'solutions' could play a significant role in each case type, but there are no detailed published guidelines in existence. To help inform clinical practice it was decided to undertake a literature review followed by a UK and Republic of Ireland wide audit on current endodontic'solution' usage within dental schools. The literature review was undertaken under the following headings: pre-op oral rinse; file lubricants; root canal irrigants and intracanal medicaments and provides an evidence base for protocol development for both primary and retreatment cases.The audit project and the protocols developed from the findings of both the literature review and audit will be presented in Part 2.

Neural tube defects – recent advances, unsolved questions and controversies

PubMed Central

Copp, Andrew J.; Stanier, Philip; Greene, Nicholas D. E.

2014-01-01

Neural tube defects (NTDs) are severe congenital malformations affecting around 1 in every 1000 pregnancies. Here we review recent advances and currently unsolved issues in the NTD field. An innovation in clinical management has come from the demonstration that closure of open spina bifida lesions in utero can diminish neurological dysfunction in children. Primary prevention by folic acid has been enhanced through introduction of mandatory food fortification in some countries, although not yet in UK. Genetic predisposition comprises the majority of NTD risk, and genes that regulate folate one-carbon metabolism and planar cell polarity have been strongly implicated. The sequence of human neural tube closure events remains controversial, but study of mouse NTD models shows that anencephaly, open spina bifida and craniorachischisis result from failure of primary neurulation, while skin-covered spinal dysraphism results from defective secondary neurulation. Other ‘NTD’ malformations, such as encephalocele, are likely to be post-neurulation disorders. PMID:23790957

Color banding on Georges Bank as viewed by coastal zone color scanner

NASA Technical Reports Server (NTRS)

Yentsch, C. S.; Phinney, D. A.; Campbell, J. W.

1994-01-01

Observations of Georges Bank by coastal zone color scanner (CZCS) show bandlike patterns that appear to be related to the large sand dunes and ridges which dominate the bottom topography there. Ship measurements of temperature and chlorophyll on Georges Bank in July 1979 also reflect the influence of the underwater dune fields. The cause of the banding in the CZCS data is unknown but is speculated to be the creation of alternating zones of divergence and convergence by tidal currents as the water flows over the underwater dune-trough configuration. The banding observed by CZCS appears to be seasonal, following the sequence of primary production in the Gulf of Maine, and is believed to be important to biological processes as a site of new production and/or as an effective transport mechanism. Any future models that attempt to interrelate tidal mixing and primary production must consider bottom topography and secondary flows.

Advances in clinical immunology in 2015.

PubMed

Chinen, Javier; Notarangelo, Luigi D; Shearer, William T

2016-12-01

Advances in clinical immunology in the past year included the report of practice parameters for the diagnosis and management of primary immunodeficiencies to guide the clinician in the approach to these relatively uncommon disorders. We have learned of new gene defects causing immunodeficiency and of new phenotypes expanding the spectrum of conditions caused by genetic mutations such as a specific regulator of telomere elongation (RTEL1) mutation causing isolated natural killer cell deficiency and mutations in ras-associated RAB (RAB27) resulting in immunodeficiency without albinism. Advances in diagnosis included the increasing use of whole-exome sequencing to identify gene defects and the measurement of serum free light chains to identify secondary hypogammaglobulinemias. For several primary immunodeficiencies, improved outcomes have been reported after definitive therapy with hematopoietic stem cell transplantation and gene therapy. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the Red Tree Vole (Phenacomys longicaudus) in the Pacific Northwest United States

USGS Publications Warehouse

Miller, Mark P.; Bellinger, R.M.; Forsman, E.D.; Haig, Susan M.

2006-01-01

Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation. We examined phylogeographical patterns of red tree voles (Phenacomys longicaudus) in western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across the species' range. Cytochrome b sequences were also analysed from a subset of our samples to confirm the presence of major haplotype groups. Phylogenetic network analyses suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus' range. Spatial genetic analyses (samova and Genetic Landscape Shapes) of control region sequences demonstrated a primary genetic discontinuity separating northern and southern sampling areas, while a secondary discontinuity separated northern sampling areas into eastern and western groups divided by the Willamette Valley. The North/South discontinuity likely corresponds to a region of secondary contact between lineages rather than an overt barrier. Although the Cordilleran ice sheet (maximum a??12 000 years ago) did not move southward to directly affect the region occupied by P. longicaudus, climate change during glaciation fragmented the forest landscape that it inhabits. Signatures of historical fragmentation were reflected by positive associations between latitude and variables such as Tajima's D and patterns associated with location-specific alleles. Genetic distances between southern sampling areas were smaller, suggesting that forest fragmentation was reduced in southern vs. northern regions.

In vitro molecular magnetic resonance imaging detection and measurement of apoptosis using superparamagnetic iron oxide + antibody as ligands for nucleosomes

NASA Astrophysics Data System (ADS)

Rapley, P. L.; Witiw, C.; Rich, K.; Niccoli, S.; Tassotto, M. L.; Th'ng, J.

2012-11-01

Recent research in cell biology as well as oncology research has focused on apoptosis or programmed cell death as a means of quantifying the induced effects of treatment. A hallmark of late-stage apoptosis is nuclear fragmentation in which DNA is degraded to release nucleosomes with their associated histones. In this work, a method was developed for detecting and measuring nucleosome concentration in vitro with magnetic resonance imaging (MRI). The indirect procedure used a commercially available secondary antibody-superparamagnetic iron oxide (SPIO) particle complex as a contrast agent that bound to primary antibodies against nucleosomal histones H4, H2A and H2B. Using a multiple-echo spin-echo sequence on a 1.5 T clinical MRI scanner, significant T2 relaxation enhancement as a function of in vitro nucleosomal concentration was measured. In addition, clustering or aggregation of the contrast agent was demonstrated with its associated enhancement in T2 effects. The T2 clustering enhancement showed a complex dependence on relative concentrations of nucleosomes, primary antibody and secondary antibody + SPIO. The technique supports the feasibility of using MRI measurements of nucleosome concentration in blood as a diagnostic, prognostic and predictive tool in the management of cancer.

Validation of CESAR Thermal-hydraulic Module of ASTEC V1.2 Code on BETHSY Experiments

NASA Astrophysics Data System (ADS)

Tregoures, Nicolas; Bandini, Giacomino; Foucher, Laurent; Fleurot, Joëlle; Meloni, Paride

The ASTEC V1 system code is being jointly developed by the French Institut de Radioprotection et Sûreté Nucléaire (IRSN) and the German Gesellschaft für Anlagen und ReaktorSicherheit (GRS) to address severe accident sequences in a nuclear power plant. Thermal-hydraulics in primary and secondary system is addressed by the CESAR module. The aim of this paper is to present the validation of the CESAR module, from the ASTEC V1.2 version, on the basis of well instrumented and qualified integral experiments carried out in the BETHSY facility (CEA, France), which simulates a French 900 MWe PWR reactor. Three tests have been thoroughly investigated with CESAR: the loss of coolant 9.1b test (OECD ISP N° 27), the loss of feedwater 5.2e test, and the multiple steam generator tube rupture 4.3b test. In the present paper, the results of the code for the three analyzed tests are presented in comparison with the experimental data. The thermal-hydraulic behavior of the BETHSY facility during the transient phase is well reproduced by CESAR: the occurrence of major events and the time evolution of main thermal-hydraulic parameters of both primary and secondary circuits are well predicted.

A gatekeeping procedure to test a primary and a secondary endpoint in a group sequential design with multiple interim looks.

PubMed

Tamhane, Ajit C; Gou, Jiangtao; Jennison, Christopher; Mehta, Cyrus R; Curto, Teresa

2018-03-01

Glimm et al. (2010) and Tamhane et al. (2010) studied the problem of testing a primary and a secondary endpoint, subject to a gatekeeping constraint, using a group sequential design (GSD) with K=2 looks. In this article, we greatly extend the previous results to multiple (K>2) looks. If the familywise error rate (FWER) is to be controlled at a preassigned α level then it is clear that the primary boundary must be of level α. We show under what conditions one α-level primary boundary is uniformly more powerful than another. Based on this result, we recommend the choice of the O'Brien and Fleming (1979) boundary over the Pocock (1977) boundary for the primary endpoint. For the secondary endpoint the choice of the boundary is more complicated since under certain conditions the secondary boundary can be refined to have a nominal level α'>α, while still controlling the FWER at level α, thus boosting the secondary power. We carry out secondary power comparisons via simulation between different choices of primary-secondary boundary combinations. The methodology is applied to the data from the RALES study (Pitt et al., 1999; Wittes et al., 2001). An R library package gsrsb to implement the proposed methodology is made available on CRAN. © 2017, The International Biometric Society.

A proposed Primary Health Early Warning Score (PHEWS) with emphasis on early detection of sepsis in the elderly.

PubMed

Anderson, Ian

2016-03-01

There are several secondary care early warning scores which alert for severe illness including sepsis. None are specifically adjusted for primary care. A Primary Health Early Warning Score (PHEWS) is proposed which incorporates practical parameters from both secondary and primary care.

Development of the precerebellar nuclei in the rat: IV. The anterior precerebellar extramural migratory stream and the nucleus reticularis tegmenti pontis and the basal pontine gray.

PubMed

Altman, J; Bayer, S A

1987-03-22

Sequential thymidine radiograms from rats injected on days E16, E17, E18, and E19 and killed 2 hours after injection and at daily intervals up to day E22 were used to establish the site of origin, migratory route, and settling patterns of neurons of the nucleus reticularis tegmenti pontis and basal pontine gray. The nucleus reticularis tegmenti pontis neurons, which are produced predominantly on days E15 and E16, derive from the primary precerebellar neuroepithelium. These cells, unlike those of the lateral reticular and external cuneate nuclei, take an anteroventral subpial route, forming the anterior precerebellar extramural migratory stream. This migratory stream reaches the anterior pole of the pons by day E18. In rats injected on day E16 and killed on day E18 some of the cells that reach the pons are unlabeled, indicating that they represent the early component of neurons generated on day E15. The cells labeled on day E16 begin to settle in the pons on day E19, 3 days after their production. These cells, migrating in an orderly temporal sequence, form a posterodorsal-to-anteroventral gradient in the nucleus reticularis tegmenti pontis. Unlike the neurons of all the other precerebellar nuclei, the basal pontine gray neurons derive from the secondary precerebellar neuroepithelium. The secondary precerebellar neuroepithelium forms on day E16 as an outgrowth of the primary precerebellar neuroepithelium, and it remains mitotically active through day E19, spanning the entire period of basal pontine gray neurogenesis. The secondary precerebellar neuroepithelium is surrounded by a horizontal layer of postmitotic cells, representing the head-waters of the anterior precerebellar extramural migratory stream. In rats injected on day E18 and killed on day E19 the cells are labeled in the proximal half of the stream around the medulla but those closer to the pons are unlabeled, indicating an orderly sequence of migration. In rats injected on day E18 and killed on day E20 the labeled cells reach the pole of the pons. In the basal pontine gray the sequentially generated neurons settle in a precise order. The neurons generated on day E16 form a small core posteriorly and the neurons generated on days E17, E18, and E19 form regular concentric rings around the core in an inside-out sequence.

Convergence of an iterative procedure for large-scale static analysis of structural components

NASA Technical Reports Server (NTRS)

Austin, F.; Ojalvo, I. U.

1976-01-01

The paper proves convergence of an iterative procedure for calculating the deflections of built-up component structures which can be represented as consisting of a dominant, relatively stiff primary structure and a less stiff secondary structure, which may be composed of one or more substructures that are not connected to one another but are all connected to the primary structure. The iteration consists in estimating the deformation of the primary structure in the absence of the secondary structure on the assumption that all mechanical loads are applied directly to the primary structure. The j-th iterate primary structure deflections at the interface are imposed on the secondary structure, and the boundary loads required to produce these deflections are computed. The cycle is completed by applying the interface reaction to the primary structure and computing its updated deflections. It is shown that the mathematical condition for convergence of this procedure is that the maximum eigenvalue of the equation relating primary-structure deflection to imposed secondary-structure deflection be less than unity, which is shown to correspond with the physical requirement that the secondary structure be more flexible at the interface boundary.

Distant Secondary Craters and Age Constraints on Young Martian Terrains

NASA Technical Reports Server (NTRS)

McEwen, A.; Preblich, B.; Turtle, E.; Studer, D.; Artemieva, N.; Golombek, M.; Hurst, M.; Kirk, R.; Burr, D.

2005-01-01

Are small (less than approx. 1 km diameter) craters on Mars and the Moon dominated by primary impacts, by secondary impacts of much larger primary craters, or are both primaries and secondaries significant? This question is critical to age constraints for young terrains and for older terrains covering small areas, where only small craters are superimposed on the unit. If the martian rayed crater Zunil is representative of large impact events on Mars, then the density of secondaries should exceed the density of primaries at diameters a factor of 1000 smaller than that of the largest contributing primary crater. On the basis of morphology and depth/diameter measurements, most small craters on Mars could be secondaries. Two additional observations (discussed below) suggest that the production functions of Hartmann and Neukum predict too many primary craters smaller than a few hundred meters in diameter. Fewer small, high-velocity impacts may explain why there appears to be little impact regolith over Amazonian terrains. Martian terrains dated by small craters could be older than reported in recent publications.

CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.

PubMed

Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

2017-05-15

B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study. Copyright © 2017 by The American Association of Immunologists, Inc.

Dual coil ignition system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huberts, Garlan J.; Qu, Qiuping; Czekala, Michael Damian

2017-03-28

A dual coil ignition system is provided. The dual coil ignition system includes a first inductive ignition coil including a first primary winding and a first secondary winding, and a second inductive ignition coil including a second primary winding and a second secondary winding, the second secondary winding connected in series to the first secondary winding. The dual coil ignition system further includes a diode network including a first diode and a second diode connected between the first secondary winding and the second secondary winding.

Identification of GATC- and CCGG- recognizing Type II REases and their putative specificity-determining positions using Scan2S—a novel motif scan algorithm with optional secondary structure constraints

PubMed Central

Niv, Masha Y.; Skrabanek, Lucy; Roberts, Richard J.; Scheraga, Harold A.; Weinstein, Harel

2008-01-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering. PMID:17972284

Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.

PubMed

Niv, Masha Y; Skrabanek, Lucy; Roberts, Richard J; Scheraga, Harold A; Weinstein, Harel

2008-05-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering.

Evidence for an Evolutionary Cheater Strategy--Relationships Between Primary and Secondary Psychopathy, Parenting, and Shame and Guilt.

PubMed

Lyons, Minna T

2015-01-01

In the present study, shame and guilt proneness were investigated in relation to primary and secondary psychopathy, looking at parental care as a possible mediator. A sample of 388 volunteers participated in an on-line study, completing several self-report measurements. Primary psychopathy, robust to parental care and sex of the participant, was associated with lower guilt proneness after a private transgression and lower negative self-evaluations after a public transgression. Secondary psychopathy was not associated with guilt or shame proneness. Paternal care played a mediating role between primary psychopathy and guilt, but only in male participants. High paternal care was associated with lower guilt repair in high psychopathy males, suggesting that a positive father-son relationship might be essential for development of exploitive strategies in primary psychopathy. The results highlight the fundamental differences between primary and secondary psychopathy, and provide support for the idea that primary psychopathy is an evolutionary cheater-strategy.

Discovery and Characterization of Eclipsing Binary Stars and Transiting Planets in Young Benchmark Clusters: The Pleiades and Hyades

NASA Astrophysics Data System (ADS)

Stassun, Keivan; David, Trevor J.; Conroy, Kyle E.; Hillenbrand, Lynne; Stauffer, John R.; Pepper, Joshua; Rebull, Luisa M.; Cody, Ann Marie

2016-06-01

Prior to K2, only one eclipsing binary in the Pleiades was known (HD 23642). We present the discovery and characterization of three additional eclipsing binaries (EBs) in this ~120 Myr old benchmark open cluster. Unlike HD 23642, all three of the new EBs are low mass (Mtot < 1 M⊙) and thus their components are still undergoing pre-main-sequence contraction at the Pleiades age. Low mass EBs are rare, especially in the pre-main-sequence phase, and thus these systems are valuable for constraining theoretical stellar evolution models. One of the three new EBs is single-lined with a K-type primary (HII 2407). The second (HCG 76) comprises two nearly equal-mass 0.3 M⊙ stars, with masses and radii measured with precisions of better than 3% and 5%, respectively. The third (MHO 9) has an M-type primary with a secondary that is possibly quite close to the hydrogen-burning limit, but needs additional follow-up observations to better constrain its parameters. We use the precise parameters of HCG 76 to test the predictions of stellar evolution models, and to derive an independent distance to the Pleiades of 132±5 pc. Finally, we present tentative evidence for differential rotation in the primary component of the newly discovered Pleiades EB HII 2407, and we also characterize a newly discovered transiting Neptune-sized planet orbiting an M-dwarf in the Hyades.

Influence of fuel ethanol content on primary emissions and secondary aerosol formation potential for a modern flex-fuel gasoline vehicle

NASA Astrophysics Data System (ADS)

Timonen, Hilkka; Karjalainen, Panu; Saukko, Erkka; Saarikoski, Sanna; Aakko-Saksa, Päivi; Simonen, Pauli; Murtonen, Timo; Dal Maso, Miikka; Kuuluvainen, Heino; Bloss, Matthew; Ahlberg, Erik; Svenningsson, Birgitta; Pagels, Joakim; Brune, William H.; Keskinen, Jorma; Worsnop, Douglas R.; Hillamo, Risto; Rönkkö, Topi

2017-04-01

The effect of fuel ethanol content (10, 85 and 100 %) on primary emissions and on subsequent secondary aerosol formation was investigated for a Euro 5 flex-fuel gasoline vehicle. Emissions were characterized during a New European Driving Cycle (NEDC) using a comprehensive set-up of high time-resolution instruments. A detailed chemical composition of the exhaust particulate matter (PM) was studied using a soot particle aerosol mass spectrometer (SP-AMS), and secondary aerosol formation was studied using a potential aerosol mass (PAM) chamber. For the primary gaseous compounds, an increase in total hydrocarbon emissions and a decrease in aromatic BTEX (benzene, toluene, ethylbenzene and xylenes) compounds was observed when the amount of ethanol in the fuel increased. In regard to particles, the largest primary particulate matter concentrations and potential for secondary particle formation was measured for the E10 fuel (10 % ethanol). As the ethanol content of the fuel increased, a significant decrease in the average primary particulate matter concentrations over the NEDC was found. The PM emissions were 0.45, 0.25 and 0.15 mg m-3 for E10, E85 and E100, respectively. Similarly, a clear decrease in secondary aerosol formation potential was observed with a larger contribution of ethanol in the fuel. The secondary-to-primary PM ratios were 13.4 and 1.5 for E10 and E85, respectively. For E100, a slight decrease in PM mass was observed after the PAM chamber, indicating that the PM produced by secondary aerosol formation was less than the PM lost through wall losses or the degradation of the primary organic aerosol (POA) in the chamber. For all fuel blends, the formed secondary aerosol consisted mostly of organic compounds. For E10, the contribution of organic compounds containing oxygen increased from 35 %, measured for primary organics, to 62 % after the PAM chamber. For E85, the contribution of organic compounds containing oxygen increased from 42 % (primary) to 57 % (after the PAM chamber), whereas for E100 the amount of oxidized organics remained the same (approximately 62 %) with the PAM chamber when compared to the primary emissions.

Control of NOx Emissions from Stationary Combustion Sources

EPA Science Inventory

In general, NOx control technologies are categorized as being either primary control technologies or secondary control technologies. Primary control technologies reduce the formation of NOx in the primary combustion zone. In contrast, secondary control technologies destroy the NO...

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

Rolled-up transformer structure for a radiofrequency integrated circuit (RFIC)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xiuling; Huang, Wen

A rolled-up transformer structure comprises a multilayer sheet having a rolled configuration comprising multiple turns about a longitudinal axis. The multilayer sheet comprises more than one conductive pattern layer on a strain-relieved layer, including a first conductive film and a second conductive film separated from the first conductive film in a thickness direction. The first conductive film comprises an even number of primary conductive strips, where each primary conductive strip has a length extending in the rolling direction, and the second conductive film comprises an even number of secondary conductive strips, where each secondary conductive strip has a length extendingmore » in the rolling direction. In the rolled configuration, turns of the primary conductive strips and turns of the secondary conductive strips wrap around the longitudinal axis. The primary conductive strips serve as a primary winding and the secondary conductive strips serve as a secondary winding of the rolled-up transformer structure.« less

A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data.

PubMed

You, Qi; Yan, Hengyu; Liu, Yue; Yi, Xin; Zhang, Kang; Xu, Wenying; Su, Zhen

2017-05-01

The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts. Here, we used the model plant Arabidopsis thaliana to improve the ability to identify candidate promoter locations in intergenic miRNAs and to determine rules for identifying primary transcription start sites of miRNAs by integrating high-throughput omics data, such as the DNase I hypersensitive sites, chromatin immunoprecipitation-sequencing of polymerase II and H3K4me3, as well as high throughput transcriptomic data. As a result, 93% of refined primary transcripts could be confirmed by the primer pairs from a previous study. Cis-element and secondary structure analyses also supported the feasibility of our results. This work will contribute to the primary transcriptional regulatory analysis of miRNAs, and the conserved regulatory pattern may be a suitable miRNA characteristic in other plant species.

Secondary dystonia in a botulinum toxin clinic: clinical characteristics, neuroanatomical substrate and comparison with idiopathic dystonia.

PubMed

Strader, Scott; Rodnitzky, Robert L; Gonzalez-Alegre, Pedro

2011-12-01

The analysis of patients with secondary dystonia has been valuable to explore the anatomical, pharmacological and physiological bases of this disorder. The goal of this study is to compare the clinical characteristics of patients with primary and secondary dystonia and analyze the neuroanatomical bases of a subgroup of patients with lesion-induced dystonia. We identified patients evaluated in our Botulinum Toxin Clinic from 1/2000 to 7/2009 with an ICD code for "dystonia". Medical records of all subjects were reviewed, recording demographic, clinical, therapeutic and neuroimaging data. A total of 230 patients were included in the study. Idiopathic/primary dystonia was diagnosed in 162 and secondary dystonia in 58, while in 10 the etiology was uncertain. We found a female predominance (2.4:1 and 1.9:1 for primary and secondary dystonia, respectively). The cervical region was most commonly affected in primary dystonia and the limbs in secondary cases. The age at presentation was higher in primary (54.4 ± 14.1) than secondary (49 ± 17.9) dystonia. Among patients with secondary dystonia, a focal lesion was the presumed etiology in 32, with localizing diagnostic studies available in 16. The most common lesions were strokes involving the corticospinal pathway. All of those patients exhibited limb dystonia, except one with cervical dystonia following a thalamic infarct. In conclusion, primary and secondary dystonias are more prevalent in women, suggesting a sex-related predisposition to the development of this movement disorder. Lesion-induced dystonia most frequently involves the limbs and is caused by lesions in the cerebral cortex and subcortical white matter. Copyright © 2011 Elsevier Ltd. All rights reserved.

Trends in nitrogen and phosphorus cycling are consistent and constrained during tropical secondary forest succession: is secondary forest young primary forest from a nutrient perspective?

NASA Astrophysics Data System (ADS)

Sullivan, B. W.; Nasto, M.; Alvarez-Clare, S.; Cole, R. J.; Reed, S.; Chazdon, R.; Davidson, E. A.; Cleveland, C. C.

2015-12-01

Extensive deforestation of tropical rainforest often leads to agricultural abandonment and secondary forest regeneration. The land area of secondary rainforest is soon likely to exceed that of primary forest, highlighting the importance of secondary tropical rainforest in the global carbon (C) cycle. Secondary forests often grow rapidly, but the role soil nutrients play in regulating secondary forest productivity remains unsettled. Consistent with biogeochemical theory, a landmark study from a set of sites in the Amazon Basin showed that secondary forests had low nitrogen (N) availability and relatively higher phosphorus (P) availability immediately after abandonment, but that as succession proceeded, N availability "recuperated" and there was relatively less P available. To address whether such changes in N and P availability during secondary forest growth are common, we reviewed 38 studies in lowland tropical rainforest that reported changes in 23 different metrics of N and P cycling during secondary succession. We calculated slopes (rates of change) during secondary succession for each metric in each study, and analyzed patterns in these rates of change. Significant trends during secondary succession were more evident in soils than in plants, but in most cases, the variability among studies was surprisingly low. Both soil N and P availability increased through succession, at least in surface soil. Such consistent changes imply substantial biogeochemical resilience of tropical forest soils in spite of differing land use histories and species compositions among studies. In most cases, slopes were similar whether primary forest was included in, or excluded from, our analysis, suggesting that secondary succession eventually leads to similar biogeochemical conditions as those found in primary forest. Our results suggesting consistent changes in N and P availability during succession provide a biogeochemical rationale for the conservation and restoration value of tropical secondary forests, and may be of utility to coupled C-nutrient models projecting primary productivity in a dynamic tropical biome.

Modeling secondary accidents identified by traffic shock waves.

PubMed

Junhua, Wang; Boya, Liu; Lanfang, Zhang; Ragland, David R

2016-02-01

The high potential for occurrence and the negative consequences of secondary accidents make them an issue of great concern affecting freeway safety. Using accident records from a three-year period together with California interstate freeway loop data, a dynamic method for more accurate classification based on the traffic shock wave detecting method was used to identify secondary accidents. Spatio-temporal gaps between the primary and secondary accident were proven be fit via a mixture of Weibull and normal distribution. A logistic regression model was developed to investigate major factors contributing to secondary accident occurrence. Traffic shock wave speed and volume at the occurrence of a primary accident were explicitly considered in the model, as a secondary accident is defined as an accident that occurs within the spatio-temporal impact scope of the primary accident. Results show that the shock waves originating in the wake of a primary accident have a more significant impact on the likelihood of a secondary accident occurrence than the effects of traffic volume. Primary accidents with long durations can significantly increase the possibility of secondary accidents. Unsafe speed and weather are other factors contributing to secondary crash occurrence. It is strongly suggested that when police or rescue personnel arrive at the scene of an accident, they should not suddenly block, decrease, or unblock the traffic flow, but instead endeavor to control traffic in a smooth and controlled manner. Also it is important to reduce accident processing time to reduce the risk of secondary accident. Copyright © 2015 Elsevier Ltd. All rights reserved.

Secondary Interpretation of CT Examinations: Frequency and Payment in the Medicare Fee-for-Service Population.

PubMed

Lu, Michael T; Hallett, Travis R; Hemingway, Jennifer; Hughes, Danny R; Hoffmann, Udo; Duszak, Richard

2016-09-01

Secondary interpretation of diagnostic imaging examinations (providing a second formal interpretation for imaging performed at another institution) may reduce repeat imaging after transfer of care. Recently, CMS requested information to guide payment policy. We aimed to study historic trends in submitted claims and payments for secondary interpretation services in the Medicare fee-for-service population. Applying current procedural terminology codes by body part to Medicare Part B aggregate claims files, we identified all CT interpretation services rendered between 1999 and 2012. Secondary interpretation services were identified using combined code modifiers 26 and 77, in accordance with CMS billing guidelines. The frequencies of billed and denied services were extracted for primary and secondary CT interpretation services. Primary versus secondary interpretation denial rates were calculated and compared. Of all 227 million Medicare Part B claims for CT services, 299,468 (0.13%) were for secondary interpretation services. From 1999 to 2012, growth in secondary interpretation claims outpaced that in primary interpretation claims (+811% versus +56%; compound annual growth rate 17% versus 3.2%). As a percentage of all services, secondary interpretations increased from 0.05% in 1999 to 0.30% in 2012. Denial rates for second interpretations decreased from 1999 to 2012 (12.7% to 7.0%), and now approach those for primary interpretations (5.4% in 2012). Medicare claims for secondary interpretation of CT examinations are growing but account for less than 1% of all billed CT interpretation services. Denial rates are similar to those of primary interpretation services. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Time-resolved characterization of primary particle emissions and secondary particle formation from a modern gasoline passenger car

NASA Astrophysics Data System (ADS)

Karjalainen, Panu; Timonen, Hilkka; Saukko, Erkka; Kuuluvainen, Heino; Saarikoski, Sanna; Aakko-Saksa, Päivi; Murtonen, Timo; Bloss, Matthew; Dal Maso, Miikka; Simonen, Pauli; Ahlberg, Erik; Svenningsson, Birgitta; Brune, William Henry; Hillamo, Risto; Keskinen, Jorma; Rönkkö, Topi

2016-07-01

Changes in vehicle emission reduction technologies significantly affect traffic-related emissions in urban areas. In many densely populated areas the amount of traffic is increasing, keeping the emission level high or even increasing. To understand the health effects of traffic-related emissions, both primary (direct) particulate emission and secondary particle formation (from gaseous precursors in the exhaust emissions) need to be characterized. In this study, we used a comprehensive set of measurements to characterize both primary and secondary particulate emissions of a Euro 5 level gasoline passenger car. Our aerosol particle study covers the whole process chain in emission formation, from the tailpipe to the atmosphere, and also takes into account differences in driving patterns. We observed that, in mass terms, the amount of secondary particles was 13 times higher than the amount of primary particles. The formation, composition, number and mass of secondary particles was significantly affected by driving patterns and engine conditions. The highest gaseous and particulate emissions were observed at the beginning of the test cycle when the performance of the engine and the catalyst was below optimal. The key parameter for secondary particle formation was the amount of gaseous hydrocarbons in primary emissions; however, also the primary particle population had an influence.

Correlation between molecular secondary ion yield and cluster ion sputtering for samples with different stopping powers

NASA Astrophysics Data System (ADS)

Heile, A.; Muhmann, C.; Lipinsky, D.; Arlinghaus, H. F.

2012-07-01

In static SIMS, the secondary ion yield, defined as detected ions per primary ion, can be increased by altering several primary ion parameters. For many years, no quantitative predictions could be made for the secondary ion yield enhancement of molecular ions. For thick samples of organic compounds, a power dependency of the secondary ion yield on the sputtering yield was shown. For this article, samples with thick molecular layers and (sub-)monolayers composed of various molecules were prepared on inorganic substrates such as silicon, silver, and gold, and subsequently analyzed. For primary ion bombardment, monoatomic (Ne+, Ar+, Ga+, Kr+, Xe+, Bi+) as well as polyatomic (Bin+, Bin++) primary ions were used within an energy range of 10-50 keV. The power dependency was found to hold true for the different samples; however, the exponent decreased with increasing stopping power. Based on these findings, a rule of thumb is proposed for the prediction of the lower limit of the secondary ion yield enhancement as a function of the primary ion species. Additionally, effects caused by the variation of the energy deposition are discussed, including the degree of molecular fragmentation and the non-linear increase of the secondary ion yield when polyatomic primary ions are used.

[Clinical study of aged patients with secondary benign paroxysmal positional vertigo].

PubMed

Zhu, Z J; Wei, L P; Xu, Z X; Xu, H J; Liu, Q; Luo, N

2017-09-07

Objective: To investigate the clinical features and evaluate the efficacy of manual reduction in treatment of age patients with secondary benign paroxysmal positional vertigo (s-BPPV). Methods: Thirty-two cases of aged patients ( the s-BPPV group: including 19 cases of female and 13 males, age from 60 to 86 years old)with secondary benign paroxysmal positional vertigo from Jul. 2013 to Sep. 2015 in our hospital were retrospectively analyzed. The results were compared with 121 patients( the primary group: including 82 cases of female and 39males, aged from 60 to 86 years old)with aged primary benign paroxysmal positional vertigo(p -BPPV). All the patients were followed up for 12 months. Statistical data analysis was carried out with SPSS 19.0. Results: 20.92%(32/153)of all the observed elderly patients with BPPV was the aged s-BPPV. The sex ratio and onset age had no significant difference between the two groups(χ(2)=0.79, P >0.05; t =0.37, P >0.05). The rate of two or more semicircular canal involvement in the secondary group(21.88%) was higher than that in primary group(6.61%)(χ(2)=6.67, P <0.05). Bilateral semicircular canals were involved in 5 of the 32 cases in secondary group(15.63%) and 4 of the 121 cases in aged primary group(3.31%), The difference was significant(χ(2)=6.94, P <0.05). The effective rate after first manual reduction was 57.50%(23/40)in secondary group and 82.31%(107/130)in primary group, the difference was significant(χ(2)=10.46, P <0.05). The total effective rate were 87.50%(35/40) after more than once manual reduction in secondary group and 91.54%(119/130) in primary group, the difference was not significant(χ(2)= 0.59, P >0.05). The numbers of circulation of the first successful manual reduction management were (3.9±1.3)times in secondary group and (2.1±1.1)times in primary group, the difference was significant( t =3.15, P <0.05). The recurrence rate was 37.50%(15/40) in the secondary group and 16.15%(21/130)in primary group after during follow-up for 12 months, the difference was statistically significant(χ(2)=8.35, P <0.05). Conclusions: It's shown that the aged patients with secondary BPPV is not rare in clinical practice, sudden deafness and head trauma are frequent more than other reasons. The aged patients with secondary BPPV are prone to injury in multi-semicircular and bilateral canal compared with the primary BPPV. The effective rate after first manual reduction of secondary BPPV is lower than primary BPPV, it's needed more circulation of first success in manual reduction management. The total effective rates are not significant in two groups and recurrence rate is relatively high in secondary group.

Primary and secondary sources of formaldehyde in urban atmospheres: Houston Texas region

NASA Astrophysics Data System (ADS)

Parrish, D. D.; Ryerson, T. B.; Mellqvist, J.; Johansson, J.; Fried, A.; Richter, D.; Walega, J. G.; Washenfelder, R. A.; de Gouw, J. A.; Peischl, J.; Aikin, K. C.; McKeen, S. A.; Frost, G. J.; Fehsenfeld, F. C.; Herndon, S. C.

2011-12-01

We evaluate the rates of secondary production and primary emission of formaldehyde (CH2O) from petrochemical industrial facilities and on-road vehicles in the Houston Texas region. This evaluation is based upon ambient measurements collected during field studies in 2000, 2006 and 2009. The predominant CH2O source (92 ± 4% of total) is secondary production formed during the atmospheric oxidation of highly reactive volatile organic compounds (HRVOCs) emitted from the petrochemical facilities. Smaller contributions are primary emissions from these facilities (4 ± 2%), and secondary production (~3%) and primary emissions (~1%) from vehicles. The primary emissions from both sectors are well quantified by current emission inventories. Since secondary production dominates, control efforts directed at primary CH2O emissions cannot address the large majority of CH2O sources in the Houston area, although there may still be a role for such efforts. Ongoing efforts to control alkene emissions from the petrochemical facilities, as well as volatile organic compound emissions from the motor vehicle fleet, will effectively reduce the CH2O concentrations in the Houston region. We have not addressed other emission sectors, such as off-road mobile sources or secondary formation from biogenic hydrocarbons. Previous analyses based on correlations between ambient concentrations of CH2O and various marker species have suggested much larger primary emissions of CH2O, but those results neglect confounding effects of dilution and loss processes, and do not demonstrate the causes of the observed correlations. Similar problems must be suspected in any source apportionment analysis of secondary species based upon correlations of ambient concentrations of pollutants.

Primary and secondary sources of formaldehyde in urban atmospheres: Houston Texas region

NASA Astrophysics Data System (ADS)

Parrish, D. D.; Ryerson, T. B.; Mellqvist, J.; Johansson, J.; Fried, A.; Richter, D.; Walega, J. G.; Washenfelder, R. A.; de Gouw, J. A.; Peischl, J.; Aikin, K. C.; McKeen, S. A.; Frost, G. J.; Fehsenfeld, F. C.; Herndon, S. C.

2012-04-01

We evaluate the rates of secondary production and primary emission of formaldehyde (CH2O) from petrochemical industrial facilities and on-road vehicles in the Houston Texas region. This evaluation is based upon ambient measurements collected during field studies in 2000, 2006 and 2009. The predominant CH2O source (92 ± 4% of total) is secondary production formed during the atmospheric oxidation of highly reactive volatile organic compounds (HRVOCs) emitted from the petrochemical facilities. Smaller contributions are primary emissions from these facilities (4 ± 2%), and secondary production (~3%) and primary emissions (~1%) from vehicles. The primary emissions from both sectors are well quantified by current emission inventories. Since secondary production dominates, control efforts directed at primary CH2O emissions cannot address the large majority of CH2O sources in the Houston area, although there may still be a role for such efforts. Ongoing efforts to control alkene emissions from the petrochemical facilities, as well as volatile organic compound emissions from the motor vehicle fleet, will effectively reduce the CH2O concentrations in the Houston region. We do not address other emission sectors, such as off-road mobile sources or secondary formation from biogenic hydrocarbons. Previous analyses based on correlations between ambient concentrations of CH2O and various marker species have suggested much larger primary emissions of CH2O, but those results neglect confounding effects of dilution and loss processes, and do not demonstrate the causes of the observed correlations. Similar problems must be suspected in any source apportionment analysis of secondary species based upon correlations of ambient concentrations of pollutants.

Importance of secondary damage in downer cows.

PubMed

Poulton, P J; Vizard, A L; Anderson, G A; Pyman, M F

2016-05-01

To investigate the relative importance in downer cows of the primary cause of recumbency in comparison with secondary complications. Downer dairy cows were monitored during their recumbency under field conditions in South Gippsland, Victoria, Australia. The cause of the original recumbency of the 218 cows was determined and secondary damage, status on day 7 and final outcome were recorded. Some type of secondary damage was found in 183/218 (84%) cows, of which 173/218 (79%) had damage deemed to be clinically important. By day 7, 52 (24%) had recovered and 69 (32%) eventually recovered. Of the 149 (68%) cows that were euthanased or died, 23 (15%) were deemed to have been lost solely from the primary cause, 107 (72%) from secondary damage and 19 (13%) from a combination of both. There was no difference in recovery among the five broad groups of causes of primary recumbency. Secondary damage was very common and presented in a large variety of ways, with many cows having multiple types of secondary damage concurrently. For most cows the secondary damage was more important than the initial primary damage in determining their fate. © 2016 Australian Veterinary Association.

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)

PubMed Central

2008-01-01

Background Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment. Results The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae. Conclusion In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics. PMID:18655698

Randomized trials are frequently fragmented in multiple secondary publications.

PubMed

Ebrahim, Shanil; Montoya, Luis; Kamal El Din, Mostafa; Sohani, Zahra N; Agarwal, Arnav; Bance, Sheena; Saquib, Juliann; Saquib, Nazmus; Ioannidis, John P A

2016-11-01

To assess the frequency and features of secondary publications of randomized controlled trials (RCTs). For 191 RCTs published in high-impact journals in 2009, we searched for secondary publications coauthored by at least one same author of the primary trial publication. We evaluated the probability of having secondary publications, characteristics of the primary trial publication that predict having secondary publications, types of secondary analyses conducted, and statistical significance of those analyses. Of 191 primary trials, 88 (46%) had a total of 475 secondary publications by 2/2014. Eight trials had >10 (up to 51) secondary publications each. In multivariable modeling, the risk of having subsequent secondary publications increased 1.32-fold (95% CI 1.05-1.68) per 10-fold increase in sample size, and 1.71-fold (95% CI 1.19-2.45) in the presence of a design article. In a sample of 197 secondary publications examined in depth, 193 tested different hypotheses than the primary publication. Of the 193, 43 tested differences between subgroups, 85 assessed predictive factors associated with an outcome of interest, 118 evaluated different outcomes than the original article, 71 had differences in eligibility criteria, and 21 assessed different durations of follow-up; 176 (91%) presented at least one analysis with statistically significant results. Approximately half of randomized trials in high-impact journals have secondary publications published with a few trials followed by numerous secondary publications. Almost all of these publications report some statistically significant results. Copyright © 2016 Elsevier Inc. All rights reserved.

The attribution of primary and secondary emotions to the in-group and to the out-group: the case of equal status countries.

PubMed

Rohmann, Anette; Niedenthal, Paula M; Brauer, Markus; Castano, Emanuele; Leyens, Jacques-Philippe

2009-12-01

We examined the attribution of primary and secondary emotions in the context of equal status groups with a non-conflictual relationship, that is, Germans and French. In Study 1 (N = 169), we found that in such an intergroup context, there was no differential attribution of secondary emotions but an over-attribution of primary emotions to the out-group. Only high identifiers tended to attribute more secondary emotions to the in-group than to the out-group. In Study 2 (N = 423), the role of the identification with the in-group and a superordinate group (Europe) in the process of infrahumanization was examined. Participants' national versus European identification was primed. The results did not differ between these two conditions. As in Study 1, an over-attribution of primary emotions to the out-group was observed. Concerning the secondary emotions, the classical infrahumanization effect occurred, that is, an over-attribution of secondary emotions to the in-group.

Conservation of the sequence of the Alzheimer's disease amyloid peptide in dog, polar bear and five other mammals by cross-species polymerase chain reaction analysis.

PubMed

Johnstone, E M; Chaney, M O; Norris, F H; Pascual, R; Little, S P

1991-07-01

Neuritic plaque and cerebrovascular amyloid deposits have been detected in the aged monkey, dog, and polar bear and have rarely been found in aged rodents (Biochem. Biophy. Res. Commun., 12 (1984) 885-890; Proc. Natl. Acad. Sci. U.S.A., 82 (1985) 4245-4249). To determine if the primary structure of the 42-43 residue amyloid peptide is conserved in species that accumulate plaques, the region of the amyloid precursor protein (APP) cDNA that encodes the peptide region was amplified by the polymerase chain reaction and sequenced. The deduced amino acid sequence was compared to those species where amyloid accumulation has not been detected. The DNA sequences of dog, polar bear, rabbit, cow, sheep, pig and guinea pig were compared and a phylogenetic tree was generated. We conclude that the amino acid sequence of dog and polar bear and other mammals which may form amyloid plaques is conserved and the species where amyloid has not been detected (mouse, rat) may be evolutionarily a distinct group. In addition, the predicted secondary structure of mouse and rat amyloid that differs from that of amyloid bearing species is its lack of propensity to form a beta sheeted structure. Thus, a cross-species examination of the amyloid peptide may suggest what is essential for amyloid deposition.

The 28S–18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor

PubMed Central

Schnare, Murray N.; Collings, James C.; Spencer, David F.; Gray, Michael W.

2000-01-01

In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from ∼11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an ∼55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A′ pre-rRNA processing sites within the 5′ external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5′ ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C.fasciculata and Trypanosoma brucei involves 3′-terminal addition of three A residues that are not present in the corresponding DNA sequences. PMID:10982863

Specific binding of a HeLa cell nuclear protein to RNA sequences in the human immunodeficiency virus transactivating region.

PubMed Central

Gaynor, R; Soultanakis, E; Kuwabara, M; Garcia, J; Sigman, D S

1989-01-01

The transactivator protein, tat, encoded by the human immunodeficiency virus is a key regulator of viral transcription. Activation by the tat protein requires sequences downstream of the transcription initiation site called the transactivating region (TAR). RNA derived from the TAR is capable of forming a stable stem-loop structure and the maintenance of both the stem structure and the loop sequences located between +19 and +44 is required for complete in vivo activation by tat. Gel retardation assays with RNA from both wild-type and mutant TAR constructs generated in vitro with SP6 polymerase indicated specific binding of HeLa nuclear proteins to the TAR. To characterize this RNA-protein interaction, a method of chemical "imprinting" has been developed using photoactivated uranyl acetate as the nucleolytic agent. This reagent nicks RNA under physiological conditions at all four nucleotides in a reaction that is independent of sequence and secondary structure. Specific interaction of cellular proteins with TAR RNA could be detected by enhanced cleavages or imprints surrounding the loop region. Mutations that either disrupted stem base-pairing or extensively changed the primary sequence resulted in alterations in the cleavage pattern of the TAR RNA. Structural features of the TAR RNA stem-loop essential for tat activation are also required for specific binding of the HeLa cell nuclear protein. Images PMID:2544877

Treatment Sequencing for Childhood ADHD: A Multiple-Randomization Study of Adaptive Medication and Behavioral Interventions.

PubMed

Pelham, William E; Fabiano, Gregory A; Waxmonsky, James G; Greiner, Andrew R; Gnagy, Elizabeth M; Pelham, William E; Coxe, Stefany; Verley, Jessica; Bhatia, Ira; Hart, Katie; Karch, Kathryn; Konijnendijk, Evelien; Tresco, Katy; Nahum-Shani, Inbal; Murphy, Susan A

2016-01-01

Behavioral and pharmacological treatments for children with attention deficit/hyperactivity disorder (ADHD) were evaluated to address whether endpoint outcomes are better depending on which treatment is initiated first and, in case of insufficient response to initial treatment, whether increasing dose of initial treatment or adding the other treatment modality is superior. Children with ADHD (ages 5-12, N = 146, 76% male) were treated for 1 school year. Children were randomized to initiate treatment with low doses of either (a) behavioral parent training (8 group sessions) and brief teacher consultation to establish a Daily Report Card or (b) extended-release methylphenidate (equivalent to .15 mg/kg/dose bid). After 8 weeks or at later monthly intervals as necessary, insufficient responders were rerandomized to secondary interventions that either increased the dose/intensity of the initial treatment or added the other treatment modality, with adaptive adjustments monthly as needed to these secondary treatments. The group beginning with behavioral treatment displayed significantly lower rates of observed classroom rule violations (the primary outcome) at study endpoint and tended to have fewer out-of-class disciplinary events. Further, adding medication secondary to initial behavior modification resulted in better outcomes on the primary outcomes and parent/teacher ratings of oppositional behavior than adding behavior modification to initial medication. Normalization rates on teacher and parent ratings were generally high. Parents who began treatment with behavioral parent training had substantially better attendance than those assigned to receive training following medication. Beginning treatment with behavioral intervention produced better outcomes overall than beginning treatment with medication.

Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection.

PubMed

Weingarden, Alexa R; Chen, Chi; Bobr, Aleh; Yao, Dan; Lu, Yuwei; Nelson, Valerie M; Sadowsky, Michael J; Khoruts, Alexander

2014-02-15

Fecal microbiota transplantation (FMT) has emerged as a highly effective therapy for refractory, recurrent Clostridium difficile infection (CDI), which develops following antibiotic treatments. Intestinal microbiota play a critical role in the metabolism of bile acids in the colon, which in turn have major effects on the lifecycle of C. difficile bacteria. We hypothesized that fecal bile acid composition is altered in patients with recurrent CDI and that FMT results in its normalization. General metabolomics and targeted bile acid analyses were performed on fecal extracts from patients with recurrent CDI treated with FMT and their donors. In addition, 16S rRNA gene sequencing was used to determine the bacterial composition of pre- and post-FMT fecal samples. Taxonomic bacterial composition of fecal samples from FMT recipients showed rapid change and became similar to the donor after the procedure. Pre-FMT fecal samples contained high concentrations of primary bile acids and bile salts, while secondary bile acids were nearly undetectable. In contrast, post-FMT fecal samples contained mostly secondary bile acids, as did non-CDI donor samples. Therefore, our analysis showed that FMT resulted in normalization of fecal bacterial community structure and metabolic composition. Importantly, metabolism of bile salts and primary bile acids to secondary bile acids is disrupted in patients with recurrent CDI, and FMT corrects this abnormality. Since individual bile salts and bile acids have pro-germinant and inhibitory activities, the changes suggest that correction of bile acid metabolism is likely a major mechanism by which FMT results in a cure and prevents recurrence of CDI.

Absolute Dimensions of the F-type Eclipsing Binary V2154 Cygni

NASA Astrophysics Data System (ADS)

Bright, Jane C.; Torres, Guillermo

2017-11-01

We report spectroscopic observations of the 2.63 day, detached, F-type main-sequence eclipsing binary V2154 Cyg. We use our observations together with existing uvby photometric measurements to derive accurate absolute masses and radii for the stars that are good to better than 1.5%. We obtain masses of {M}1=1.269+/- 0.017 {M}⊙ and {M}2=0.7542+/- 0.0059 {M}⊙ , radii of {R}1=1.477+/- 0.012 {R}⊙ and {R}2=0.7232+/- 0.0091 {R}⊙ , and effective temperatures of 6770 ± 150 K and 5020 ± 150 K for the primary and secondary stars, respectively. Both components appear to have their rotations synchronized with the motion in the circular orbit. A comparison of the properties of the primary with current stellar evolution models gives good agreement for a metallicity of [{Fe}/{{H}}]=-0.17, which is consistent with photometric estimates, and an age of about 2.2 Gyr. On the other hand, the K2 secondary is larger than predicted for its mass by about 4%. Similar discrepancies are known to exist for other cool stars, and are generally ascribed to stellar activity. The system is in fact an X-ray source, and we argue that the main site of the activity is the secondary star. Indirect estimates give a strength of about 1 kG for the average surface magnetic field on that star. A previously known close visual companion to V2154 Cyg is shown to be physically bound, making the system a hierarchical triple.

Photochemical dimerization and functionalization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and silanes

DOEpatents

Crabtree, Robert H.; Brown, Stephen H.

1989-01-01

The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and primary, secondary and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

Photochemical dimerization and functionalization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and silanes

DOEpatents

Crabtree, R.H.; Brown, S.H.

1989-10-17

The space-time yield and/or the selectivity of the photochemical dimerization of alkanes, ethers, primary and secondary alcohols, phosphine oxides and primary, secondary and tertiary silanes with Hg and U.V. light is enhanced by refluxing the substrate in the irradiated reaction zone at a temperature at which the dimer product condenses and remains condensed promptly upon its formation. Cross-dimerization of the alkanes, ethers and silanes with primary alcohols is disclosed, as is the functionalization to aldehydes of the alkanes with carbon monoxide.

Apparatus and method for mixing fuel in a gas turbine nozzle

DOEpatents

Johnson, Thomas Edward; Ziminsky, Willy Steve; Berry, Jonathan Dwight

2014-08-12

A nozzle includes a fuel plenum and an air plenum downstream of the fuel plenum. A primary fuel channel includes an inlet in fluid communication with the fuel plenum and a primary air port in fluid communication with the air plenum. Secondary fuel channels radially outward of the primary fuel channel include a secondary fuel port in fluid communication with the fuel plenum. A shroud circumferentially surrounds the secondary fuel channels. A method for mixing fuel and air in a nozzle prior to combustion includes flowing fuel to a fuel plenum and flowing air to an air plenum downstream of the fuel plenum. The method further includes injecting fuel from the fuel plenum through a primary fuel passage, injecting fuel from the fuel plenum through secondary fuel passages, and injecting air from the air plenum through the primary fuel passage.

Transcriptome analysis of Petunia axillaris flowers reveals genes involved in morphological differentiation and metabolite transport

PubMed Central

Amano, Ikuko; Kitajima, Sakihito; Suzuki, Hideyuki; Koeduka, Takao

2018-01-01

The biosynthesis of plant secondary metabolites is associated with morphological and metabolic differentiation. As a consequence, gene expression profiles can change drastically, and primary and secondary metabolites, including intermediate and end-products, move dynamically within and between cells. However, little is known about the molecular mechanisms underlying differentiation and transport mechanisms. In this study, we performed a transcriptome analysis of Petunia axillaris subsp. parodii, which produces various volatiles in its corolla limbs and emits metabolites to attract pollinators. RNA-sequencing from leaves, buds, and limbs identified 53,243 unigenes. Analysis of differentially expressed genes, combined with gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, showed that many biological processes were highly enriched in limbs. These included catabolic processes and signaling pathways of hormones, such as gibberellins, and metabolic pathways, including phenylpropanoids and fatty acids. Moreover, we identified five transporter genes that showed high expression in limbs, and we performed spatiotemporal expression analyses and homology searches to infer their putative functions. Our systematic analysis provides comprehensive transcriptomic information regarding morphological differentiation and metabolite transport in the Petunia flower and lays the foundation for establishing the specific mechanisms that control secondary metabolite biosynthesis in plants. PMID:29902274

Signal transduction in artichoke [Cynara cardunculus L. subsp. scolymus (L.) Hayek] callus and cell suspension cultures under nutritional stress.

PubMed

Lattanzio, Vincenzo; Caretto, Sofia; Linsalata, Vito; Colella, Giovanni; Mita, Giovanni

2018-06-01

Stimulated production of secondary phenolic metabolites and proline was studied by using cell cultures of artichoke [Cynara cardunculus L. subsp. scolymus (L.) Hayek] submitted to nutritional stress. Artichoke cell cultures accumulated phenolic secondary metabolites in a pattern similar to that seen in artichoke leaves and heads (capitula). This paper shows that both callus and cell suspension cultures under nutritional stress accumulated phenolic compounds and proline, at the same time their biomass production was negatively affected by nutrient deficiency. The results obtained strongly suggest that plant tissues respond to nutrient deprivation by a defensive costly mechanism, which determines the establishment of a mechanism of trade-off between growth and adaptive response. Furthermore, the results of this research suggest that perception of abiotic stress and increased phenolic metabolites are linked by a sequence of biochemical processes that also involves the intracellular free proline and the oxidative pentose phosphate pathway. The main conclusion of this paper is that, once calli and cell suspension cultures respond to nutrient deficiency, in acclimated cells the establishment of a negative correlation between primary metabolism (growth) and secondary metabolism (defence compounds) is observed. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

PubMed

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-03-31

With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

PubMed Central

Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

2008-01-01

Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules. PMID:18373878

Improved Model for Predicting the Free Energy Contribution of Dinucleotide Bulges to RNA Duplex Stability.

PubMed

Tomcho, Jeremy C; Tillman, Magdalena R; Znosko, Brent M

2015-09-01

Predicting the secondary structure of RNA is an intermediate in predicting RNA three-dimensional structure. Commonly, determining RNA secondary structure from sequence uses free energy minimization and nearest neighbor parameters. Current algorithms utilize a sequence-independent model to predict free energy contributions of dinucleotide bulges. To determine if a sequence-dependent model would be more accurate, short RNA duplexes containing dinucleotide bulges with different sequences and nearest neighbor combinations were optically melted to derive thermodynamic parameters. These data suggested energy contributions of dinucleotide bulges were sequence-dependent, and a sequence-dependent model was derived. This model assigns free energy penalties based on the identity of nucleotides in the bulge (3.06 kcal/mol for two purines, 2.93 kcal/mol for two pyrimidines, 2.71 kcal/mol for 5'-purine-pyrimidine-3', and 2.41 kcal/mol for 5'-pyrimidine-purine-3'). The predictive model also includes a 0.45 kcal/mol penalty for an A-U pair adjacent to the bulge and a -0.28 kcal/mol bonus for a G-U pair adjacent to the bulge. The new sequence-dependent model results in predicted values within, on average, 0.17 kcal/mol of experimental values, a significant improvement over the sequence-independent model. This model and new experimental values can be incorporated into algorithms that predict RNA stability and secondary structure from sequence.

Novel Approach to Analyzing MFE of Noncoding RNA Sequences

PubMed Central

George, Tina P.; Thomas, Tessamma

2016-01-01

Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers. PMID:27695341

Novel Approach to Analyzing MFE of Noncoding RNA Sequences.

PubMed

George, Tina P; Thomas, Tessamma

2016-01-01

Genomic studies have become noncoding RNA (ncRNA) centric after the study of different genomes provided enormous information on ncRNA over the past decades. The function of ncRNA is decided by its secondary structure, and across organisms, the secondary structure is more conserved than the sequence itself. In this study, the optimal secondary structure or the minimum free energy (MFE) structure of ncRNA was found based on the thermodynamic nearest neighbor model. MFE of over 2600 ncRNA sequences was analyzed in view of its signal properties. Mathematical models linking MFE to the signal properties were found for each of the four classes of ncRNA analyzed. MFE values computed with the proposed models were in concordance with those obtained with the standard web servers. A total of 95% of the sequences analyzed had deviation of MFE values within ±15% relative to those obtained from standard web servers.

Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice.

PubMed

Jang, Su; Lee, Yunjoo; Lee, Gileung; Seo, Jeonghwan; Lee, Dongryung; Yu, Yoye; Chin, Joong Hyoun; Koh, Hee-Jong

2018-01-15

Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle. In total, 142 polymorphic sites, which constructed 58 haplotypes, were detected in coding regions of ten panicle development gene and 35 sequence variants in six genes were significantly associated with panicle-related traits. Rice cultivars were clustered according to their sequence variant profiles. One of the four resultant clusters, which contained only indica and tong-il varieties, exhibited the largest average number of favorable alleles and highest average number of spikelets per panicle, suggesting that the favorable allele combination found in this cluster was beneficial in increasing the number of spikelets per panicle. Favorable alleles identified in this study can be used to develop functional markers for rice breeding programs. Furthermore, stacking several favorable alleles has the potential to substantially improve the number of spikelets per panicle in rice.

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

Selection, Characterization and Interaction Studies of a DNA Aptamer for the Detection of Bifidobacterium bifidum

PubMed Central

Hu, Lujun; Wang, Linlin; Lu, Wenwei; Zhao, Jianxin; Zhang, Hao; Chen, Wei

2017-01-01

A whole-bacterium-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure was adopted in this study for the selection of an ssDNA aptamer that binds to Bifidobacterium bifidum. After 12 rounds of selection targeted against B. bifidum, 30 sequences were obtained and divided into seven families according to primary sequence homology and similarity of secondary structure. Four FAM (fluorescein amidite) labeled aptamer sequences from different families were selected for further characterization by flow cytometric analysis. The results reveal that the aptamer sequence CCFM641-5 demonstrated high-affinity and specificity for B. bifidum compared with the other sequences tested, and the estimated Kd value was 10.69 ± 0.89 nM. Additionally, sequence truncation experiments of the aptamer CCFM641-5 led to the conclusion that the 5′-primer and 3′-primer binding sites were essential for aptamer-target binding. In addition, the possible component of the target B. bifidum, bound by the aptamer CCFM641-5, was identified as a membrane protein by treatment with proteinase. Furthermore, to prove the potential application of the aptamer CCFM641-5, a colorimetric bioassay of the sandwich-type structure was used to detect B. bifidum. The assay had a linear range of 104 to 107 cfu/mL (R2 = 0.9834). Therefore, the colorimetric bioassay appears to be a promising method for the detection of B. bifidum based on the aptamer CCFM641-5. PMID:28441340

Draft genome sequence of the marine bacterium Streptomyces griseoaurantiacus M045, which produces novel manumycin-type antibiotics with a pABA core component.

PubMed

Li, Fuchao; Jiang, Peng; Zheng, Huajun; Wang, Shengyue; Zhao, Guoping; Qin, Song; Liu, Zhaopu

2011-07-01

Streptomyces griseoaurantiacus M045, isolated from marine sediment, produces manumycin and chinikomycin antibiotics. Here we present a high-quality draft genome sequence of S. griseoaurantiacus M045, the first marine Streptomyces species to be sequenced and annotated. The genome encodes several gene clusters for biosynthesis of secondary metabolites and has provided insight into genomic islands linking secondary metabolism to functional adaptation in marine S. griseoaurantiacus M045.

Insights into the phylogenetic positions of photosynthetic bacteria obtained from 5S rRNA and 16S rRNA sequence data

NASA Technical Reports Server (NTRS)

Fox, G. E.

1985-01-01

Comparisons of complete 16S ribosomal ribonucleic acid (rRNA) sequences established that the secondary structure of these molecules is highly conserved. Earlier work with 5S rRNA secondary structure revealed that when structural conservation exists the alignment of sequences is straightforward. The constancy of structure implies minimal functional change. Under these conditions a uniform evolutionary rate can be expected so that conditions are favorable for phylogenetic tree construction.

Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites▿

PubMed Central

Song, Ju Yeon; Jeong, Haeyoung; Yu, Dong Su; Fischbach, Michael A.; Park, Hong-Seog; Kim, Jae Jong; Seo, Jeong-Sun; Jensen, Susan E.; Oh, Tae Kwang; Lee, Kye Joon; Kim, Jihyun F.

2010-01-01

Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics. PMID:20889745

U enrichment and Th/U fractionation in Archean boninites: Implications for paleo-ocean oxygenation and U cycling at juvenile subduction zones

NASA Astrophysics Data System (ADS)

Manikyamba, C.; Said, Nuru; Santosh, M.; Saha, Abhishek; Ganguly, Sohini; Subramanyam, K. S. V.

2018-05-01

Phanerozoic boninites record enrichments of U over Th, giving Th/U: 0.5-1.6, relative to intraoceanic island arc tholeiites (IAT) where Th/U averages 2.6. Uranium enrichment is attributed to incorporation of shallow, oxidized fluids, U-rich but Th-poor, from the slab into the melt column of boninites which form in near-trench to forearc settings of suprasubduction zone ophiolites. Well preserved Archean komatiite-tholeiite, plume-derived, oceanic volcanic sequences have primary magmatic Th/U ratios of 4.4-3.6, and Archean convergent margin IAT volcanic sequences, having REE and HFSE compositions similar to Phanerozoic IAT equivalents, preserve primary Th/U of 4-3.6. The best preserved Archean boninites of the 3.0 Ga Olondo and 2.7 Ga Gadwal greenstone belts, hosted in convergent margin ophiolite sequences, also show relative enrichments of U over Th, with low average Th/U ∼3 relative to coeval IAT, and Phanerozoic counterparts which are devoid of crustal contamination and therefore erupted in an intraoceanic setting, with minimal contemporaneous submarine hydrothermal alteration. Later enrichment of U is unlikely as Th-U-Nb-LREE patterns are coherent in these boninites whereas secondary effects induce dispersion of Th/U ratios. The variation in Th/U ratios from Archean to Phanerozoic boninites of greenstone belts to ophiolitic sequences reflect on genesis of boninitic lavas at different tectono-thermal regimes. Consequently, if the explanation for U enrichment in Phanerozoic boninites also applies to Archean examples, the implication is that U was soluble in oxygenated Archean marine water up to 600 Ma before the proposed great oxygenation event (GOE) at ∼2.4 Ga. This interpretation is consistent with large Ce anomalies in some hydrothermally altered Archean volcanic sequences aged 3.0-2.7 Ga.

40 CFR 421.184 - Standards of performance for new sources.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Secondary Germanium and Gallium Subcategory § 421.184 Standards of performance for new sources. Any new... liquor. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant or pollutant... air pollution control. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant...

40 CFR 421.184 - Standards of performance for new sources.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Secondary Germanium and Gallium Subcategory § 421.184 Standards of performance for new sources. Any new... liquor. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant or pollutant... air pollution control. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant...

40 CFR 421.184 - Standards of performance for new sources.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Secondary Germanium and Gallium Subcategory § 421.184 Standards of performance for new sources. Any new... liquor. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant or pollutant... air pollution control. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant...

40 CFR 421.184 - Standards of performance for new sources.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Secondary Germanium and Gallium Subcategory § 421.184 Standards of performance for new sources. Any new... liquor. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant or pollutant... air pollution control. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant...

40 CFR 421.184 - Standards of performance for new sources.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Secondary Germanium and Gallium Subcategory § 421.184 Standards of performance for new sources. Any new... liquor. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant or pollutant... air pollution control. NSPS for the Primary and Secondary Germanium and Gallium Subcategory Pollutant...

Emergence of Secondary Trigger Sites after Primary Migraine Surgery.

PubMed

Punjabi, Ayesha; Brown, Matthew; Guyuron, Bahman

2016-04-01

Surgical decompression of a migraine headache may unmask headaches originating from secondary sites. A retrospective chart review investigated the incidence and characteristics of secondary trigger sites to identify clinical patterns that could aid in predicting and perhaps reducing postoperative migraines. One hundred eighty-five charts for migraine patients who underwent surgery at the senior author's (B.G.) practice were reviewed. Sites from which migraine headaches initiated or occurred independently were considered primary. The sites that were not active at the time of preoperative evaluation but became active after surgery were considered secondary. Bivariate analysis was performed to characterize postoperative migraines. Of 185 patients, 33 (17.8 percent) developed secondary migraine headache trigger sites. Of patients with primary site I (frontal) symptoms, 20.83 percent had site III (septonasal) symptoms unmasked after surgery (versus 7 percent for patients with other primary sites; p = 0.04). Of the patients with site II (temporal) migraines, 17.14 percent had secondary frontal symptoms (versus 5.68 percent; p = 0.04). Primary site II symptoms predicted postoperative site IV (occipital) symptoms (11.43 versus 1.1 percent; p = 0.008), and primary occipital symptoms predicted postoperative temporal symptoms (11.1 versus 2.33 percent; p = 0.04). The authors observed that 17.8 percent of patients develop postoperative migraine headache triggers that are not reported during the initial assessment. Knowledge of secondary migraine emergence patterns, and the presence of some preoperative symptoms, can aid in predicting the migraines that will arise from a new site postoperatively. Therapeutic, IV.

Treatment of primary and secondary syphilis. Serological response.

PubMed

Fiumara, N J

1980-06-27

One hundred thirty-eight patients with primary syphillis and 161 patients with secondary syphilis were treated with penicillin G benzathine, 2.4 million units given intramuscularly weekly for two weeks, for a total of 4.8 million units. All 138 patients with primary syphilis had a rapid resolution of their lesions, and all became seronegative within one year. Similarly, the 161 patients with secondary syphilis were cured clinically, and all achieved seronegativity within 24 months.

Size-velocity distribution of large ejecta fragments

NASA Technical Reports Server (NTRS)

Vickery, A. M.

1986-01-01

The characteristics of three primary extraterrestrial craters and the associated craters were examined to generate a size-velocity distribution for large ejecta fragments. The lunar craters Copernicus and Aristillus and the Martian crater Dv on Olympus Mons were used. Attention was focused on the radial distances between the primary and secondary crater centers and the diameters of the secondaries. The primary craters selected are all relatively young, which avoided contamination of the data from secondaries from other primaries. Attempts were made to account for the speed of the hypervelocity impacts and the elemental compositions of the impactors. An apparent velocity cutoff of about 1 km/sec was observed for the secondaries, which implies that no meteoroid impacts can accelerate ejecta to escape velocities from the moon or Mars.

40 CFR 50.2 - Scope.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS NATIONAL PRIMARY AND SECONDARY AMBIENT AIR QUALITY STANDARDS § 50.2 Scope. (a) National primary and secondary ambient air quality standards under section 109 of the Act are set forth in this part. (b) National primary ambient air quality...

78 FR 53237 - Airworthiness Directives; Airbus Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-29

... control secondary computers (FCSCs), rather than flight control primary computers (FCPCs). This document... control primary computers (FCPCs); modifying two flight control secondary computers (FCSCs); revising the... the AD, which specify FCSCs, instead of flight control primary computers FCPCs. No other part of the...

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

PubMed

Medema, Marnix H; Blin, Kai; Cimermancic, Peter; de Jager, Victor; Zakrzewski, Piotr; Fischbach, Michael A; Weber, Tilmann; Takano, Eriko; Breitling, Rainer

2011-07-01

Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide variety of microbes. However, rapidly and reliably pinpointing all the potential gene clusters for secondary metabolites in dozens of newly sequenced genomes has been extremely challenging, due to their biochemical heterogeneity, the presence of unknown enzymes and the dispersed nature of the necessary specialized bioinformatics tools and resources. Here, we present antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view. antiSMASH is available at http://antismash.secondarymetabolites.org.

Case A and B evolution towards electron capture supernova

NASA Astrophysics Data System (ADS)

Siess, L.; Lebreuilly, U.

2018-06-01

Context. Most super-asymptotic giant branch (SAGB) stars are expected to end their life as oxygen-neon white dwarfs rather than electron capture supernovae (ECSN). The reason is ascribed to the ability of the second dredge-up to significantly reduce the mass of the He core and of the efficient AGB winds to remove the stellar envelope before the degenerate core reaches the critical mass for the activation of electron capture reactions. Aims: In this study, we investigate the formation of ECSN through case A and case B mass transfer. In these scenarios, when Roche lobe overflow stops, the primary has become a helium star. With a small envelope left, the second dredge-up is prevented, potentially opening new paths to ECSN. Methods: We compute binary models using our stellar evolution code BINSTAR. We consider three different secondary masses of 8, 9, and 10 M⊙ and explore the parameter space, varying the companion mass, orbital period, and input physics. Results: Assuming conservative mass transfer, with our choice of secondary masses all case A systems enter contact either during the main sequence or as a consequence of reversed mass transfer when the secondary overtakes its companion during core helium burning. Case B systems are able to produce ECSN progenitors in a relatively small range of periods (3 ≲ P(d) ≤ 30) and primary masses (10.9 ≤ M/M⊙≤ 11.5). Changing the companion mass has little impact on the primary's fate as long as the mass ratio M1/M2 remains less than 1.4-1.5, above which evolution to contact becomes unavoidable. We also find that allowing for systemic mass loss substantially increases the period interval over which ECSN can occur. This change in the binary physics does not however affect the primary mass range. We finally stress that the formation of ECSN progenitors through case A and B mass transfer is very sensitive to adopted binary and stellar physics. Conclusions: Close binaries provide additional channels for ECSN but the parameter space is rather constrained likely making ECSN a rare event.

Variable compression ratio device for internal combustion engine

DOEpatents

Maloney, Ronald P.; Faletti, James J.

2004-03-23

An internal combustion engine, particularly suitable for use in a work machine, is provided with a combustion cylinder, a cylinder head at an end of the combustion cylinder and a primary piston reciprocally disposed within the combustion cylinder. The cylinder head includes a secondary cylinder and a secondary piston reciprocally disposed within the secondary cylinder. An actuator is coupled with the secondary piston for controlling the position of the secondary piston dependent upon the position of the primary piston. A communication port establishes fluid flow communication between the combustion cylinder and the secondary cylinder.

PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.

PubMed

Ganesan, K; Parthasarathy, S

2011-12-01

Annotation of any newly determined protein sequence depends on the pairwise sequence identity with known sequences. However, for the twilight zone sequences which have only 15-25% identity, the pair-wise comparison methods are inadequate and the annotation becomes a challenging task. Such sequences can be annotated by using methods that recognize their fold. Bowie et al. described a 3D1D profile method in which the amino acid sequences that fold into a known 3D structure are identified by their compatibility to that known 3D structure. We have improved the above method by using the predicted secondary structure information and employ it for fold recognition from the twilight zone sequences. In our Protein Secondary Structure 3D1D (PSS-3D1D) method, a score (w) for the predicted secondary structure of the query sequence is included in finding the compatibility of the query sequence to the known fold 3D structures. In the benchmarks, the PSS-3D1D method shows a maximum of 21% improvement in predicting correctly the α + β class of folds from the sequences with twilight zone level of identity, when compared with the 3D1D profile method. Hence, the PSS-3D1D method could offer more clues than the 3D1D method for the annotation of twilight zone sequences. The web based PSS-3D1D method is freely available in the PredictFold server at http://bioinfo.bdu.ac.in/servers/ .

Identification of Causes of the Occupational Stress for Health Providers at Different Levels of Health Care.

PubMed

Trifunovic, Natasa; Jatic, Zaim; Kulenovic, Alma Dzubur

2017-06-01

To identify and compare the stressors in the work environment experienced by employees in primary health care and secondary health care, amongphysiciansand nurses. The survey was conducted to identify types of stressors by assessing health care workers employed in the primary and secondary health care services of the Public Institution, the Health Centre of the Sarajevo Canton, using a questionnaire about stress in the workplace. Among all study participants stressors connected to the organization of work, finance and communication were found to affect their mental health most strongly. The results show a significant difference between primary and secondary health care in experience of stressors related to the organization of work, communication, and stressors related to the emotional and physical risks. Primary health care physicians report a significantly higher experience of stress and impact on mental health compared with other physicians related to emotional difficulties when working in the field of palliative care. Our results also indicate a significant difference between primary and secondary health providers in experiencing stressors related to the organization of work, such as: on-call duty shifts, an inadequate working environment and in the assessment of administrative work overload. The survey identified the most intense stressors for doctors and nurses at primary and secondary levels of health care services. The results of the study indicate that doctors and nurses have a different hierarchy of stressors, as well as subjects at Primary and Secondary Health Care. The results of the study indicate that subjects et Primary Health Care perceive more stressful organizational, emotional and communicational problems.

Comparison of endotoxin levels found in primary and secondary endodontic infections.

PubMed

Gomes, Brenda P F A; Endo, Marcos S; Martinho, Frederico C

2012-08-01

This clinical study was conducted to compare the levels of endotoxins (lipopolysaccharides [LPSs]) found in primary and secondary endodontic infections with apical periodontitis by correlating LPS contents with clinical/radiographic findings. In addition, the presence of target gram-negative anaerobic bacteria was also investigated. Samples were taken from 15 root canals with primary infections and 15 with secondary infections by using paper points. The limulus amebocyte lysate assay was used to quantify endotoxins, and the polymerase chain reaction technique (16S rDNA) was used for bacterial investigation. Endotoxins were detected in 100% of the root canal samples collected from primary (15/15) and secondary (15/15) infections with median values of 7.49 EU/mL and 3.96 EU/mL, respectively (P < .05). The median value of endotoxins found in the presence of clinical symptoms was significantly higher than in asymptomatic teeth with primary infections (P < .05). A positive correlation was found between endotoxin contents and a larger size of the radiolucent area (>3 mm) (P < .05). Prevotella nigrescens (10/15, 4/15), Fusobacterium nucleatum (5/15, 1/15), Treponema denticola (3/15, 1/15), and Treponema socranskii (5/15, 1/15) were detected in teeth with primary and secondary infections, respectively. P. endodontalis was present only in teeth with primary infections (5/15). Teeth with primary endodontic infections had higher contents of endotoxins and a more complex gram-negative bacterial community than teeth with secondary infections. Moreover, the levels of endotoxins were related to the severity of bone destruction in periapical tissues as well as the development of clinical features in teeth with primary infections. Copyright © 2012 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Clinical effectiveness of secondary interventions for restenosis after renal artery stenting

PubMed Central

Simone, Thomas A.; Brooke, Benjamin S.; Goodney, Philip P.; Walsh, Daniel B.; Stone, David H.; Powell, Richard J.; Cronenwett, Jack L.; Nolan, Brian W.

2013-01-01

Objective Secondary interventions for renal artery restenosis (RAS) after renal artery stenting are common, despite limited data about their effectiveness. This study was designed to evaluate the outcomes of endovascular treatment of recurrent RAS. Methods We conducted a retrospective review of patients who underwent renal artery stenting between 2001 and 2011 at Dartmouth-Hitchcock Medical Center. Patients who required secondary interventions were compared with control patients who underwent only primary interventions for RAS. Multivariate regression models were used to identify factors associated with successful outcomes, as measured by changes in blood pressure, estimated glomerular filtration rate, and number of antihypertensive medications required. Results Sixty-five secondary (57 patients) renal interventions were undertaken for recurrent RAS associated with progressive hypertension or renal dysfunction and compared with outcomes after 216 primary (180 patients) renal artery stenting procedures. Patients undergoing primary vs secondary interventions did not differ significantly in the number of preoperative antihypertensive medications used, comorbid conditions, or blood pressure. All primary and secondary interventions were performed with stents and showed no difference in procedural complications. At a mean follow-up of 23 months (range, 1–128 months), similar improvements in renal function and blood pressure were found between patients undergoing primary and secondary interventions, and there was no difference in rates of restenosis or survival between cohorts. Regression models showed that the use of embolic protection devices was associated with improved renal function after primary (odds ratio [OR], 2.0; 95% confidence interval [CI], 1.1–3.8; P < .05) and secondary (OR, 4.7; 95% CI, 1.7–12.5; P < .05) interventions, whereas statin therapy was associated with improved renal (OR, 2.0; 95% CI, 1.3–3.2; P < .05) and blood pressure response (OR, 4.1; 95% CI, 1.1–14.9; P < .05) after secondary interventions. Conclusions Patients undergoing secondary interventions for recurrent RAS have outcomes that are comparable with those for primary interventions. These data suggest that repeated endovascular procedures for RAS can be undertaken with similar expectations for clinical improvement and may be further improved by routine use of embolic protection devices and statin therapy. PMID:23688626

Lethal neonatal case and review of primary short-chain enoyl-CoA hydratase (SCEH) deficiency associated with secondary lymphocyte pyruvate dehydrogenase complex (PDC) deficiency.

PubMed

Bedoyan, Jirair K; Yang, Samuel P; Ferdinandusse, Sacha; Jack, Rhona M; Miron, Alexander; Grahame, George; DeBrosse, Suzanne D; Hoppel, Charles L; Kerr, Douglas S; Wanders, Ronald J A

2017-04-01

Mutations in ECHS1 result in short-chain enoyl-CoA hydratase (SCEH) deficiency which mainly affects the catabolism of various amino acids, particularly valine. We describe a case compound heterozygous for ECHS1 mutations c.836T>C (novel) and c.8C>A identified by whole exome sequencing of proband and parents. SCEH deficiency was confirmed with very low SCEH activity in fibroblasts and nearly absent immunoreactivity of SCEH. The patient had a severe neonatal course with elevated blood and cerebrospinal fluid lactate and pyruvate concentrations, high plasma alanine and slightly low plasma cystine. 2-Methyl-2,3-dihydroxybutyric acid was markedly elevated as were metabolites of the three branched-chain α-ketoacids on urine organic acids analysis. These urine metabolites notably decreased when lactic acidosis decreased in blood. Lymphocyte pyruvate dehydrogenase complex (PDC) activity was deficient, but PDC and α-ketoglutarate dehydrogenase complex activities in cultured fibroblasts were normal. Oxidative phosphorylation analysis on intact digitonin-permeabilized fibroblasts was suggestive of slightly reduced PDC activity relative to control range in mitochondria. We reviewed 16 other cases with mutations in ECHS1 where PDC activity was also assayed in order to determine how common and generalized secondary PDC deficiency is associated with primary SCEH deficiency. For reasons that remain unexplained, we find that about half of cases with primary SCEH deficiency also exhibit secondary PDC deficiency. The patient died on day-of-life 39, prior to establishing his diagnosis, highlighting the importance of early and rapid neonatal diagnosis because of possible adverse effects of certain therapeutic interventions, such as administration of ketogenic diet, in this disorder. There is a need for better understanding of the pathogenic mechanisms and phenotypic variability in this relatively recently discovered disorder. Copyright © 2017 Elsevier Inc. All rights reserved.

Keeping the Promise: Five Benefits of Girls' Secondary Education

ERIC Educational Resources Information Center

Rihani, May A.

2006-01-01

Countries around the world have achieved huge gains in primary education, reaching a world average of 83.8 percent in net primary enrollment. However, large numbers of students still do not complete primary education, and even fewer continue on to secondary school. Since so few children complete primary school, those who do must be able to…

Identification of ribonucleotide reductase mutation causing temperature-sensitivity of herpes simplex virus isolates from whitlow by deep sequencing.

PubMed

Daikoku, Tohru; Oyama, Yukari; Yajima, Misako; Sekizuka, Tsuyoshi; Kuroda, Makoto; Shimada, Yuka; Takehara, Kazuhiko; Miwa, Naoko; Okuda, Tomoko; Sata, Tetsutaro; Shiraki, Kimiyasu

2015-06-01

Herpes simplex virus 2 caused a genital ulcer, and a secondary herpetic whitlow appeared during acyclovir therapy. The secondary and recurrent whitlow isolates were acyclovir-resistant and temperature-sensitive in contrast to a genital isolate. We identified the ribonucleotide reductase mutation responsible for temperature-sensitivity by deep-sequencing analysis.

Chromium effects on glucose tolerance and insulin sensitivity in persons at risk for diabetes mellitus.

PubMed

Ali, Ather; Ma, Yingying; Reynolds, Jesse; Wise, John Pierce; Inzucchi, Silvio E; Katz, David L

2011-01-01

To investigate the effects of daily chromium picolinate supplementation on serum measures of glucose tolerance and insulin sensitivity in patients at high risk for type 2 diabetes mellitus. We conducted a randomized, double-blind, placebo-controlled, modified cross-over clinical trial with 6-month sequences of intervention and placebo followed by a 6-month postintervention assessment. Adult patients with impaired fasting glucose, impaired glucose tolerance, or metabolic syndrome were enrolled. Participants received 6-month sequences of chromium picolinate or placebo at 1 of 2 dosages (500 or 1000 mcg daily). Primary outcome measures were change in fasting plasma glucose, 2-hour plasma glucose during oral glucose tolerance testing, fasting and 2-hour insulin, and homeostasis model assessment of insulin resistance (HOMA-IR). Secondary outcomes included anthropometric measures, blood pressure, endothelial function, hemoglobin A1c, lipids, and urinary microalbumin. Fifty-nine participants were enrolled. No changes were seen in glucose level, insulin level, or HOMA-IR (all P>.05) after 6 months of chromium at either dosage level (500 mcg or 1000 mcg daily) when compared with placebo. None of the secondary outcomes improved with either chromium dosage compared with placebo (P>.05). Chromium supplementation does not appear to ameliorate insulin resistance or impaired glucose metabolism in patients at risk for type 2 diabetes and thus is unlikely to attenuate diabetes risk.

Coexistence of Wolbachia with Buchnera aphidicola and a Secondary Symbiont in the Aphid Cinara cedri

PubMed Central

Gómez-Valero, Laura; Soriano-Navarro, Mario; Pérez-Brocal, Vicente; Heddi, Abdelaziz; Moya, Andrés; García-Verdugo, José Manuel; Latorre, Amparo

2004-01-01

Intracellular symbiosis is very common in the insect world. For the aphid Cinara cedri, we have identified by electron microscopy three symbiotic bacteria that can be characterized by their different sizes, morphologies, and electrodensities. PCR amplification and sequencing of the 16S ribosomal DNA (rDNA) genes showed that, in addition to harboring Buchnera aphidicola, the primary endosymbiont of aphids, C. cedri harbors a secondary symbiont (S symbiont) that was previously found to be associated with aphids (PASS, or R type) and an α-proteobacterium that belongs to the Wolbachia genus. Using in situ hybridization with specific bacterial probes designed for symbiont 16S rDNA sequences, we have shown that Wolbachia was represented by only a few minute bacteria surrounding the S symbionts. Moreover, the observed B. aphidicola and the S symbionts had similar sizes and were housed in separate specific bacterial cells, the bacteriocytes. Interestingly, in contrast to the case for all aphids examined thus far, the S symbionts were shown to occupy a similarly sized or even larger bacteriocyte space than B. aphidicola. These findings, along with the facts that C. cedri harbors the B. aphidicola strain with the smallest bacterial genome and that the S symbionts infect all Cinara spp. analyzed so far, suggest the possibility of bacterial replacement in these species. PMID:15375144

Simulating secondary waterflooding in heterogeneous rocks with variable wettability using an image-based, multiscale pore network model

NASA Astrophysics Data System (ADS)

Bultreys, Tom; Van Hoorebeke, Luc; Cnudde, Veerle

2016-09-01

The two-phase flow properties of natural rocks depend strongly on their pore structure and wettability, both of which are often heterogeneous throughout the rock. To better understand and predict these properties, image-based models are being developed. Resulting simulations are however problematic in several important classes of rocks with broad pore-size distributions. We present a new multiscale pore network model to simulate secondary waterflooding in these rocks, which may undergo wettability alteration after primary drainage. This novel approach permits to include the effect of microporosity on the imbibition sequence without the need to describe each individual micropore. Instead, we show that fluid transport through unresolved pores can be taken into account in an upscaled fashion, by the inclusion of symbolic links between macropores, resulting in strongly decreased computational demands. Rules to describe the behavior of these links in the quasistatic invasion sequence are derived from percolation theory. The model is validated by comparison to a fully detailed network representation, which takes each separate micropore into account. Strongly and weakly water-and oil-wet simulations show good results, as do mixed-wettability scenarios with different pore-scale wettability distributions. We also show simulations on a network extracted from a micro-CT scan of Estaillades limestone, which yields good agreement with water-wet and mixed-wet experimental results.

Aberrant differentiation of the axially condensed tail bud mesenchyme in human embryos with lumbosacral myeloschisis.

PubMed

Saitsu, Hirotomo; Yamada, Shigehito; Uwabe, Chigako; Ishibashi, Makoto; Shiota, Kohei

2007-03-01

Development of the posterior neural tube (PNT) in human embryos is a complicated process that involves both primary and secondary neurulation. Recently, we histologically examined 20 human embryos around the stage of posterior neuropore closure and found that the axially condensed mesenchyme (AM) intervened between the neural plate/tube and the notochord in the junctional region of the primary and secondary neural tubes. The AM appeared to be incorporated into the most ventral part of the primary neural tube, and no cavity was observed in the AM. In this study, we report three cases of human embryos with myeloschisis in which the open primary neural tube and the closed secondary neural tube overlap dorsoventrally. In all three cases, part of the closed neural tube was located ventrally to the open neural tube in the lumbosacral region. The open and closed neural tubes appeared to be part of the primary and the AM-derived secondary neural tubes, respectively. Thus, these findings suggest that, in those embryos with myeloschisis, the AM may not be incorporated into the ventral part of the primary neural tube but aberrantly differentiate into the secondary neural tube containing cavities, leading to dorsoventral overlapping of the primary and secondary neural tubes. The aberrant differentiation of the AM in embryos with lumbosacral myeloschisis suggests that the AM plays some roles in normal as well as abnormal development of the human posterior neural tube.

Monogamy versus Consensual Non-Monogamy: Alternative Approaches to Pursuing a Strategically Pluralistic Mating Strategy.

PubMed

Mogilski, Justin K; Memering, Stacy L; Welling, Lisa L M; Shackelford, Todd K

2017-02-01

This study examined the frequency of partner-directed mate retention behaviors and several self- and partner-rated romantic relationship evaluations (i.e., sociosexuality, relationship satisfaction, mate value, and partner ideal measures) within monogamous and consensually non-monogamous (CNM) relationships. Measures were compared (1) between monogamous and CNM participants and (2) between two concurrent partners within each CNM relationship (i.e., primary and secondary partners). We found that individuals in currently monogamous relationships (n = 123) performed more mate retention behaviors compared to those currently in CNM relationships (n = 76). Within CNM relationships, participants reported engaging in more mate retention behaviors with primary partners compared to secondary partners. Likewise, CNM participants reported talking about their extra-dyadic sexual experiences and downplaying these sexual experiences more often with their primary partner compared to their secondary partner. There were no significant differences between ratings of monogamous and primary partners in participants' overall relationship satisfaction. However, monogamous participants reported less satisfaction with the amount of communication and openness they had with their partner compared to CNM participants' reports of their primary partner, but not secondary partner. By comparison, CNM participants reported higher overall relationship satisfaction with primary compared to secondary partners and considered their primary partner to be more desirable as a long-term mate than their secondary partner. We interpret these results within the context of previous research on monogamous and CNM relationships and hypothesize that these relationship configurations are alternative strategies for pursuing a strategically pluralistic mating strategy.

OUTLINE OF VOCATIONAL TRAINING IN ZAMBIA.

ERIC Educational Resources Information Center

Australian Dept. of Labour and National Service, Perth.

THE 1963 POPULATION OF ZAMBIA WAS APPROXIMATELY 3.5 MILLION. THE 8-YEAR PRIMARY EDUCATION PROGRAM IS FOLLOWED BY SECONDARY, SECONDARY TECHNICAL, AND TRADE SCHOOL OPTIONS. THERE IS AN INCREASE IN ADULT EDUCATION AT THE PRIMARY AND SECONDARY LEVELS. CRAFT AND TECHNICIAN LEVEL PROGRAMS ARE CONDUCTED AT NORTHERN TECHNICAL COLLEGE AND ITS ANCILLARY…

40 CFR 421.182 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2012 CFR

2012-07-01

... CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.182 Effluent limitations guidelines...) Still liquor. BPT Limitations for the Primary and Secondary Germanium and Gallium Subcategory Pollutant... Secondary Germanium and Gallium Subcategory Pollutant or pollutant property Maximum for any 1 day Maximum...

40 CFR 421.182 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2010 CFR

2010-07-01

... CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.182 Effluent limitations guidelines...) Still liquor. BPT Limitations for the Primary and Secondary Germanium and Gallium Subcategory Pollutant... Secondary Germanium and Gallium Subcategory Pollutant or pollutant property Maximum for any 1 day Maximum...

40 CFR 421.182 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2014 CFR

2014-07-01

... CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.182 Effluent limitations guidelines...) Still liquor. BPT Limitations for the Primary and Secondary Germanium and Gallium Subcategory Pollutant... Secondary Germanium and Gallium Subcategory Pollutant or pollutant property Maximum for any 1 day Maximum...

40 CFR 421.182 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2013 CFR

2013-07-01

... CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.182 Effluent limitations guidelines...) Still liquor. BPT Limitations for the Primary and Secondary Germanium and Gallium Subcategory Pollutant... Secondary Germanium and Gallium Subcategory Pollutant or pollutant property Maximum for any 1 day Maximum...

40 CFR 421.182 - Effluent limitations guidelines representing the degree of effluent reduction attainable by the...

Code of Federal Regulations, 2011 CFR

2011-07-01

... CATEGORY Primary and Secondary Germanium and Gallium Subcategory § 421.182 Effluent limitations guidelines...) Still liquor. BPT Limitations for the Primary and Secondary Germanium and Gallium Subcategory Pollutant... Secondary Germanium and Gallium Subcategory Pollutant or pollutant property Maximum for any 1 day Maximum...

Secondary Analysis of National Longitudinal Transition Study 2 Data

ERIC Educational Resources Information Center

Hicks, Tyler A.; Knollman, Greg A.

2015-01-01

This review examines published secondary analyses of National Longitudinal Transition Study 2 (NLTS2) data, with a primary focus upon statistical objectives, paradigms, inferences, and methods. Its primary purpose was to determine which statistical techniques have been common in secondary analyses of NLTS2 data. The review begins with an…

Association between Secondary and Primary Sjögren's Syndrome in a Large Collection of Lupus Families.

PubMed

Aggarwal, Rachna; Anaya, Juan-Manuel; Koelsch, Kristi A; Kurien, Biji T; Scofield, R Hal

2015-01-01

Objective. Systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS) share clinical and immunogenetic features and may occur together. We undertook this study to determine the risk of primary SS among SLE-unaffected relatives of SLE patients and whether or not primary and secondary SS tended to occur in the same families. Methods. We collected clinical and serological data on 2694 SLE patients, 7390 SLE-unaffected relatives of the SLE patients, and 1470 matched controls. Results. Of the 2694 subjects with SLE, 548 had secondary SS, while 71 of their 7390 SLE-unaffected relatives had primary SS. None of the 1470 controls had SS as defined herein (p = 5 × 10(-5) compared to SLE-unaffected relatives). Of the 71 SLE-unaffected relatives with primary SS, 18 (25.3%) had an SLE-affected family member with secondary SS, while only 530 of the 7319 (7.2%) SLE-unaffected relatives without SS did so (p = 1 × 10(-8)). Conclusion. Among families identified for the presence of SLE, primary and secondary SS tend to occur within the same families. These results highlight the commonalities between these two forms of SS, which in fact correspond to the same disease.

Challenging Cosmic Ray Propagation with Antiprotons: Evidence for a "Fresh" Nuclei Component?

NASA Technical Reports Server (NTRS)

Moskalenko, Igor V.; Strong, Andrew W.; Mashnik, Stepan G.; Ormes, Jonathan F.

2002-01-01

Recent measurements of the cosmic ray (CR) antiproton flux have been shown to challenge existing CR propagation models. It was shown that the reacceleration models designed to match secondary to primary nuclei ratio (e.g., Boron/Carbon) produce too few antiprotons, while the traditional non-reacceleration models can reproduce the antiproton flux but fall short of explaining the low-energy decrease in the secondary to primary nuclei ratio. Matching both the secondary to primary nuclei ratio and antiproton flux requires artificial breaks in the diffusion coefficient and the primary injection spectrum suggesting the need for other approaches. In the present paper we discuss one possibility to overcome these difficulties. Using the measured antiproton flux to fix the diffusion coefficient, we show that the spectra of primary nuclei as measured in the heliosphere may contain a fresh local unprocessed component at low energies, thus decreasing the measured secondary to primary nuclei ratio. A model reproducing antiprotons, B/C ratio, and abundances up to Ni is presented.

Mining co-occurrence and sequence patterns from cancer diagnoses in New York State.

PubMed

Wang, Yu; Hou, Wei; Wang, Fusheng

2018-01-01

The goal of this study is to discover disease co-occurrence and sequence patterns from large scale cancer diagnosis histories in New York State. In particular, we want to identify disparities among different patient groups. Our study will provide essential knowledge for clinical researchers to further investigate comorbidities and disease progression for improving the management of multiple diseases. We used inpatient discharge and outpatient visit records from the New York State Statewide Planning and Research Cooperative System (SPARCS) from 2011-2015. We grouped each patient's visit history to generate diagnosis sequences for seven most popular cancer types. We performed frequent disease co-occurrence mining using the Apriori algorithm, and frequent disease sequence patterns discovery using the cSPADE algorithm. Different types of cancer demonstrated distinct patterns. Disparities of both disease co-occurrence and sequence patterns were observed from patients within different age groups. There were also considerable disparities in disease co-occurrence patterns with respect to different claim types (i.e., inpatient, outpatient, emergency department and ambulatory surgery). Disparities regarding genders were mostly found where the cancer types were gender specific. Supports of most patterns were usually higher for males than for females. Compared with secondary diagnosis codes, primary diagnosis codes can convey more stable results. Two disease sequences consisting of the same diagnoses but in different orders were usually with different supports. Our results suggest that the methods adopted can generate potentially interesting and clinically meaningful disease co-occurrence and sequence patterns, and identify disparities among various patient groups. These patterns could imply comorbidities and disease progressions.

Method And Apparatus For Production Of Bi-213 From The Activity Ac-225 Source

DOEpatents

Egorov, Oleg B.; O'Hara, Matthew J.

2005-12-06

A method and apparatus for isolating and purifying a .sup.213 Bi radioactive isotope from an .sup.225 Ac source using a primary column and a primary sorbent which preferentially retains .sup.225 Ac over .sup.213 Bi when exposed to a compatible solvent in combination with a secondary column having a secondary sorbent which retains .sup.213 Bi when exposed to a mixture of the compatible solvent and .sup.213 Bi. A "compatible solvent" is a solvent which will preferentially remove .sup.213 Bi radioactive isotopes from a primary sorbent without removing .sup.225 Ac radioactive isotopes, and then allow .sup.213 Bi radioactive isotopes removed from the primary sorbent to be retained on a secondary sorbent, without having to dilute or otherwise chemically or physically modify the compatible solvent in between exposure to the primary and secondary sorbents.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Jin; Zhang, Yingchen; Krad, Ibrahim

Power system frequency needs to be maintained close to its nominal value at all times to avoid machine damage, under-frequency load-shedding and even blackouts. Adequate primary frequency response and secondary frequency response are the primary forces to correct an energy imbalance at the second to minute level. As wind energy becomes a larger portion of the world's energy portfolio, there are greater oppotunities for wind to provide frequency response services. This paper addresses one area of frequency control that has been missing in previous work - the reliabilty impacts and interactions between primary and secondary frequency control. The lack ofmore » a commercially available tools to simulate the interaction of these two responses has limited the energy industry's understanding of when the depletion of primary control reserve will impact the performance of secondary conrol response or vice versa. To investigate this issue, in this paper we develop a multi-area frequency response integration model with combined primary and secondary frequency control capabilities.« less

Method and apparatus for constructing an underground barrier wall structure

DOEpatents

Dwyer, Brian P.; Stewart, Willis E.; Dwyer, Stephen F.

2002-01-01

A method and apparatus for constructing a underground barrier wall structure using a jet grout injector subassembly comprising a pair of primary nozzles and a plurality of secondary nozzles, the secondary nozzles having a smaller diameter than the primary nozzles, for injecting grout in directions other than the primary direction, which creates a barrier wall panel having a substantially uniform wall thickess. This invention addresses the problem of the weak "bow-tie" shape that is formed during conventional jet injection when using only a pair of primary nozzles. The improvement is accomplished by using at least four secondary nozzles, of smaller diameter, located on both sides of the primary nozzles. These additional secondary nozzles spray grout or permeable reactive materials in other directions optimized to fill in the thin regions of the bow-tie shape. The result is a panel with increased strength and substantially uniform wall thickness.

RNAstructure: software for RNA secondary structure prediction and analysis.

PubMed

Reuter, Jessica S; Mathews, David H

2010-03-15

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

A New Classification for Pathologies of Spinal Meninges-Part 2: Primary and Secondary Intradural Arachnoid Cysts.

PubMed

Klekamp, Jörg

2017-08-01

Spinal intradural arachnoid cysts are rare causes of radiculopathy or myelopathy. Treatment options include resection, fenestration, or cyst drainage. To classify intradural spinal arachnoid cysts and present results of their treatment. Among 1519 patients with spinal space occupying lesions, 130 patients demonstrated intradural arachnoid cysts. Neuroradiological and surgical features were reviewed and clinical data analyzed. Twenty-one patients presented arachnoid cysts as a result of an inflammatory leptomeningeal reaction related to meningitis, subarachnoid hemorrhage, intrathecal injections, intradural surgery, or trauma, ie, secondary cysts. For the remaining 109 patients, no such history could be elucidated, ie, primary cysts. Forty-six percent of primary and 86% of secondary cysts were associated with syringomyelia. Patients presented after an average history of 53 ± 88 months. There were 122 thoracic and 7 lumbar cysts plus 1 cervical cyst. Fifty-nine patients with primary and 15 patients with secondary cysts underwent laminotomies with complete or partial cyst resection and duraplasty. Mean follow-up was 57 ± 52 months. In the first postoperative year, profound improvements for primary cysts were noted, in contrast to marginal changes for secondary cysts. Progression-free survival for 10 years following surgery was determined as 83% for primary compared to 15% for secondary cysts. Despite differences in clinical presentation, progression-free survival was almost identical for patients with or without syringomyelia. Complete or partial resection leads to favorable short- and long-term results for primary arachnoid cysts. For secondary cysts, surgery can only provide clinical stabilization for a limited time due to the often extensive arachnoiditis. Copyright © 2017 by the Congress of Neurological Surgeons

Human immunodeficiency virus type 1 LTR TATA and TAR region sequences required for transcriptional regulation.

PubMed Central

Garcia, J A; Harrich, D; Soultanakis, E; Wu, F; Mitsuyasu, R; Gaynor, R B

1989-01-01

The human immunodeficiency virus (HIV) type 1 LTR is regulated at the transcriptional level by both cellular and viral proteins. Using HeLa cell extracts, multiple regions of the HIV LTR were found to serve as binding sites for cellular proteins. An untranslated region binding protein UBP-1 has been purified and fractions containing this protein bind to both the TAR and TATA regions. To investigate the role of cellular proteins binding to both the TATA and TAR regions and their potential interaction with other HIV DNA binding proteins, oligonucleotide-directed mutagenesis of both these regions was performed followed by DNase I footprinting and transient expression assays. In the TATA region, two direct repeats TC/AAGC/AT/AGCTGC surround the TATA sequence. Mutagenesis of both of these direct repeats or of the TATA sequence interrupted binding over the TATA region on the coding strand, but only a mutation of the TATA sequence affected in vivo assays for tat-activation. In addition to TAR serving as the site of binding of cellular proteins, RNA transcribed from TAR is capable of forming a stable stem-loop structure. To determine the relative importance of DNA binding proteins as compared to secondary structure, oligonucleotide-directed mutations in the TAR region were studied. Local mutations that disrupted either the stem or loop structure were defective in gene expression. However, compensatory mutations which restored base pairing in the stem resulted in complete tat-activation. This indicated a significant role for the stem-loop structure in HIV gene expression. To determine the role of TAR binding proteins, mutations were constructed which extensively changed the primary structure of the TAR region, yet left stem base pairing, stem energy and the loop sequence intact. These mutations resulted in decreased protein binding to TAR DNA and defects in tat-activation, and revealed factor binding specifically to the loop DNA sequence. Further mutagenesis which inverted this stem and loop mutation relative to the HIV LTR mRNA start site resulted in even larger decreases in tat-activation. This suggests that multiple determinants, including protein binding, the loop sequence, and RNA or DNA secondary structure, are important in tat-activation and suggests that tat may interact with cellular proteins binding to DNA to increase HIV gene expression. Images PMID:2721501

Generalized Autobalanced Ramsey Spectroscopy of Clock Transitions

NASA Astrophysics Data System (ADS)

Yudin, V. I.; Taichenachev, A. V.; Basalaev, M. Yu.; Zanon-Willette, T.; Pollock, J. W.; Shuker, M.; Donley, E. A.; Kitching, J.

2018-05-01

When performing precision measurements, the quantity being measured is often perturbed by the measurement process itself. Such measurements include precision frequency measurements for atomic clock applications carried out with Ramsey spectroscopy. With the aim of eliminating probe-induced perturbations, a method of generalized autobalanced Ramsey spectroscopy (GABRS) is presented and rigorously substantiated. The usual local-oscillator frequency control loop is augmented with a second control loop derived from secondary Ramsey sequences interspersed with the primary sequences and with a different Ramsey period. This second loop feeds back to a secondary clock variable and ultimately compensates for the perturbation of the clock frequency caused by the measurements in the first loop. We show that such a two-loop scheme can lead to perfect compensation for measurement-induced light shifts and does not suffer from the effects of relaxation, time-dependent pulse fluctuations and phase-jump modulation errors that are typical of other hyper-Ramsey schemes. Several variants of GABRS are explored based on different secondary variables including added relative phase shifts between Ramsey pulses, external frequency-step compensation, and variable second-pulse duration. We demonstrate that a universal antisymmetric error signal, and hence perfect compensation at a finite modulation amplitude, is generated only if an additional frequency step applied during both Ramsey pulses is used as the concomitant variable parameter. This universal technique can be applied to the fields of atomic clocks, high-resolution molecular spectroscopy, magnetically induced and two-photon probing schemes, Ramsey-type mass spectrometry, and the field of precision measurements. Some variants of GABRS can also be applied for rf atomic clocks using coherent-population-trapping-based Ramsey spectroscopy of the two-photon dark resonance.

Polygyny and its fitness consequences for primary and secondary female pied flycatchers

PubMed Central

Huk, Thomas; Winkel, Wolfgang

2006-01-01

In polygynous species with biparental care, the amount of paternal support often varies considerably. In the pied flycatcher (Ficedula hypoleuca), females mated with monogamous males receive more male assistance during the nestling phase than females mated with bigynous males, as the latter have to share their mates with another female. Bigynous males, however, give more support to their primary broods than to their secondary broods. Using a long-term dataset (31 years), the present study revealed that direct reproductive success, i.e. number of fledglings, was lower in females that mated with bigynous males, especially in secondary broods without male assistance, than in females that mated with monogamous males. Secondary broods with male assistance were more affected than primary broods. Female survival was independent of mating status. In primary broods, a delayed compensation for inferior direct reproductive success was found in terms of the number of grandoffspring, a phenomenon that did not occur in secondary broods. Delayed compensation in primary broods refers to indirect effects, i.e. good genes. According to the sexy son hypothesis, genetically superior (i.e. sexy) males may have sons with a higher number of broods belonging to a polygynous breeding status than do sons from broods with a monogamous father. This was indeed the case for sons descending from primary broods, but not for sons descending from secondary broods. PMID:16769641

Which features of primary care affect unscheduled secondary care use? A systematic review

PubMed Central

Huntley, Alyson; Lasserson, Daniel; Wye, Lesley; Morris, Richard; Checkland, Kath; England, Helen; Salisbury, Chris; Purdy, Sarah

2014-01-01

Objectives To conduct a systematic review to identify studies that describe factors and interventions at primary care practice level that impact on levels of utilisation of unscheduled secondary care. Setting Observational studies at primary care practice level. Participants Studies included people of any age of either sex living in Organisation for Economic Co-operation and Development (OECD) countries with any health condition. Primary and secondary outcome measures The primary outcome measure was unscheduled secondary care as measured by emergency department attendance and emergency hospital admissions. Results 48 papers were identified describing potential influencing features on emergency department visits (n=24 studies) and emergency admissions (n=22 studies). Patient factors associated with both outcomes were increased age, reduced socioeconomic status, lower educational attainment, chronic disease and multimorbidity. Features of primary care affecting unscheduled secondary care were more complex. Being able to see the same healthcare professional reduced unscheduled secondary care. Generally, better access was associated with reduced unscheduled care in the USA. Proximity to healthcare provision influenced patterns of use. Evidence relating to quality of care was limited and mixed. Conclusions The majority of research was from different healthcare systems and limited in the extent to which it can inform policy. However, there is evidence that continuity of care is associated with reduced emergency department attendance and emergency hospital admissions. PMID:24860000

Scanning secondary derived crashes from disabled and abandoned vehicle incidents on uninterrupted flow highways.

PubMed

Chimba, Deo; Kutela, Boniphace

2014-09-01

Extent of secondary crashes derived from primary incidents involving abandoned and disabled vehicles are presented in this paper. Using years 2004 to 2010 incident and crash data on selected Tennessee freeways, the study identified secondary crashes that resulted from disabled and abandoned vehicle primary incidents. The relationship between time and distance gaps before the secondary crash with respect to individual incident characteristics were evaluated through descriptive statistics and linear regression. The time and distance gap analysis indicated that a large portion of secondary crashes occurred within 20 min after the primary incidents and within a distance of 0.5 miles upstream. While 76% of incidents involved shoulder, most secondary crashes were related to the closing of right lanes. Overall, 58% of the secondary crashes occurred within 30 min after the occurrence of the primary incidents. Most of the vehicles in the incidents that involved towing and caused secondary crashes were towed or removed out of the travel way within 60 min from the time of occurrence. The study found that most (95%) secondary crashes were property damage only (PDO), while 49% were rear-end crashes. The negative binomial model was used to evaluate the impact of roadway geometry and traffic factors associated with frequency of these secondary crashes. It was found that the posted speed limit, congested segments, segments with high percentages of trucks, and peak hour volumes increased the likelihood of secondary crash occurrence. Roadway segments with wider medians, shoulders, and multilanes decrease the likelihood of secondary crashes caused by abandoned and disabled vehicles as the primary incidents. Practical applications The paper recommends that wider shoulders be provided on any section of freeway to accommodate abandoned or disabled vehicles to avoid blocking of travel lane(s). Copyright © 2014 National Safety Council and Elsevier Ltd. All rights reserved.

Cardiac emergencies and problems of the critical care patient.

PubMed

Marr, Celia M

2004-04-01

Cardiac disease and dysfunction can occur as a primary disorder(ie, with pathology situated in one or more of the cardiac structures) or can be classified as a secondary problem when it occurs in patients with another primary problem that has affected the heart either directly or indirectly. Primary cardiac problems are encountered in horses presented to emergency clinics; however,this occurs much less frequently in equine critical patients than cardiac problems arising secondary to other conditions. Nevertheless,if primary or secondary cardiac problems are not identified and addressed, they certainly contribute to the morbidity and mortality of critical care patients.

[Evaluation and management of hyperhidrosis].

PubMed

Menzinger, Sébastien; Quenan, Sandrine

2017-03-29

Hyperhidrosis is excessive sweating beyond what is expected for thermoregulatory needs. Nearly 3 % of the population has hyperhidrosis. It may be primary or secondary to medications or general medical conditions, including diabetes mellitus, hyperthyroidism, Parkinson disease, etc. History taking and clinical examination are essential to differentiate primary from secondary origins. Blood tests and a consultation with a specialist (endocrinologist, neurologist) is sometimes necessary to establish the diagnosis. The management of secondary hyperhidrosis involves the treatment of the underlying cause. For primary hyperhidrosis, it depends on its severity and the sites affected. This article will review the treatments for primary hyperhidrosis.

Syncom 4 deploy, LDEF retrieval highlight 10-day Columbia flight

NASA Technical Reports Server (NTRS)

1989-01-01

The objectives of Space Shuttle Mission STS-32 are described along with major flight activities, prelaunch and launch operations, trajectory sequence of events, and landing and post-landing operations. The primary objectives of STS-32 are the deployment of a Navy synchronous communications satellite (Syncom 4) and the retrieval of the Long Duration Exposure Facility (LDEF) launched from the Challenger in April 1984. Secondary STS-32 payloads include a protein crystal growth experiment, the Fluids Experiment Apparatus (FEA) for the investigation of microgravity materials processing, the Mesoscale Lighting Experiment, the Latitude-Longitude Locator Experiment, the Americal Flight Echocardiograph, and an experiment to investigate neurospora circadian rhythms in a microgravity environment.

Crater dimensions from apollo data and supplemental sources

USGS Publications Warehouse

Pike, R.J.

1976-01-01

A catalog of crater dimensions that were compiled mostly from the new Apollo-based Lunar Topographic Orthophotomaps is presented in its entirety. Values of crater diameter, depth, rim height, flank width, circularity, and floor diameter (where applicable) are tabulated for a sample of 484 craters on the Moon and 22 craters on Earth. Systematic techniques of mensuration are detailed. The lunar craters range in size from 400 m to 300 km across and include primary impact craters of the main sequence, secondary impact craters, craterlets atop domes and cones, and dark-halo craters. The terrestrial craters are between 10 m and 22.5 km in diameter and were formed by meteorite impact. ?? 1976 D. Reidel Publishing Company.

Improvement of wireless power transmission efficiency of implantable subcutaneous devices by closed magnetic circuit mechanism.

PubMed

Jo, Sung-Eun; Joung, Sanghoon; Suh, Jun-Kyo Francis; Kim, Yong-Jun

2012-09-01

Induction coils were fabricated based on flexible printed circuit board for inductive transcutaneous power transmission. The coil had closed magnetic circuit (CMC) structure consisting of inner and outer magnetic core. The power transmission efficiency of the fabricated device was measured in the air and in vivo condition. It was confirmed that the CMC coil had higher transmission efficiency than typical air-core coil. The power transmission efficiency during a misalignment between primary coil and implanted secondary coil was also evaluated. The decrease of mutual inductance between the two coils caused by the misalignment led to a low efficiency of the inductive link. Therefore, it is important to properly align the primary coil and implanted secondary coil for effective power transmission. To align the coils, a feedback coil was proposed. This was integrated on the backside of the primary coil and enabled the detection of a misalignment of the primary and secondary coils. As a result of using the feedback coil, the primary and secondary coils could be aligned without knowledge of the position of the implanted secondary coil.

On the Study of Cognitive Bidirectional Relaying with Asymmetric Traffic Demands

NASA Astrophysics Data System (ADS)

Ji, Xiaodong

2015-05-01

In this paper, we consider a cognitive radio network scenario, where two primary users want to exchange information with each other and meanwhile, one secondary node wishes to send messages to a cognitive base station. To meet the target quality of service (QoS) of the primary users and raise the communication opportunity of the secondary nodes, a cognitive bidirectional relaying (BDR) scheme is examined. First, system outage probabilities of conventional direct transmission and BDR schemes are presented. Next, a new system parameter called operating region is defined and calculated, which indicates in which position a secondary node can be a cognitive relay to assist the primary users. Then, a cognitive BDR scheme is proposed, giving a transmission protocol along with a time-slot splitting algorithm between the primary and secondary transmissions. Information-theoretic metric of ergodic capacity is studied for the cognitive BDR scheme to evaluate its performance. Simulation results show that with the proposed scheme, the target QoS of the primary users can be guaranteed, while increasing the communication opportunity for the secondary nodes.

[Appraisal of occupational stress and strain in primary and secondary school teachers].

PubMed

Wang, Z; Lan, Y; Li, J; Wang, M

2001-09-01

This study was conducted to assess occupational stress and strain in primary and secondary school teachers. A test of occupational stress and strain was carried out by using Occupational Stress Inventory Revised Edition (OSI-R) in 1460 primary and secondary school teachers (teacher group) and 319 mental workers in non-educational area (non-teacher group as control). The results showed the level of occupational stress in role overload and physical environment in the teacher group was significantly higher than that in the non-teacher group (P < 0.05). In teacher group the level of occupational stress and strain increased with age; the occupational stress and strain in male teachers were significantly higher than those in female teachers (P < 0.01); the occupational stress and strain in secondary school teachers were significantly higher than those in primary school teachers. These results indicate: to protect and promote primary and secondary school teacher's health, particularly male teachers' health, to mitigate their work pressure and to raise the quality of education are important tasks in the area of occupational health.

Email communication at the medical primary-secondary care interface: a qualitative exploration.

PubMed

Sampson, Rod; Barbour, Rosaline; Wilson, Philip

2016-07-01

There is little published research into the influence of email communication between primary and secondary care clinicians on patient care. To explore the use of email communication between clinicians across the primary- secondary care interface, and how this may relate to patient care. A qualitative study involving primary and secondary care services in the NHS Highland Health Board area, Scotland. Ten GPs and 12 hospital consultants were purposively sampled to reflect diversity. Eligible clinicians were invited to take part in a semi-structured interview. Data were analysed using a thematic analysis approach. Key themes that emerged for clinicians included general perceptions of email; using email in practice (managing workload, impact on patient journeys, and 'quick answers'); system issues (variability and governance); relational aspects; and email skills. Email communication between primary and secondary care clinicians generally has a positive impact on patient access to specialist expertise. Governance issues around the use of clinical email need to be defined. There may currently be a two-tier health service for those patients (and their GPs) requiring 'quick answers'. © British Journal of General Practice 2016.

A regional programme to improve skin cancer management.

PubMed

McGeoch, Graham R; Sycamore, Mark J; Shand, Brett I; Simcock, Jeremy W

2015-12-01

In 2008, public specialist and general practice services in Canterbury were unable to manage demand for skin cancer treatment. Local clinicians decided the solution was to develop a see-and-treat skin excision clinic staffed by plastic surgeons and general practitioners (GPs), and the introduction of subsidised excisions in general practice. This paper describes the collaboration between clinicians, managers and funders and the results and quality management measures of these initiatives. There is an increasing incidence of skin cancer. GPs in Canterbury were unable to meet increasing demand for skin cancer treatment because some lacked confidence and competence in skin cancer management. There was no public funding for primary care management of skin cancer, driving patients to fully funded secondary care services. Secondary care services were at capacity, with no coordinated programme across primary and secondary care. The programme has resulted in a greater number of skin cancers being treated by the public health system, a reduction in waiting times for treatment, and fewer minor skin lesions being referred to secondary care. Quality measures have been achieved and are improving steadily. Development of the programme has improved working relationships between primary and secondary care clinicians. The strategy was to facilitate the working relationship between primary and secondary care and increase the capacity for skin lesion excisions in both sectors. Skin cancer management can be improved by a coordinated approach between primary and secondary care.

The transition from primary to secondary school in mainstream education for children with autism spectrum disorder.

PubMed

Mandy, William; Murin, Marianna; Baykaner, Ozlem; Staunton, Sara; Hellriegel, Josselyn; Anderson, Seonaid; Skuse, David

2016-01-01

The transition from primary to secondary education (hereafter 'school transition') is a major ecological shift that poses considerable social, emotional, academic and organisational challenges. It is commonly assumed that this school transition is especially difficult for children with autism spectrum disorder, but that idea is mainly based on anecdotal evidence and requires systematic investigation. We describe change and continuity for children with autism spectrum disorder (N = 28, mean age = 11.29 years, mean full-scale IQ = 87.86) transitioning in mainstream education from primary to secondary school. Levels of psychopathology, adaptive functioning and peer victimisation were measured by parent, self and teacher report in the last year of primary school, and again after one term of secondary school. At follow-up, all participants were still in their secondary school, and there was no evidence for a marked escalation of difficulties during the transition. Instead, we observed high levels of psychopathology and maladaption at baseline which persisted across the transition and were in some cases under-recognised. By parent report, levels of bullying fell from primary to secondary school. Future research should investigate factors, such as school characteristics, that influence the move to secondary education in autism spectrum disorder, to inform the development of interventions to promote successful school transition. © The Author(s) 2015.

Comparison of Global Transcriptional Responses of Chicken Following Primary and Secondary Eimeria acervulina Infections

USDA-ARS?s Scientific Manuscript database

In the current study, we compared chicken gene transcriptional profiles following primary and secondary infections with Eimeria acervulina using a 9.6K avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA). Gene Ontology analysis showed that primary infection significantly modulated ...

Salience of Primary and Secondary Colours in Infancy

ERIC Educational Resources Information Center

Franklin, Anna; Pitchford, Nicola; Hart, Lynsey; Davies, Ian R. L.; Clausse, Samantha; Jennings, Siobhan

2008-01-01

Primary colour terms ("black", "white", "red", "green", "yellow", and "blue") are more fundamental in colour language than secondary colour terms ("pink", "purple", "orange", "brown", and "grey"). Here, we assess whether this distinction exists in the absence of language, by investigating whether primary colours attract and sustain preverbal…

A Population Study of Wide-Separation Brown Dwarf Companions to Main Sequence Stars

NASA Technical Reports Server (NTRS)

Smith, Jeffrey J.

2005-01-01

Increased interest in infrared astronomy has opened the frontier to study cooler objects that shed significant light on the formation of planetary systems. Brown dwarf research provides a wealth of information useful for sorting through a myriad of proposed formation theories. Our study combines observational data from 2MASS with rigorous computer simulations to estimate the true population of long-range (greater than 1000 AU) brown dwarf companions in the solar neighborhood (less than 25 pc from Earth). Expanding on Gizis et al. (2001), we have found the margin of error in previous estimates to be significantly underestimated after we included orbit eccentricity, longitude of pericenter, angle of inclination, field star density, and primary and secondary luminosities as parameters influencing the companion systems in observational studies. We apply our simulation results to current L- and T-dwarf catalogs to provide updated estimates on the frequency of wide-separation brown dwarf companions to main sequence stars.

Colorimetric biosensing of targeted gene sequence using dual nanoparticle platforms

PubMed Central

Thavanathan, Jeevan; Huang, Nay Ming; Thong, Kwai Lin

2015-01-01

We have developed a colorimetric biosensor using a dual platform of gold nanoparticles and graphene oxide sheets for the detection of Salmonella enterica. The presence of the invA gene in S. enterica causes a change in color of the biosensor from its original pinkish-red to a light purplish solution. This occurs through the aggregation of the primary gold nanoparticles–conjugated DNA probe onto the surface of the secondary graphene oxide–conjugated DNA probe through DNA hybridization with the targeted DNA sequence. Spectrophotometry analysis showed a shift in wavelength from 525 nm to 600 nm with 1 μM of DNA target. Specificity testing revealed that the biosensor was able to detect various serovars of the S. enterica while no color change was observed with the other bacterial species. Sensitivity testing revealed the limit of detection was at 1 nM of DNA target. This proves the effectiveness of the biosensor in the detection of S. enterica through DNA hybridization. PMID:25897217

Absolute dimensions and masses of eclipsing binaries. V. IQ Persei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lacy, C.H.; Frueh, M.L.

1985-08-01

New photometric and spectroscopic observations of the 1.7 day eclipsing binary IQ Persei (B8 + A6) have been analyzed to yield very accurate fundamental properties of the system. Reticon spectroscopic observations obtained at McDonald Observatory were used to determine accurate radial velocities of both stars in this slightly eccentric large light-ratio binary. A new set of VR light curves obtained at McDonald Observatory were analyzed by synthesis techniques, and previously published UBV light curves were reanalyzed to yield accurate photometric orbits. Orbital parameters derived from both sets of photometric observations are in excellent agreement. The absolute dimensions, masses, luminosities, andmore » apsidal motion period (140 yr) derived from these observations agree well with the predictions of theoretical stellar evolution models. The A6 secondary is still very close to the zero-age main sequence. The B8 primary is about one-third of the way through its main-sequence evolution. 27 references.« less

The School Malaise Trap Program: Coupling educational outreach with scientific discovery

PubMed Central

Breton, Vanessa; Berzitis, Emily; Hebert, Paul D. N.

2017-01-01

The School Malaise Trap Program (SMTP) provides a technologically sophisticated and scientifically relevant educational experience that exposes students to the diversity of life, enhancing their understanding of biodiversity while promoting environmental stewardship. Since 2013, the SMTP has allowed 15,000 students at 350 primary and secondary schools to explore insect diversity in Canadian schoolyards. Students at each school collected hundreds of insects for an analysis of DNA sequence variation that enabled their rapid identification to a species. Through this hands-on approach, they participated in a learning exercise that conveys a real sense of scientific discovery. As well, the students contributed valuable data to the largest biodiversity genomics initiative ever undertaken: the International Barcode of Life project. To date, the SMTP has sequenced over 80,000 insect specimens, which includes representatives of 7,990 different species, nearly a tenth of the Canadian fauna. Both surprisingly and importantly, the collections generated the first DNA barcode records for 1,288 Canadian species. PMID:28437475

Effect of Compliant Walls on Secondary Instabilities in Boundary-Layer Transition

NASA Technical Reports Server (NTRS)

Joslin, Ronald D.; Morris, Philip J.

1991-01-01

For aerodynamic and hydrodynamic vehicles, it is highly desirable to reduce drag and noise levels. A reduction in drag leads to fuel savings. In particular for submersible vehicles, a decrease in noise levels inhibits detection. A suggested means to obtain these reduction goals is by delaying the transition from laminar to turbulent flow in external boundary layers. For hydrodynamic applications, a passive device which shows promise for transition delays is the compliant coating. In previous studies with a simple mechanical model representing the compliant wall, coatings were found that provided transition delays as predicted from the semi-empirical e(sup n) method. Those studies were concerned with the linear stage of transition where the instability of concern is referred to as the primary instability. For the flat-plate boundary layer, the Tollmien-Schlichting (TS) wave is the primary instability. In one of those studies, it was shown that three-dimensional (3-D) primary instabilities, or oblique waves, could dominate transition over the coatings considered. From the primary instability, the stretching and tilting of vorticity in the shear flow leads to a secondary instability mechanism. This has been theoretical described by Herbert based on Floquet theory. In the present study, Herbert's theory is used to predict the development of secondary instabilities over isotropic and non-isotropic compliant walls. Since oblique waves may be dominant over compliant walls, a secondary theory extention is made to allow for these 3-D primary instabilities. The effect of variations in primary amplitude, spanwise wavenumber, and Reynolds number on the secondary instabilities are examined. As in the rigid wall case, over compliant walls the subharmonic mode of secondary instability dominates for low-amplitude primary disturbances. Both isotropic and non-isotropic compliant walls lead to reduced secondary growth rates compared to the rigid wall results. For high frequencies, the non-isotropic wall suppresses the amplification of the secondary instabilities, while instabilities over the isotropic wall may grow with an explosive rate similar to the rigid wall results. For the more important lower frequencies, both isotropic and non-isotropic compliant walls suppress the amplification of secondary instabilities compared to the rigid wall results. The twofold major discovery and demonstration of the present investigation are: (1) the use of passive devices, such as compliant walls, can lead to significant reductions in the secondary instability growth rates and amplification; (2) suppressing the primary growth rates and subsequent amplification enable delays in the growth of the explosive secondary instability mechanism.

Fibrin promotes development and function of macaque primary follicles during encapsulated three-dimensional culture.

PubMed

Xu, J; Lawson, M S; Yeoman, R R; Molskness, T A; Ting, A Y; Stouffer, R L; Zelinski, M B

2013-08-01

Does fibrin introduced into the extracellular matrix affect the growth and maturation of individual primate follicles during encapsulated three-dimensional (3D) culture? While not altering follicle survival, fibrin-alginate (FIBRIN) improves macaque primary, but not secondary, follicle development during encapsulated 3D culture in terms of growth, steroidogenesis, anti-Müllerian hormone (AMH)/vascular endothelial growth factor (VEGF) production and oocyte maturation. Efforts to grow non-human primate ovarian follicles from the secondary to the antral stage during encapsulated 3D culture have been successful. However, the growth and maturation of primary follicles in vitro has not been reported in primates, especially in chemically defined conditions. In vitro follicle maturation was investigated using the rhesus macaque (Macaca mulatta). Ovaries (n = 7 pairs) were obtained during the early follicular phase of the menstrual cycle (cycle day 1-4). Primary (80-120 µm diameter) and secondary (125-225 µm diameter) follicles were isolated mechanically, randomly assigned to experimental groups, encapsulated into alginate (0.25% w/v) or FIBRIN (25 mg/ml fibrinogen-0.25% alginate) and cultured for 13 and 5 weeks, respectively. Individual follicles were cultured in alpha minimum essential medium supplemented with FSH. Follicle survival and growth were assessed by microscopy. Follicles that reached the antral stage were treated with recombinant hCG. Metaphase II (MII) oocytes were inseminated via ICSI. Follicle morphology was evaluated by hematoxylin and eosin (H&E) staining. Immunohistochemistry was performed for cytochrome P450 family 17 subfamily A polypeptide 1 (CYP17A1) and 19 subfamily A polypeptide 1 (CYP19A1). Culture medium was analyzed for estradiol (E2) and progesterone by chemiluminescence, androstenedione (A4) by radioimmunoassay, as well as anti-Müllerian hormone (AMH) and vascular endothelial growth factor (VEGF) by enzyme-linked immunosorbent assay. A total of 105 primary and 133 secondary follicles were collected. The presence of fibrin in the alginate matrix had no effect on either primary or secondary follicle survival. Growing primary and secondary follicles formed an antrum at Weeks 9 and 3, respectively. The percentage of growing follicles was higher (P < 0.05) for primary follicles cultured in FIBRIN than alginate at Week 13. The diameters were larger for the growing secondary follicles cultured in alginate than FIBRIN at Week 5 (P < 0.05). H&E staining revealed the typical morphology for small antral follicles. CPY17A1 immunostaining was detected in theca cells, while CYP19A1 was observed in granulosa cells. E2 increased (P < 0.05) during antrum formation in growing follicles at Week 9 for primary and Week 3 for secondary follicles. AMH levels in medium from growing primary follicles increased (P < 0.05) after Week 4 with peak levels at Weeks 9-11. AMH increased (P < 0.05) in growing secondary follicles at Weeks 3-5. VEGF levels in medium were elevated (P < 0.05) in growing primary follicles at Week 9. VEGF increased (P < 0.05) in medium from growing secondary follicles at Weeks 3-5. E2, AMH and VEGF production was higher (P < 0.05) in primary follicle culture with FIBRIN than alginate alone. One primary follicle cultured in FIBRIN (1 of 5 follicles harvested) and a secondary follicle cultured in alginate alone (1 of 15 follicles harvested) yielded an MII oocyte. The fertilized oocyte from primary follicle culture arrested without cell division after fertilization, while the oocyte from secondary follicle culture cleaved and reached the morula stage. The study reports on in vitro development and function of individual macaque follicles, that is limited to the interval from the primary and secondary stage to the small antral stage. The findings await translation to human ovarian follicles. The 3D model for primate follicle development offers a unique opportunity to investigate the growth and regulation of primate primary, as well as secondary follicles, and their enclosed oocytes, as they grow to the antral stage by monitoring and manipulating factors or signaling pathways in vitro. Since primate primary follicles, in addition to secondary follicles, can be cultured to the antral stage to provide mature oocytes, they represent an additional source of pre-antral follicles for in vitro follicle maturation with the potential to provide gametes for assisted reproductive technology as an option for fertility preservation in women, including patients with cancer. This work was supported by The Oncofertility Consortium (NIH U54 RR024347-HD058294, PL1-EB008542), NIH U54-HD18185 (Eunice Kennedy Shriver Specialized Cooperative Centers Program in Reproduction and Infertility Research), NIH ORWH/NICHD 2K12HD043488 (BIRCWH), Oregon National Primate Research Center 8P51OD011092. There are no conflicts of interest.

Dielectrokinetic chromatography devices

DOEpatents

Chirica, Gabriela S; Fiechtner, Gregory J; Singh, Anup K

2014-12-16

Disclosed herein are methods and devices for dielectrokinetic chromatography. As disclosed, the devices comprise microchannels having at least one perturber which produces a non-uniformity in a field spanning the width of the microchannel. The interaction of the field non-uniformity with a perturber produces a secondary flow which competes with a primary flow. By decreasing the size of the perturber the secondary flow becomes significant for particles/analytes in the nanometer-size range. Depending on the nature of a particle/analyte present in the fluid and its interaction with the primary flow and the secondary flow, the analyte may be retained or redirected. The composition of the primary flow can be varied to affect the magnitude of primary and/or secondary flows on the particles/analytes and thereby separate and concentrate it from other particles/analytes.

Dielectrokinetic chromatography and devices thereof

DOEpatents

Chirica, Gabriela S; Fiechtner, Gregory J; Singh, Anup K

2014-04-22

Disclosed herein are methods and devices for dielectrokinetic chromatography. As disclosed, the devices comprise microchannels having at least one perturber which produces a non-uniformity in a field spanning the width of the microchannel. The interaction of the field non-uniformity with a perturber produces a secondary flow which competes with a primary flow. By decreasing the size of the perturber the secondary flow becomes significant for particles/analytes in the nanometer-size range. Depending on the nature of a particle/analyte present in the fluid and its interaction with the primary flow and the secondary flow, the analyte may be retained or redirected. The composition of the primary flow can be varied to affect the magnitude of primary and/or secondary flows on the particles/analytes and thereby separate and concentrate it from other particles/analytes.

Method and system for low-NO.sub.x dual-fuel combustion of liquid and/or gaseous fuels

DOEpatents

Gard, Vincent; Chojnacki, Dennis A; Rabovitser, Ioseph K

2014-12-02

A method and apparatus for combustion in which a pressurized preheated liquid fuel is atomized and a portion thereof flash vaporized, creating a mixture of fuel vapor and liquid droplets. The mixture is mixed with primary combustion oxidant, producing a fuel/primary oxidant mixture which is then injected into a primary combustion chamber in which the fuel/primary oxidant mixture is partially combusted, producing a secondary gaseous fuel containing hydrogen and carbon oxides. The secondary gaseous fuel is mixed with a secondary combustion oxidant and injected into the second combustion chamber wherein complete combustion of the secondary gaseous fuel is carried out. The resulting second stage flue gas containing very low amounts of NO.sub.x is then vented from the second combustion chamber.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aronhime, Natan; Zoghlin, Eli; Keylin, Vladimir

Fe-Ni based metal amorphous nanocomposites (MANCs) are investigated in the pseudo-binary alloys (Fe 100–xNi x) 80Nb 4Si 2B 14. To optimize the soft magnetic properties of the nanocomposites, primary and secondary crystallization kinetics must be understood. As such, primary and secondary crystallization temperatures are determined by differential scanning calorimetry, and activation energies are calculated, along with the resulting crystalline phases. Time-temperature-transformation diagrams for primary and secondary crystallization in (Fe 70Ni 30) 80Nb 4Si 2B 14 are presented. Saturation magnetization and Curie temperature are determined. In conclusion, the shape of magnetization vs. time curves for (Fe 30Ni 70) 80Nb 4Si 2Bmore » 14 at various temperatures suggest that the secondary crystal product often consumes some of the primary crystalline product.« less

Aged particles derived from emissions of coal-fired power plants: The TERESA field results

PubMed Central

Kang, Choong-Min; Gupta, Tarun; Ruiz, Pablo A.; Wolfson, Jack M.; Ferguson, Stephen T.; Lawrence, Joy E.; Rohr, Annette C.; Godleski, John; Koutrakis, Petros

2013-01-01

The Toxicological Evaluation of Realistic Emissions Source Aerosols (TERESA) study was carried out at three US coal-fired power plants to investigate the potential toxicological effects of primary and photochemically aged (secondary) particles using in situ stack emissions. The exposure system designed successfully simulated chemical reactions that power plant emissions undergo in a plume during transport from the stack to receptor areas (e.g., urban areas). Test atmospheres developed for toxicological experiments included scenarios to simulate a sequence of atmospheric reactions that can occur in a plume: (1) primary emissions only; (2) H2SO4 aerosol from oxidation of SO2; (3) H2SO4 aerosol neutralized by gas-phase NH3; (4) neutralized H2SO4 with secondary organic aerosol (SOA) formed by the reaction of α-pinene with O3; and (5) three control scenarios excluding primary particles. The aged particle mass concentrations varied significantly from 43.8 to 257.1 μg/m3 with respect to scenario and power plant. The highest was found when oxidized aerosols were neutralized by gas-phase NH3 with added SOA. The mass concentration depended primarily on the ratio of SO2 to NOx (particularly NO) emissions, which was determined mainly by coal composition and emissions controls. Particulate sulfate (H2SO4 + neutralized sulfate) and organic carbon (OC) were major components of the aged particles with added SOA, whereas trace elements were present at very low concentrations. Physical and chemical properties of aged particles appear to be influenced by coal type, emissions controls and the particular atmospheric scenarios employed. PMID:20462390

An Analysis of Cryptographically Significant Boolean Functions With High Correlation Immunity by Reconfigurable Computer

DTIC Science & Technology

2010-12-01

with high correlation immunity and then evaluate these functions for other desirable cryptographic features. C. METHOD The only known primary methods...out if not used) # ---------------------------------- # PRIMARY = < primary file 1> < primary file 2> #SECONDARY = <secondary file 1...finding the fuction value for a //set u and for each value of v. end end

The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition.

PubMed

Jauch, Ralf; Ng, Calista K L; Narasimhan, Kamesh; Kolatkar, Prasanna R

2012-04-01

It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.

Public's Views toward Return of Secondary Results in Genomic Sequencing: It's (Almost) All about the Choice.

PubMed

Ryan, Kerry A; De Vries, Raymond G; Uhlmann, Wendy R; Roberts, J Scott; Gornick, Michele C

2017-12-01

The therapeutic use of genomic sequencing creates novel and unresolved questions about cost, clinical efficacy, access, and the disclosure of sequencing results. The disclosure of the secondary results of sequencing poses a particularly challenging ethical problem. Experts disagree about which results should be shared and public input - especially important for the creation of disclosure policies - is complicated by the complex nature of genetics. Recognizing the value of deliberative democratic methods for soliciting informed public opinion on matters like these, we recruited participants from a clinical research site for an all-day deliberative democracy (DD) session. Participants were introduced to the clinical and ethical issues associated with genomic sequencing, after which they discussed the tradeoffs and offered their opinions about policies for the return of secondary results. Participants (n = 66; mean age = 57 (SD = 15); 70% female; 76% white) were divided into 10 small groups (5 to 8 participants each) allowing interactive deliberation on policy options for the return of three categories of secondary results: 1) medically actionable results; 2) risks for adult-onset disorders identified in children; and 3) carrier status for autosomal recessive disorders. In our qualitative analysis of the session transcripts, we found that while participants favored choice and had a preference for making information available, they also acknowledged the risks (and benefits) of learning such information. Our research reveals the nuanced reasoning used by members of the public when weighing the pros and cons of receiving genomic information, enriching our understanding of the findings of surveys of attitudes regarding access to secondary results.

Comparison of breeding bird and vegetation communities in primary and secondary forests of Great Smoky Mountains National Park

USGS Publications Warehouse

Simons, Theodore R.; Shriner, Susan A.; Farnsworth, George L.

2006-01-01

We compared breeding bird communities and vegetation characteristics at paired point locations in primary (undisturbed) and mature secondary forest (70-100 years old) sites in Great Smoky Mountains National Park, USA to understand how sites logged prior to creation of the park compare to undisturbed sites following 70 years of protection from human disturbance. We found that bird and vegetation communities are currently similar, but retain some differences in species composition. Rank abundance curves for primary and secondary forest bird communities showed very similar patterns of species dominance. Species composition was also similar on the two sites which shared 24 of the 25 most frequently recorded species. Nonetheless, comparisons of density estimates derived from distance sampling showed three bird species were more abundant on primary forest sites and that one bird species was significantly more abundant on secondary forest sites. Notably, comparisons based on raw counts (unadjusted for potential differences in detectability) produced somewhat different results. Analyses of vegetation samples for the paired sites also showed relative similarity, but with some differences between primary and secondary forests. Primary forest sites had more large trees (trees greater than 50 cm diameter at breast height) and late successional species. Primary forest sites had a denser tall shrub layer while secondary forest sites had a denser canopy layer. Nonetheless, tree species richness, basal area of live trees and number of standing snags did not differ between primary and secondary forest sites. Results indicate that breeding bird communities on sites within the park that were logged commercially 70 years ago are currently quite similar to bird communities on sites with no history of human disturbance. Similarities between the bird communities on previously disturbed and undisturbed sites in Great Smoky Mountains National Park may exceed those on more fragmented landscapes because large patches of primary forest, adjacent to commercially logged sites, remained in the park when it was established in 1935. These patches of primary forest may have served as source areas for commercially logged sites.

Variants in Nebulin (NEB) Are Linked to the Development of Familial Primary Angle Closure Glaucoma in Basset Hounds

PubMed Central

Ahram, Dina F.; Grozdanic, Sinisa D.; Kecova, Helga; Henkes, Arjen; Collin, Rob W. J.; Kuehn, Markus H.

2015-01-01

Several dog breeds are susceptible to developing primary angle closure glaucoma (PACG), which suggests a genetic basis for the disease. We have identified a four-generation Basset Hound pedigree with characteristic autosomal recessive PACG that closely recapitulates PACG in humans. Our aim is to utilize gene mapping and whole exome sequencing approaches to identify PACG-causing sequence variants in the Basset. Extensive clinical phenotyping of all pedigree members was conducted. SNP-chip genotyping was carried out in 9 affected and 15 unaffected pedigree members. Two-point and multipoint linkage analyses of genome-wide SNP data were performed using Superlink-Online SNP-1.1 and a locus was mapped to chromosome 19q with a maximum LOD score of 3.24. The locus contains 12 Ensemble predicted canine genes and is syntenic to a region on chromosome 2 in the human genome. Using exome-sequencing analysis, a possibly damaging, non-synonymous variant in the gene Nebulin (NEB) was found to segregate with PACG which alters a phylogenetically conserved Lysine residue. The association of this variants with PACG was confirmed in a secondary cohort of unrelated Basset Hounds (p = 3.4 × 10-4, OR = 15.3 for homozygosity). Nebulin, a protein that promotes the contractile function of sarcomeres, was found to be prominently expressed in the ciliary muscles of the anterior segment. Our findings may provide insight into the molecular mechanisms that underlie PACG. The phenotypic similarities of disease presentation in dogs and humans may enable the translation of findings made in this study to patients with PACG. PMID:25938837

Variants in Nebulin (NEB) Are Linked to the Development of Familial Primary Angle Closure Glaucoma in Basset Hounds.

PubMed

Ahram, Dina F; Grozdanic, Sinisa D; Kecova, Helga; Henkes, Arjen; Collin, Rob W J; Kuehn, Markus H

2015-01-01

Several dog breeds are susceptible to developing primary angle closure glaucoma (PACG), which suggests a genetic basis for the disease. We have identified a four-generation Basset Hound pedigree with characteristic autosomal recessive PACG that closely recapitulates PACG in humans. Our aim is to utilize gene mapping and whole exome sequencing approaches to identify PACG-causing sequence variants in the Basset. Extensive clinical phenotyping of all pedigree members was conducted. SNP-chip genotyping was carried out in 9 affected and 15 unaffected pedigree members. Two-point and multipoint linkage analyses of genome-wide SNP data were performed using Superlink-Online SNP-1.1 and a locus was mapped to chromosome 19q with a maximum LOD score of 3.24. The locus contains 12 Ensemble predicted canine genes and is syntenic to a region on chromosome 2 in the human genome. Using exome-sequencing analysis, a possibly damaging, non-synonymous variant in the gene Nebulin (NEB) was found to segregate with PACG which alters a phylogenetically conserved Lysine residue. The association of this variants with PACG was confirmed in a secondary cohort of unrelated Basset Hounds (p = 3.4 × 10-4, OR = 15.3 for homozygosity). Nebulin, a protein that promotes the contractile function of sarcomeres, was found to be prominently expressed in the ciliary muscles of the anterior segment. Our findings may provide insight into the molecular mechanisms that underlie PACG. The phenotypic similarities of disease presentation in dogs and humans may enable the translation of findings made in this study to patients with PACG.

Adapted cuing technique: facilitating sequential phoneme production.

PubMed

Klick, S L

1994-09-01

ACT is a visual cuing technique designed to facilitate dyspraxic speech by highlighting the sequential production of phonemes. In using ACT, cues are presented in such a way as to suggest sequential, coarticulatory movement in an overall pattern of motion. While using ACT, the facilitator's hand moves forward and back along the side of her (or his) own face. Finger movements signal specific speech sounds in formations loosely based on the manual alphabet for the hearing impaired. The best movements suggest the flowing, interactive nature of coarticulated phonemes. The synergistic nature of speech is suggested by coordinated hand motions which tighten and relax, move quickly or slowly, reflecting the motions of the vocal tract at various points during production of phonemic sequences. General principles involved in using ACT include a primary focus on speech-in-motion, the monitoring and fading of cues, and the presentation of stimuli based on motor-task analysis of phonemic sequences. Phonemic sequences are cued along three dimensions: place, manner, and vowel-related mandibular motion. Cuing vowels is a central feature of ACT. Two parameters of vowel production, focal point of resonance and mandibular closure, are cued. The facilitator's hand motions reflect the changing shape of the vocal tract and the trajectory of the tongue that result from the coarticulation of vowels and consonants. Rigid presentation of the phonemes is secondary to the facilitator's primary focus on presenting the overall sequential movement. The facilitator's goal is to self-tailor ACT in response to the changing needs and abilities of the client.(ABSTRACT TRUNCATED AT 250 WORDS)

Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.

PubMed

Lorenzo, J Ramiro; Alonso, Leonardo G; Sánchez, Ignacio E

2015-01-01

Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".

Primary and Secondary Control among Children Undergoing Medical Procedures: Adjustment as a Function of Coping Style.

ERIC Educational Resources Information Center

Weisz, John R.; And Others

1994-01-01

Obtained reports of coping and goals from 33 children being treated for leukemia. Coping strategies were classified as primary control coping (attempts to alter objective conditions), secondary control coping (attempts to adjust to objective conditions), or relinquished control (no attempt to cope). Secondary control coping was positively…

Using Design-Based Research to Improve the Lesson Study Approach to Professional Development in Camden (London)

ERIC Educational Resources Information Center

Brown, Chris; Taylor, Carol; Ponambalum, Lorna

2016-01-01

The Haverstock Primary to Secondary Transition Project was designed to improve the experience of transition to secondary school for vulnerable pupils in Camden (London). The project used lesson study to help primary and secondary practitioners work collaboratively, to develop effective cross-phase pedagogical approaches to teaching…

OUTLINE OF VOCATIONAL TRAINING IN SINGAPORE.

ERIC Educational Resources Information Center

Australian Dept. of Labour and National Service, Perth.

IN 1964 SINGAPORE HAD A POPULATION OF 1,844,200. EDUCATION IS FREE FOR THE 6 PRIMARY YEARS. SUCCESSFUL STUDENTS ATTEND AN ACADEMIC SECONDARY, A SECONDARY COMMERCIAL, OR A SECONDARY TECHNICAL SCHOOL. A 2-YEAR PREUNIVERSITY, A POLYTECHNIC, AND A TEACHERS' COLLEGE ARE ALSO AVAILABLE. UNSUCCESSFUL PRIMARY STUDENTS RECEIVE 2 YEARS ADDITIONAL WORK AT A…

Numerical simulations of primary and secondary hydrogen ENA fluxes at 1 AU

DOE PAGES

Zirnstein, Eric; Heerikhuisen, Jacob; Pogorelov, Nikolai

2012-11-20

The interaction between the solar wind (SW) and the local interstellar medium (LISM) creates energetic neutral atoms (ENAs), mainly Hydrogen (H), at energies similar to ions in the SW. H ENAs are born from charge exchanges between SW protons and LISM H atoms. A large portion of measurable primary ENAs are born in the inner heliosheath (IHS), where the heated and condensed SW plasma has a large thermal component to direct ENAs back toward 1 AU. Secondary ENAs, however, require secondary charge exchanges before being detected at 1 AU. Primary ENAs born in the supersonic and subsonic SW may exitmore » the HP, charge exchange into pick-up ions (PUIs), and charge exchange again to become secondary ENAs. Recent IBEX observations show a ribbon of flux dominating the entire sky. It is possible that the IBEX ribbon is created through secondary charge exchange processes. In this article we present a numerical code that calculates primary and secondary H ENA fluxes by integrating along ENA trajectories. Here we will provide descriptions of the code and preliminary results.« less

Early presentation of primary glioblastoma.

PubMed

Faguer, R; Tanguy, J-Y; Rousseau, A; Clavreul, A; Menei, P

2014-08-01

Clinical and neuroimaging findings of glioblastomas (GBM) at an early stage have rarely been described and those tumors are most probably under-diagnosed. Furthermore, their genetic alterations, to our knowledge, have never been previously reported. We report the clinical as well as neuroimaging findings of four early cases of patients with GBM. In our series, early stage GBM occurred at a mean age of 57 years. All patients had seizures as their first symptom. In all early stages, MRI showed a hyperintense signal on T2-weighted sequences and an enhancement on GdE-T1WI sequences. A hyperintense signal on diffusion sequences with a low ADC value was also found. These early observed occurrences of GBM developed rapidly and presented the MRI characteristics of classic GBM within a few weeks. The GBM size was multiplied by 32 in one month. Immunohistochemical analysis indicated the de novo nature of these tumors, i.e. absence of mutant IDH1 R132H protein expression, which is a diagnostic marker of low-grade diffuse glioma and secondary GBM. A better knowledge of early GBM presentation would allow a more suitable management of the patients and may improve their prognosis. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations

PubMed Central

Bodini, Margherita; Ronchini, Chiara; Giacò, Luciano; Russo, Anna; Melloni, Giorgio E. M.; Luzi, Lucilla; Sardella, Domenico; Volorio, Sara; Hasan, Syed K.; Ottone, Tiziana; Lavorgna, Serena; Lo-Coco, Francesco; Candoni, Anna; Fanin, Renato; Toffoletti, Eleonora; Iacobucci, Ilaria; Martinelli, Giovanni; Cignetti, Alessandro; Tarella, Corrado; Bernard, Loris; Pelicci, Pier Giuseppe

2015-01-01

The analyses carried out using 2 different bioinformatics pipelines (SomaticSniper and MuTect) on the same set of genomic data from 133 acute myeloid leukemia (AML) patients, sequenced inside the Cancer Genome Atlas project, gave discrepant results. We subsequently tested these 2 variant-calling pipelines on 20 leukemia samples from our series (19 primary AMLs and 1 secondary AML). By validating many of the predicted somatic variants (variant allele frequencies ranging from 100% to 5%), we observed significantly different calling efficiencies. In particular, despite relatively high specificity, sensitivity was poor in both pipelines resulting in a high rate of false negatives. Our findings raise the possibility that landscapes of AML genomes might be more complex than previously reported and characterized by the presence of hundreds of genes mutated at low variant allele frequency, suggesting that the application of genome sequencing to the clinic requires a careful and critical evaluation. We think that improvements in technology and workflow standardization, through the generation of clear experimental and bioinformatics guidelines, are fundamental to translate the use of next-generation sequencing from research to the clinic and to transform genomic information into better diagnosis and outcomes for the patient. PMID:25499761

Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins.

PubMed

Raimondi, Daniele; Orlando, Gabriele; Pancsa, Rita; Khan, Taushif; Vranken, Wim F

2017-08-18

Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities as features. The EFoldMine predictions give insights into the folding process, as illustrated by a qualitative comparison with independent experimental observations. Furthermore, on a quantitative proteome scale, the predicted early folding residues tend to become the residues that interact the most in the folded structure, and they are often residues that display evolutionary covariation. The connection of the EFoldMine predictions with both folding pathway data and the folded protein structure suggests that the initial statistical behavior of the protein chain with respect to local structure formation has a lasting effect on its subsequent states.

Mapping PDB chains to UniProtKB entries.

PubMed

Martin, Andrew C R

2005-12-01

UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file. We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping. The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.

Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils.

PubMed

Ranjan, Kshitij; Paula, Fabiana S; Mueller, Rebecca C; Jesus, Ederson da C; Cenciani, Karina; Bohannan, Brendan J M; Nüsslein, Klaus; Rodrigues, Jorge L M

2015-01-01

The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils.

Forest-to-pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils

PubMed Central

Ranjan, Kshitij; Paula, Fabiana S.; Mueller, Rebecca C.; Jesus, Ederson da C.; Cenciani, Karina; Bohannan, Brendan J. M.; Nüsslein, Klaus; Rodrigues, Jorge L. M.

2015-01-01

The Amazon rainforest is well known for its rich plant and animal diversity, but its bacterial diversity is virtually unexplored. Due to ongoing and widespread deforestation followed by conversion to agriculture, there is an urgent need to quantify the soil biological diversity within this tropical ecosystem. Given the abundance of the phylum Verrucomicrobia in soils, we targeted this group to examine its response to forest-to-pasture conversion. Both taxonomic and phylogenetic diversities were higher for pasture in comparison to primary and secondary forests. The community composition of Verrucomicrobia in pasture soils was significantly different from those of forests, with a 11.6% increase in the number of sequences belonging to subphylum 3 and a proportional decrease in sequences belonging to the class Spartobacteria. Based on 99% operational taxonomic unit identity, 40% of the sequences have not been detected in previous studies, underscoring the limited knowledge regarding the diversity of microorganisms in tropical ecosystems. The abundance of Verrucomicrobia, measured with quantitative PCR, was strongly correlated with soil C content (r = 0.80, P = 0.0016), indicating their importance in metabolizing plant-derived carbon compounds in soils. PMID:26284056

Molecular taxonomy of Dunaliella (Chlorophyceae), with a special focus on D. salina: ITS2 sequences revisited with an extensive geographical sampling

PubMed Central

2012-01-01

We used an ITS2 primary and secondary structure and Compensatory Base Changes (CBCs) analyses on new French and Spanish Dunallela salina strains to investigate their phylogenetic position and taxonomic status within the genus Dunaliella. Our analyses show a great diversity within D. salina (with only some clades not statistically supported) and reveal considerable genetic diversity and structure within Dunaliella, although the CBC analysis did not bolster the existence of different biological groups within this taxon. The ITS2 sequences of the new Spanish and French D. salina strains were very similar except for two of them: ITC5105 "Janubio" from Spain and ITC5119 from France. Although the Spanish one had a unique ITS2 sequence profile and the phylogenetic tree indicates that this strain can represent a new species, this hypothesis was not confirmed by CBCs, and clarification of its taxonomic status requires further investigation with new data. Overall, the use of CBCs to define species boundaries within Dunaliella was not conclusive in some cases, and the ITS2 region does not contain a geographical signal overall. PMID:22520929

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

PubMed

Utturkar, Sagar M; Klingeman, Dawn M; Hurt, Richard A; Brown, Steven D

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

Heavy metals in sediments, soils, and aquatic plants from a secondary anabranch of the three gorges reservoir region, China.

PubMed

Gao, Jun-Min; Sun, Xiu-Qian; Jiang, Wen-Chao; Wei, Yun-Mei; Guo, Jin-Song; Liu, Yuan-Yuan; Zhang, Ke

2016-06-01

We investigated the occurrence of cadmium (Cd), copper (Cu), chromium (Cr), nickel (Ni), lead (Pb), Znic (Zn), iron (Fe), manganese (Mn), and magnesium (Mg) in sediments, as well as in related soils and aquatic plants in the Liangtan River, a typical secondary anabranch of the Yangtze River in the Three Gorges Reservoir Region (TGRR) of China. We found that sediments accumulated more metals than soils and aquatic plants. Concentrations of the nine metals in sediments and soils followed the same sequence, while their concentrations in aquatic plants followed a different sequence. Potential adverse effects of contaminated sediments on benthic fauna were evaluated, and the results showed that the toxic effect on benthic organisms followed the sequence Zn > Ni > Cr > Cu > Cd > Pb. The potential ecological risk index analysis indicated that Cd in sediments had considerable ecological risk, whereas Cr, Cu, Zn, Ni, and Pb had low ecological risk. The potential ecological risk index (RI) of the heavy metals in sediments of the Liangtan River was 174.9, indicating moderate ecological risk. The transfer factor trend of metals for aquatic plants showed that Cd and Ni had the most and least accumulation, respectively. For Cu, Cd, Mg, Pb, and Cr, a significant positive correlation of the metal concentrations was observed between sediments and soils, but no correlations (excluding Cr) were detected between sediments and aquatic plants. Our study indicated that anthropogenic input may be the primary source of metal contamination in the Liangtan River, and that Zn and Cd pollution in the Liangtan River should be further explored.

Nanolayered Features of Collagen-like Peptides

NASA Technical Reports Server (NTRS)

Valluzzi, Regina; Bini, Elisabetta; Haas, Terry; Cebe, Peggy; Kaplan, David L.

2003-01-01

We have been investigating collagen-like model oligopeptides as molecular bases for complex ordered biomimetic materials. The collagen-like molecules incorporate aspects of native collagen sequence and secondary structure. Designed modifications to native primary and secondary structure have been incorporated to control the nanostructure and microstructure of the collagen-like materials produced. We find that the collagen-like molecules form a number of lyotropic rod liquid crystalline phases, which because of their strong temperature dependence in the liquid state can also be viewed as solvent intercalated thermotropic liquid crystals. The liquid crystalline phases formed by the molecules can be captured in the solid state by drying off solvent, resulting in solid nanopatterned (chemically and physically) thermally stable (to greater than 100 C) materials. Designed sequences which stabilize smectic phases have allowed a variety of nanoscale multilayered biopolymeric materials to be developed. Preliminary investigations suggest that chemical patterns running perpendicular to the smectic layer plane can be functionalized and used to localize a variety of organic, inorganic, and organometallic moieties in very simple multilayered nanocomposites. The phase behavior of collagen-like oligopeptide materials is described, emphasizing the correlation between mesophase, molecular orientation, and chemical patterning at the microscale and nanoscale. In many cases, the textures observed for smectic and hexatic phase collagens are remarkably similar to the complex (and not fully understood) helicoids observed in biological collagen-based tissues. Comparisons between biological morphologies and collagen model liquid crystalline (and solidified materials) textures may help us understand the molecular features which impart order and function to the extracellular matrix and to collagen-based mineralized tissues. Initial studies have utilized synthetic collagen-like peptides while future work will also focus on similar sequences generated via genetic engineering methods.

Secondary stressors and extreme events and disasters: a systematic review of primary research from 2010-2011.

PubMed

Lock, Sarah; Rubin, G James; Murray, Virginia; Rogers, M Brooke; Amlôt, Richard; Williams, Richard

2012-10-29

Introduction Extreme events and disasters, such as earthquakes and floods, cause distress and are associated with some people developing mental disorders. Primary stressors inherent in many disasters can include injuries sustained or watching someone die. The literature recognises the distress which primary stressors cause and their association with mental disorders. Secondary stressors such as a lack of financial assistance, the gruelling process of submitting an insurance claim, parents' worries about their children, and continued lack of infrastructure can manifest their effects shortly after a disaster and persist for extended periods of time. Secondary stressors, and their roles in affecting people's longer-term mental health, should not be overlooked. We draw attention in this review to the nature of secondary stressors that are commonly identified in the literature, assess how they are measured, and develop a typology of these stressors that often affect people after extreme events. Methods We searched for relevant papers from 2010 and 2011 using MEDLINE®, Embase and PsycINFO®. We selected primary research papers that evaluated the associations between secondary stressors and distress or mental disorders following extreme events, and were published in English. We extracted information on which secondary stressors were assessed, and used thematic analysis to group the secondary stressors into a typology. Results Thirty-two relevant articles published in 2010 and 2011 were identified. Many secondary stressors were poorly defined and difficult to differentiate from primary stressors or other life events. We identified 11 categories of secondary stressors, though some extend over more than one category. The categories include: economic stressors such as problems with compensation, recovery of and rebuilding homes; loss of physical possessions and resources; health-related stressors; stress relating to education and schooling; stress arising from media reporting; family and social stressors; stress arising from loss of leisure and recreation; and stress related to changes in people's views of the world or themselves. Limitations in this review include its focus on studies published in 2010 and 2011, which may have led to some secondary stressors being excluded. Assumptions have been made about whether certain items are secondary stressors, if unclear definitions made it difficult to differentiate them from primary stressors. Conclusions This is the first review, to our knowledge, that has developed a typology of secondary stressors that occur following extreme events. We discuss the differing natures of these stressors and the criteria that should be used to differentiate primary and secondary stressors. Some secondary stressors, for example, are entities in themselves, while others are persisting primary stressors that exert their effects through failure of societal responses to disasters to mitigate their immediate impacts. Future research should aim to define secondary stressors and investigate the interactions between stressors. This is essential if we are to identify which secondary stressors are amenable to interventions which might reduce their impacts on the psychosocial resilience and mental health of people who are affected by disasters. Corresponding Author: Dr Sarah Lock, Extreme Events and Health Protection, London, 151 Buckingham Palace Road, London, SW1W 9SZ. E-mail: sarah.lock@hpa.org.uk.

Secondary stressors and extreme events and disasters: a systematic review of primary research from 2010-2011

PubMed Central

Lock, Sarah; Rubin, G. James; Murray, Virginia; Rogers, M. Brooke; Amlôt, Richard; Williams, Richard

2012-01-01

Introduction Extreme events and disasters, such as earthquakes and floods, cause distress and are associated with some people developing mental disorders. Primary stressors inherent in many disasters can include injuries sustained or watching someone die. The literature recognises the distress which primary stressors cause and their association with mental disorders. Secondary stressors such as a lack of financial assistance, the gruelling process of submitting an insurance claim, parents’ worries about their children, and continued lack of infrastructure can manifest their effects shortly after a disaster and persist for extended periods of time. Secondary stressors, and their roles in affecting people’s longer-term mental health, should not be overlooked. We draw attention in this review to the nature of secondary stressors that are commonly identified in the literature, assess how they are measured, and develop a typology of these stressors that often affect people after extreme events. Methods We searched for relevant papers from 2010 and 2011 using MEDLINE®, Embase and PsycINFO®. We selected primary research papers that evaluated the associations between secondary stressors and distress or mental disorders following extreme events, and were published in English. We extracted information on which secondary stressors were assessed, and used thematic analysis to group the secondary stressors into a typology. Results Thirty-two relevant articles published in 2010 and 2011 were identified. Many secondary stressors were poorly defined and difficult to differentiate from primary stressors or other life events. We identified 11 categories of secondary stressors, though some extend over more than one category. The categories include: economic stressors such as problems with compensation, recovery of and rebuilding homes; loss of physical possessions and resources; health-related stressors; stress relating to education and schooling; stress arising from media reporting; family and social stressors; stress arising from loss of leisure and recreation; and stress related to changes in people’s views of the world or themselves. Limitations in this review include its focus on studies published in 2010 and 2011, which may have led to some secondary stressors being excluded. Assumptions have been made about whether certain items are secondary stressors, if unclear definitions made it difficult to differentiate them from primary stressors. Conclusions This is the first review, to our knowledge, that has developed a typology of secondary stressors that occur following extreme events. We discuss the differing natures of these stressors and the criteria that should be used to differentiate primary and secondary stressors. Some secondary stressors, for example, are entities in themselves, while others are persisting primary stressors that exert their effects through failure of societal responses to disasters to mitigate their immediate impacts. Future research should aim to define secondary stressors and investigate the interactions between stressors. This is essential if we are to identify which secondary stressors are amenable to interventions which might reduce their impacts on the psychosocial resilience and mental health of people who are affected by disasters. Corresponding Author: Dr Sarah Lock, Extreme Events and Health Protection, London, 151 Buckingham Palace Road, London, SW1W 9SZ. E-mail: sarah.lock@hpa.org.uk PMID:23145350

Secondary ion emission from phosphatidic acid sandwich films under atomic and molecular primary ion bombardment

NASA Astrophysics Data System (ADS)

Stapel, D.; Benninghoven, A.

2001-11-01

Secondary ion yields increase considerably when changing from atomic to molecular primary ions. Since secondary ion emission from deeper layers could result in a pronounced yield increase, the secondary ion emission depth of molecular fragments was investigated. A phosphatidic acid Langmuir-Blodgett (LB) sandwich system was applied. The well-defined layer structure of the applied sample allows the assignment of different depths of origin to the selected fragment ions. At least 93% of the detected characteristic molecular fragment ions originate from the first and second layers. This holds true for all applied atomic and molecular primary ions.