APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data.

PubMed

Ye, Congting; Long, Yuqi; Ji, Guoli; Li, Qingshun Quinn; Wu, Xiaohui

2018-06-01

Alternative polyadenylation (APA) has been increasingly recognized as a crucial mechanism that contributes to transcriptome diversity and gene expression regulation. As RNA-seq has become a routine protocol for transcriptome analysis, it is of great interest to leverage such unprecedented collection of RNA-seq data by new computational methods to extract and quantify APA dynamics in these transcriptomes. However, research progress in this area has been relatively limited. Conventional methods rely on either transcript assembly to determine transcript 3' ends or annotated poly(A) sites. Moreover, they can neither identify more than two poly(A) sites in a gene nor detect dynamic APA site usage considering more than two poly(A) sites. We developed an approach called APAtrap based on the mean squared error model to identify and quantify APA sites from RNA-seq data. APAtrap is capable of identifying novel 3' UTRs and 3' UTR extensions, which contributes to locating potential poly(A) sites in previously overlooked regions and improving genome annotations. APAtrap also aims to tally all potential poly(A) sites and detect genes with differential APA site usages between conditions. Extensive comparisons of APAtrap with two other latest methods, ChangePoint and DaPars, using various RNA-seq datasets from simulation studies, human and Arabidopsis demonstrate the efficacy and flexibility of APAtrap for any organisms with an annotated genome. Freely available for download at https://apatrap.sourceforge.io. liqq@xmu.edu.cn or xhuister@xmu.edu.cn. Supplementary data are available at Bioinformatics online.

Microarray Meta-Analysis of RNA-Binding Protein Functions in Alternative Polyadenylation

PubMed Central

Hu, Wenchao; Liu, Yuting; Yan, Jun

2014-01-01

Alternative polyadenylation (APA) is a post-transcriptional mechanism to generate diverse mRNA transcripts with different 3′UTRs from the same gene. In this study, we systematically searched for the APA events with differential expression in public mouse microarray data. Hundreds of genes with over-represented differential APA events and the corresponding experiments were identified. We further revealed that global APA differential expression occurred prevalently in tissues such as brain comparing to peripheral tissues, and biological processes such as development, differentiation and immune responses. Interestingly, we also observed widespread differential APA events in RNA-binding protein (RBP) genes such as Rbm3, Eif4e2 and Elavl1. Given the fact that RBPs are considered as the main regulators of differential APA expression, we constructed a co-expression network between APAs and RBPs using the microarray data. Further incorporation of CLIP-seq data of selected RBPs showed that Nova2 represses and Mbnl1 promotes the polyadenylation of closest poly(A) sites respectively. Altogether, our study is the first microarray meta-analysis in a mammal on the regulation of APA by RBPs that integrated massive mRNA expression data under a wide-range of biological conditions. Finally, we present our results as a comprehensive resource in an online website for the research community. PMID:24622240

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

PubMed Central

Shen, Yingjia; Venu, R.C.; Nobuta, Kan; Wu, Xiaohui; Notibala, Varun; Demirci, Caghan; Meyers, Blake C.; Wang, Guo-Liang; Ji, Guoli; Li, Qingshun Q.

2011-01-01

Polyadenylation sites mark the ends of mRNA transcripts. Alternative polyadenylation (APA) may alter sequence elements and/or the coding capacity of transcripts, a mechanism that has been demonstrated to regulate gene expression and transcriptome diversity. To study the role of APA in transcriptome dynamics, we analyzed a large-scale data set of RNA “tags” that signify poly(A) sites and expression levels of mRNA. These tags were derived from a wide range of tissues and developmental stages that were mutated or exposed to environmental treatments, and generated using digital gene expression (DGE)–based protocols of the massively parallel signature sequencing (MPSS-DGE) and the Illumina sequencing-by-synthesis (SBS-DGE) sequencing platforms. The data offer a global view of APA and how it contributes to transcriptome dynamics. Upon analysis of these data, we found that ∼60% of Arabidopsis genes have multiple poly(A) sites. Likewise, ∼47% and 82% of rice genes use APA, supported by MPSS-DGE and SBS-DGE tags, respectively. In both species, ∼49%–66% of APA events were mapped upstream of annotated stop codons. Interestingly, 10% of the transcriptomes are made up of APA transcripts that are differentially distributed among developmental stages and in tissues responding to environmental stresses, providing an additional level of transcriptome dynamics. Examples of pollen-specific APA switching and salicylic acid treatment-specific APA clearly demonstrated such dynamics. The significance of these APAs is more evident in the 3034 genes that have conserved APA events between rice and Arabidopsis. PMID:21813626

Biaxial and antiferroelectric structure of the orthogonal smectic phase of a bent-shaped molecule and helical structure in a chiral mixture system

NASA Astrophysics Data System (ADS)

Kang, Sungmin; Nguyen, Ha; Nakajima, Shunpei; Tokita, Masatoshi; Watanabe, Junji

2013-05-01

We examined the biaxial and antiferroelectric properties in the Smectic-APA (Sm-APA) phase of bent-shaped DC-S-8. The biaxiality, which results from the existence of a secondary director, was well established from birefringence observations in the homeotropically aligned Sm-APA. By entering into Sm-APA phase, the birefringence (Δn, difference between two refractive indices of short axes) continuously increased from 0 to 0.02 with decreasing temperature. The antiferroelectric switching and second harmonic generation (SHG) activity on the field-on state were also observed in the Sm-APA phase, and the evaluated spontaneous polarization (PS) value strongly depended on temperature. The temperature dependence of Δn and PS resembles each other and follows Haller's approximation, showing that the biaxiality is due to polar packing in which the molecules are preferentially packed with their bent direction arranged in the same direction, and that the phase transition of Sm-APA to Sm-A is second order. The biaxiality was further examined in chiral Sm-APA*. Doping with chiral components induced the helical twisting of the secondary director in the Sm-APA* phase, which was confirmed by observing the reflection of the circular dichroism (CD) bands in the homeotropically aligned cell. The helical pitch of Sm-APA* is tunable in the range of 300-700 nm wavelength with a variation in the chiral content of 5 to 10 weight (wt)%.

Cleavage and polyadenylation: Ending the message expands gene regulation

PubMed Central

Neve, Jonathan

2017-01-01

ABSTRACT Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3′end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease. PMID:28453393

Fatigue-induced early onset of anticipatory postural adjustments in non-fatigued muscles: support for a centrally mediated adaptation.

PubMed

Strang, Adam J; Berg, William P; Hieronymus, Mathias

2009-08-01

Muscle fatigue has been shown to result in early onset of anticipatory postural adjustments (APAs) relative to those produced in a non-fatigued state. This adaptation is thought to reflect an attempt to preserve postural stability during a focal movement performed in a fatigued state. It remains unclear, however, whether this adaptation is of central (e.g., central nervous system motor command) or peripheral (e.g., muscle contractile properties), origin. One way to confirm that this adaptation is centrally driven is to identify fatigued-induced early APA onsets in non-fatigued muscles. In this study, APAs were obtained using a rapid bilateral reaching maneuver and recorded via surface electromyography before and after conditions of rest (n = 25) or fatigue (n = 25). Fatigue was generated using isokinetic exercise of the right leg. Results showed that fatigue-induced early APA onsets occurred in fatigued and non-fatigued muscles, confirming that fatigue-induced early APA onset is a centrally mediated adaptation.

Alternative Polyadenylation in Human Diseases

PubMed Central

Chang, Jae-Woong; Yeh, Hsin-Sung

2017-01-01

Varying length of messenger RNA (mRNA) 3′-untranslated region is generated by alternating the usage of polyadenylation sites during pre-mRNA processing. It is prevalent through all eukaryotes and has emerged as a key mechanism for controlling gene expression. Alternative polyadenylation (APA) plays an important role for cell growth, proliferation, and differentiation. In this review, we discuss the functions of APA related with various physiological conditions including cellular metabolism, mRNA processing, and protein diversity in a variety of disease models. We also discuss the molecular mechanisms underlying APA regulation, such as variations in the concentration of mRNA processing factors and RNA-binding proteins, as well as global transcriptome changes under cellular signaling pathway. PMID:29271615

Development of clinical practice guidelines.

PubMed

Hollon, Steven D; Areán, Patricia A; Craske, Michelle G; Crawford, Kermit A; Kivlahan, Daniel R; Magnavita, Jeffrey J; Ollendick, Thomas H; Sexton, Thomas L; Spring, Bonnie; Bufka, Lynn F; Galper, Daniel I; Kurtzman, Howard

2014-01-01

Clinical practice guidelines (CPGs) are intended to improve mental, behavioral, and physical health by promoting clinical practices that are based on the best available evidence. The American Psychological Association (APA) is committed to generating patient-focused CPGs that are scientifically sound, clinically useful, and informative for psychologists, other health professionals, training programs, policy makers, and the public. The Institute of Medicine (IOM) 2011 standards for generating CPGs represent current best practices in the field. These standards involve multidisciplinary guideline development panels charged with generating recommendations based on comprehensive systematic reviews of the evidence. The IOM standards will guide the APA as it generates CPGs that can be used to inform the general public and the practice community regarding the benefits and harms of various treatment options. CPG recommendations are advisory rather than compulsory. When used appropriately, high-quality guidelines can facilitate shared decision making and identify gaps in knowledge.

Impact and Potential of Decision Research on Decision Aiding

DTIC Science & Technology

1987-12-01

series was generated by the APA Committee on Research Support (CORS). a committee reporting to APA’s major scientific policy-making body, the Board of... Scientific Affairs. CORS initiated the series to provide a forum for the discussion of behavioral research issues related to the defense mission...are interested mainly in the scientific or theoretical aspects of their work, and are usually not in the best position to understand its potential

Involvement of arginine 878 together with Ca2+ in mouse aminopeptidase A substrate specificity for N-terminal acidic amino-acid residues

PubMed Central

Couvineau, Pierre; de Almeida, Hugo; Maigret, Bernard; Llorens-Cortes, Catherine

2017-01-01

Aminopeptidase A (APA) is a membrane-bound zinc metalloprotease cleaving, in the brain, the N-terminal aspartyl residue of angiotensin II to generate angiotensin III, which exerts a tonic stimulatory effect on the control of blood pressure in hypertensive animals. Using a refined APA structure derived from the human APA crystal structure, we docked the specific and selective APA inhibitor, EC33 in the presence of Ca2+. We report the presence in the S1 subsite of Arg-887 (Arg-878 in mouse APA), the guanidinium moiety of which established an interaction with the electronegative sulfonate group of EC33. Mutagenic replacement of Arg-878 with an alanine or a lysine residue decreased the affinity of the recombinant enzymes for the acidic substrate, α-L-glutamyl-β-naphthylamide, with a slight decrease in substrate hydrolysis velocity either with or without Ca2+. In the absence of Ca2+, the mutations modified the substrate specificity of APA for the acidic substrate, the mutated enzymes hydrolyzing more efficiently basic and neutral substrates, although the addition of Ca2+ partially restored the acidic substrate specificity. The analysis of the 3D models of the Arg-878 mutated APAs revealed a change in the volume of the S1 subsite, which may impair the binding and/or the optimal positioning of the substrate in the active site as well as its hydrolysis. These findings demonstrate the key role of Arg-878 together with Ca2 + in APA substrate specificity for N-terminal acidic amino acid residues by ensuring the optimal positioning of acidic substrates during catalysis. PMID:28877217

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster.

PubMed

Liu, Xiaochuan; Freitas, Jaime; Zheng, Dinghai; Oliveira, Marta S; Hoque, Mainul; Martins, Torcato; Henriques, Telmo; Tian, Bin; Moreira, Alexandra

2017-12-01

Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here, using 3' region extraction and deep sequencing (3'READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in Drosophila melanogaster , expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. Cis -element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in Drosophila melanogaster undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3'UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3'UTRs and in introns, consistent with the "first come, first served" model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for Drosophila melanogaster and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate. © 2017 Liu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Renal expression of aminopeptidase A in rats with two-kidney, one-clip hypertension.

PubMed

Wolf, G; Wenzel, U; Assmann, K J; Stahl, R A

2000-12-01

Angiotensin II (ANG II) is a major factor involved in the progression of chronic renal disease. Although the generation of this vasoactive peptide has been investigated in great detail, only a few studies have hitherto addressed the metabolism of ANG II into fragments such as angiotensin III and IV (ANG III, IV) which may exert physiological effects independent of ANG II. Aminopeptidase A (APA) is the major enzyme degrading ANG II. The aim of the current study was to evaluate glomerular APA expression in rats with two-kidney, one-clip hypertension. The left renal artery was restricted with a 0.2-mm silver clip. Kidneys were harvested 1 and 4 weeks after surgery. APA enzyme and protein expression was evaluated in kidney sections. Total APA enzyme activity and mRNA expression was assessed in isolated glomeruli. Degradation of exogenous ANG II by isolated glomeruli was measured with reverse-phase high-performance liquid chromatography. APA enzyme activity, protein, and mRNA expression were stimulated in the clipped kidney 1 week after surgery compared with the contralateral kidney or normal controls. In contrast, 4 weeks after clipping APA activity and expression was higher in the contralateral kidney. In parallel to these findings, degradation of ANG II was greatest in isolated glomeruli obtained from the clipped kidney after 1 week. However, preparations from the contralateral kidney 4 weeks after surgery were more active in the metabolism of exogenous ANG II. The present study provides evidence that APA is complexly regulated in in vivo situations with an activated local renin-ANG II system. ANG II appears to play a direct role in this regulation. However, since conversion of ANG II to ANG III by APA is the initial step leading to the formation of ANG IV which may exert detrimental effects not mediated through classical ANG II receptors, a local increase in APA activity may contribute to the progression of chronic renal disease even during complete AT(1)-receptor blockade.

The state of the psychology health service provider workforce.

PubMed

Michalski, Daniel S; Kohout, Jessica L

2011-12-01

Numerous efforts to describe the health service provider or clinical workforce in psychology have been conducted during the past 30 years. The American Psychological Association (APA) has studied trends in the doctoral education pathway and the resultant effects on the broader psychology workforce. During this period, the creation and growth of the PsyD degree and the formalization of the predoctoral internship placement system (the APPIC Match) have been well noted, but efforts to gain a complete understanding of professional practice are lacking. Specifically, piecemeal research on the provider workforce has led to the study of specific subpopulations using varying approaches and definitions of those providing direct clinical service. Consequently, estimates of the supply and need for health service providers are distinctly divergent and generate protracted debate in organized psychology. The APA membership directory and the APA Doctorate Employment Surveys have traditionally been relied on for workforce analyses. Yet, these data have become characterized by limited generalizability in recent years because of declining survey response rates and the fact that APA member data may not be as representative of the entire psychology health service provider population as they were previously. The 2008 APA Survey of Psychology Health Service Providers targeted these limitations by including nonmember psychologists in the sampling frame. Results revealed emerging themes in the demographics, work settings, and delivery of health services of the psychology health service provider workforce. Future areas of research for APA and organized psychology to undertake in addressing need and demand are suggested. (PsycINFO Database Record (c) 2011 APA, all rights reserved).

Influence of chronic ethanol intake on mouse synaptosomal aspartyl aminopeptidase and aminopeptidase A: relationship with oxidative stress indicators.

PubMed

Mayas, María Dolores; Ramírez-Expósito, María Jesús; García, María Jesús; Carrera, María Pilar; Martínez-Martos, José Manuel

2012-08-01

Aminopeptidase A (APA) and aspartyl aminopeptidase (ASAP) not only act as neuromodulators in the regional brain renin-angiotensin system, but also release N-terminal acidic amino acids (glutamate and aspartate). The hyperexcitability of amino acid neurotransmitters is responsible for several neurodegenerative processes affecting the central nervous system. The purpose of the present work was to study the influence of chronic ethanol intake, a well known neurotoxic compound, on APA and ASAP activity under resting and K(+)-stimulated conditions at the synapse level. APA and ASAP activity were determined against glutamate- and aspartate-β-naphthylamide respectively in mouse frontal cortex synaptosomes and in their incubation supernatant in a Ca(2+)-containing or Ca(2+)-free artificial cerebrospinal fluid. The neurotoxic effects were analyzed by determining free radical generation, peroxidation of membrane lipids and the oxidation of synaptosomal proteins. In addition, the bioenergetic behavior of synaptosomes was analyzed under different experimental protocols. We obtained several modifications in oxidative stress parameters and a preferential inhibitor effect of chronic ethanol intake on APA and ASAP activities. Although previous in vitro studies failed to show signs of neurodegeneration, these in vivo modifications in oxidative stress parameters do not seem to be related to changes in APA and ASAP, invalidating the idea that an excess of free acidic amino acids released by APA and ASAP induces neurodegeneration. Copyright © 2012 Elsevier Inc. All rights reserved.

Molecular Regulation of Alternative Polyadenylation (APA) within the Drosophila Nervous System.

PubMed

Vallejos Baier, Raul; Picao-Osorio, Joao; Alonso, Claudio R

2017-10-27

Alternative polyadenylation (APA) is a widespread gene regulatory mechanism that generates mRNAs with different 3'-ends, allowing them to interact with different sets of RNA regulators such as microRNAs and RNA-binding proteins. Recent studies have shown that during development, neural tissues produce mRNAs with particularly long 3'UTRs, suggesting that such extensions might be important for neural development and function. Despite this, the mechanisms underlying neural APA are not well understood. Here, we investigate this problem within the Drosophila nervous system, focusing on the roles played by general cleavage and polyadenylation factors (CPA factors). In particular, we examine the model that modulations in CPA factor concentration may affect APA during development. For this, we first analyse the expression of the Drosophila orthologues of all mammalian CPA factors and note that their expression decreases during embryogenesis. In contrast to this global developmental decrease in CPA factor expression, we see that cleavage factor I (CFI) expression is actually elevated in the late embryonic central nervous system, suggesting that CFI might play a special role in neural tissues. To test this, we use the UAS/Gal4 system to deplete CFI proteins from neural tissue and observe that in this condition, multiple genes switch their APA patterns, demonstrating a role of CFI in APA control during Drosophila neural development. Furthermore, analysis of genes with 3'UTR extensions of different length leads us to suggest a novel relation between 3'UTR length and sensitivity to CPA factor expression. Our work thus contributes to the understanding of the mechanisms of APA control within the developing central nervous system. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing.

PubMed

Chen, Shi-Yi; Deng, Feilong; Jia, Xianbo; Li, Cao; Lai, Song-Jia

2017-08-09

It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus). We totally obtain 36,186 high-confidence transcripts from 14,474 genic loci, among which more than 23% of genic loci and 66% of isoforms have not been annotated yet within the current reference genome. Furthermore, about 17% of transcripts are computationally revealed to be non-coding RNAs. Up to 24,797 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events are detected within this de novo constructed transcriptome, respectively. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of rabbit genome.

Dimensional approaches to psychiatric classification: refining the research agenda for DSM-V: an introduction.

PubMed

Regier, Darrel A

2007-01-01

The American Psychiatric Association (APA) will publish the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-V), in 2012. This paper reviews the extended, multi-faceted research planning preparations that APA has undertaken, several in collaboration with the World Health Organization and the U.S. National Institutes of Health, to assess the current state of diagnosis-relevant research and to generate short- and long-term recommendations for research needed to enrich DSM-V and future psychiatric classifications. This research review and planning process has underscored widespread interest among nosologists in the US and globally regarding the potential benefits for research and clinical practice of incorporating a dimensional component into the existing categorical, or binary, classification system in the DSM. Toward this end, the APA and its partners convened an international conference in July 2006 to critically appraise the use of dimensional constructs in psychiatric diagnostic systems. Resultant papers appear in this issue of International Journal of Methods in Psychiatric Research and in a forthcoming monograph to be published by APA. Copyright (c) 2007 John Wiley & Sons, Ltd.

Not all nonnormal distributions are created equal: Improved theoretical and measurement precision.

PubMed

Joo, Harry; Aguinis, Herman; Bradley, Kyle J

2017-07-01

We offer a four-category taxonomy of individual output distributions (i.e., distributions of cumulative results): (1) pure power law; (2) lognormal; (3) exponential tail (including exponential and power law with an exponential cutoff); and (4) symmetric or potentially symmetric (including normal, Poisson, and Weibull). The four categories are uniquely associated with mutually exclusive generative mechanisms: self-organized criticality, proportionate differentiation, incremental differentiation, and homogenization. We then introduce distribution pitting, a falsification-based method for comparing distributions to assess how well each one fits a given data set. In doing so, we also introduce decision rules to determine the likely dominant shape and generative mechanism among many that may operate concurrently. Next, we implement distribution pitting using 229 samples of individual output for several occupations (e.g., movie directors, writers, musicians, athletes, bank tellers, call center employees, grocery checkers, electrical fixture assemblers, and wirers). Results suggest that for 75% of our samples, exponential tail distributions and their generative mechanism (i.e., incremental differentiation) likely constitute the dominant distribution shape and explanation of nonnormally distributed individual output. This finding challenges past conclusions indicating the pervasiveness of other types of distributions and their generative mechanisms. Our results further contribute to theory by offering premises about the link between past and future individual output. For future research, our taxonomy and methodology can be used to pit distributions of other variables (e.g., organizational citizenship behaviors). Finally, we offer practical insights on how to increase overall individual output and produce more top performers. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The APA and the Rise of Pediatric Generalist Network Research

PubMed Central

Wasserman, Richard; Serwint, Janet R.; Kuppermann, Nathan; Srivastava, Rajendu; Dreyer, Benard

2010-01-01

The Academic Pediatric Association (APA – formerly the Ambulatory Pediatric Association) first encouraged multi-institutional collaborative research among its members over thirty years ago. Individual APA members went on subsequently to figure prominently in establishing formal research networks. These enduring collaborations have been established to conduct investigations in a variety of generalist contexts. At present, four generalist networks – Pediatric Research in Office Settings (PROS), the Pediatric Emergency Care Applied Network (PECARN), the COntinuity Research NETwork (CORNET), and Pediatric Research in Inpatient Settings (PRIS) – have a track record of extensive achievement in generating new knowledge aimed at improving the health and health care of children. This review details the history, accomplishments, and future directions of these networks and summarizes the common themes, strengths, challenges and opportunities inherent in pediatric generalist network research. PMID:21282083

A vertebrate case study of the quality of assemblies derived from next-generation sequences

PubMed Central

2011-01-01

The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references. PMID:21453517

Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches.

PubMed

Lin, Hsin-Hung; Liao, Yu-Chieh

2015-01-01

Despite the ever-increasing output of next-generation sequencing data along with developing assemblers, dozens to hundreds of gaps still exist in de novo microbial assemblies due to uneven coverage and large genomic repeats. Third-generation single-molecule, real-time (SMRT) sequencing technology avoids amplification artifacts and generates kilobase-long reads with the potential to complete microbial genome assembly. However, due to the low accuracy (~85%) of third-generation sequences, a considerable amount of long reads (>50X) are required for self-correction and for subsequent de novo assembly. Recently-developed hybrid approaches, using next-generation sequencing data and as few as 5X long reads, have been proposed to improve the completeness of microbial assembly. In this study we have evaluated the contemporary hybrid approaches and demonstrated that assembling corrected long reads (by runCA) produced the best assembly compared to long-read scaffolding (e.g., AHA, Cerulean and SSPACE-LongRead) and gap-filling (SPAdes). For generating corrected long reads, we further examined long-read correction tools, such as ECTools, LSC, LoRDEC, PBcR pipeline and proovread. We have demonstrated that three microbial genomes including Escherichia coli K12 MG1655, Meiothermus ruber DSM1279 and Pdeobacter heparinus DSM2366 were successfully hybrid assembled by runCA into near-perfect assemblies using ECTools-corrected long reads. In addition, we developed a tool, Patch, which implements corrected long reads and pre-assembled contigs as inputs, to enhance microbial genome assemblies. With the additional 20X long reads, short reads of S. cerevisiae W303 were hybrid assembled into 115 contigs using the verified strategy, ECTools + runCA. Patch was subsequently applied to upgrade the assembly to a 35-contig draft genome. Our evaluation of the hybrid approaches shows that assembling the ECTools-corrected long reads via runCA generates near complete microbial genomes, suggesting that genome assembly could benefit from re-analyzing the available hybrid datasets that were not assembled in an optimal fashion.

The O-mannosylation and production of recombinant APA (45/47 KDa) protein from Mycobacterium tuberculosis in Streptomyces lividans is affected by culture conditions in shake flasks.

PubMed

Gamboa-Suasnavart, Ramsés A; Valdez-Cruz, Norma A; Cordova-Dávalos, Laura E; Martínez-Sotelo, José A; Servín-González, Luis; Espitia, Clara; Trujillo-Roldán, Mauricio A

2011-12-20

The Ala-Pro-rich O-glycoprotein known as the 45/47 kDa or APA antigen from Mycobacterium tuberculosis is an immunodominant adhesin restricted to mycobacterium genus and has been proposed as an alternative candidate to generate a new vaccine against tuberculosis or for diagnosis kits. In this work, the recombinant O-glycoprotein APA was produced by the non-pathogenic filamentous bacteria Streptomyces lividans, evaluating three different culture conditions. This strain is known for its ability to produce heterologous proteins in a shorter time compared to M. tuberculosis. Three different shake flask geometries were used to provide different shear and oxygenation conditions; and the impact of those conditions on the morphology of S. lividans and the production of rAPA was characterized and evaluated. Small unbranched free filaments and mycelial clumps were found in baffled and coiled shake flasks, but one order of magnitude larger pellets were found in conventional shake flasks. The production of rAPA is around 3 times higher in small mycelia than in larger pellets, most probably due to difficulties in mass transfer inside pellets. Moreover, there are four putative sites of O-mannosylation in native APA, one of which is located at the carboxy-terminal region. The carbohydrate composition of this site was determined for rAPA by mass spectrometry analysis, and was found to contain different glycoforms depending on culture conditions. Up to two mannoses residues were found in cultures carried out in conventional shake flasks, and up to five mannoses residues were determined in coiled and baffled shake flasks. The shear and/or oxygenation parameters determine the bacterial morphology, the productivity, and the O-mannosylation of rAPA in S. lividans. As demonstrated here, culture conditions have to be carefully controlled in order to obtain recombinant O-glycosylated proteins with similar "quality" in bacteria, particularly, if the protein activity depends on the glycosylation pattern. Furthermore, it will be an interesting exercise to determine the effect of shear and oxygen in shake flasks, to obtain evidences that may be useful in scaling-up these processes to bioreactors. Another approach will be using lab-scale bioreactors under well-controlled conditions, and study the impact of those on rAPA productivity and quality.

Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe

PubMed Central

Liu, Xiaochuan; Hoque, Mainul; Larochelle, Marc; Lemay, Jean-François; Yurko, Nathan; Manley, James L.; Bachand, François; Tian, Bin

2017-01-01

Alternative polyadenylation (APA) is a widespread mechanism that generates mRNA isoforms with distinct properties. Here we have systematically mapped and compared cleavage and polyadenylation sites (PASs) in two yeast species, S. cerevisiae and S. pombe. Although >80% of the mRNA genes in each species were found to display APA, S. pombe showed greater 3′ UTR size differences among APA isoforms than did S. cerevisiae. PASs in different locations of gene are surrounded with distinct sequences in both species and are often associated with motifs involved in the Nrd1-Nab3-Sen1 termination pathway. In S. pombe, strong motifs surrounding distal PASs lead to higher abundances of long 3′ UTR isoforms than short ones, a feature that is opposite in S. cerevisiae. Differences in PAS placement between convergent genes lead to starkly different antisense transcript landscapes between budding and fission yeasts. In both species, short 3′ UTR isoforms are more likely to be expressed when cells are growing in nutrient-rich media, although different gene groups are affected in each species. Significantly, 3′ UTR shortening in S. pombe coordinates with up-regulation of expression for genes involved in translation during cell proliferation. Using S. pombe strains deficient for Pcf11 or Pab2, we show that reduced expression of 3′-end processing factors lengthens 3′ UTR, with Pcf11 having a more potent effect than Pab2. Taken together, our data indicate that APA mechanisms in S. pombe and S. cerevisiae are largely different: S. pombe has many of the APA features of higher species, and Pab2 in S. pombe has a different role in APA regulation than its mammalian homolog, PABPN1. PMID:28916539

Journal article reporting standards for qualitative primary, qualitative meta-analytic, and mixed methods research in psychology: The APA Publications and Communications Board task force report.

PubMed

Levitt, Heidi M; Bamberg, Michael; Creswell, John W; Frost, David M; Josselson, Ruthellen; Suárez-Orozco, Carola

2018-01-01

The American Psychological Association Publications and Communications Board Working Group on Journal Article Reporting Standards for Qualitative Research (JARS-Qual Working Group) was charged with examining the state of journal article reporting standards as they applied to qualitative research and with generating recommendations for standards that would be appropriate for a wide range of methods within the discipline of psychology. These standards describe what should be included in a research report to enable and facilitate the review process. This publication marks a historical moment-the first inclusion of qualitative research in APA Style, which is the basis of both the Publication Manual of the American Psychological Association (APA, 2010) and APA Style CENTRAL, an online program to support APA Style. In addition to the general JARS-Qual guidelines, the Working Group has developed standards for both qualitative meta-analysis and mixed methods research. The reporting standards were developed for psychological qualitative research but may hold utility for a broad range of social sciences. They honor a range of qualitative traditions, methods, and reporting styles. The Working Group was composed of a group of researchers with backgrounds in varying methods, research topics, and approaches to inquiry. In this article, they present these standards and their rationale, and they detail the ways that the standards differ from the quantitative research reporting standards. They describe how the standards can be used by authors in the process of writing qualitative research for submission as well as by reviewers and editors in the process of reviewing research. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

A survey of the sorghum transcriptome using single-molecule long reads

DOE PAGES

Abdel-Ghany, Salah E.; Hamilton, Michael; Jacobi, Jennifer L.; ...

2016-06-24

Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novelmore » splice isoforms. Additionally, we uncover APA ofB11,000 expressed genes and more than 2,100 novel genes. Lastly, these results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism.« less

A survey of the sorghum transcriptome using single-molecule long reads

PubMed Central

Abdel-Ghany, Salah E.; Hamilton, Michael; Jacobi, Jennifer L.; Ngam, Peter; Devitt, Nicholas; Schilkey, Faye; Ben-Hur, Asa; Reddy, Anireddy S. N.

2016-01-01

Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ∼11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism. PMID:27339290

Self-Assembly of Human Serum Albumin: A Simplex Phenomenon

PubMed Central

Thakur, Garima; Prashanthi, Kovur; Jiang, Keren; Thundat, Thomas

2017-01-01

Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is explained through thermodynamics and chemical kinetics. PMID:28930179

Next Generation Sequence Assembly with AMOS

PubMed Central

Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, Mihai

2011-01-01

A Modular Open-Source Assembler (AMOS) was designed to offer a modular approach to genome assembly. AMOS includes a wide range of tools for assembly, including lightweight de novo assemblers Minimus and Minimo, and Bambus 2, a robust scaffolder able to handle metagenomic and polymorphic data. This protocol describes how to configure and use AMOS for the assembly of Next Generation sequence data. Additionally, we provide three tutorial examples that include bacterial, viral, and metagenomic datasets with specific tips for improving assembly quality. PMID:21400694

GENESUS: a two-step sequence design program for DNA nanostructure self-assembly.

PubMed

Tsutsumi, Takanobu; Asakawa, Takeshi; Kanegami, Akemi; Okada, Takao; Tahira, Tomoko; Hayashi, Kenshi

2014-01-01

DNA has been recognized as an ideal material for bottom-up construction of nanometer scale structures by self-assembly. The generation of sequences optimized for unique self-assembly (GENESUS) program reported here is a straightforward method for generating sets of strand sequences optimized for self-assembly of arbitrarily designed DNA nanostructures by a generate-candidates-and-choose-the-best strategy. A scalable procedure to prepare single-stranded DNA having arbitrary sequences is also presented. Strands for the assembly of various structures were designed and successfully constructed, validating both the program and the procedure.

Next generation sequence assembly with AMOS.

PubMed

Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, Mihai

2011-03-01

A Modular Open-Source Assembler (AMOS) was designed to offer a modular approach to genome assembly. AMOS includes a wide range of tools for assembly, including the lightweight de novo assemblers Minimus and Minimo, and Bambus 2, a robust scaffolder able to handle metagenomic and polymorphic data. This protocol describes how to configure and use AMOS for the assembly of Next Generation sequence data. Additionally, we provide three tutorial examples that include bacterial, viral, and metagenomic datasets with specific tips for improving assembly quality. © 2011 by John Wiley & Sons, Inc.

System and method for heating ferrite magnet motors for low temperatures

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

Reddy, Patel Bhageerath; El-Refaie, Ayman Mohamed Fawzi; Huh, Kum-Kang

A system and method for heating ferrite permanent magnets in an electrical machine is disclosed. The permanent magnet machine includes a stator assembly and a rotor assembly, with a plurality of ferrite permanent magnets disposed within the stator assembly or the rotor assembly to generate a magnetic field that interacts with a stator magnetic field to produce a torque. A controller of the electrical machine is programmed to cause a primary field current to be applied to the stator windings to generate the stator magnetic field, so as to cause the rotor assembly to rotate relative to the stator assembly.more » The controller is further programmed to cause a secondary current to be applied to the stator windings to selectively generate a secondary magnetic field, the secondary magnetic field inducing eddy currents in at least one of the stator assembly and the rotor assembly to heat the ferrite permanent magnets.« less

System and method for heating ferrite magnet motors for low temperatures

DOEpatents

Reddy, Patel Bhageerath; El-Refaie, Ayman Mohamed Fawzi; Huh, Kum-Kang

2017-07-04

A system and method for heating ferrite permanent magnets in an electrical machine is disclosed. The permanent magnet machine includes a stator assembly and a rotor assembly, with a plurality of ferrite permanent magnets disposed within the stator assembly or the rotor assembly to generate a magnetic field that interacts with a stator magnetic field to produce a torque. A controller of the electrical machine is programmed to cause a primary field current to be applied to the stator windings to generate the stator magnetic field, so as to cause the rotor assembly to rotate relative to the stator assembly. The controller is further programmed to cause a secondary current to be applied to the stator windings to selectively generate a secondary magnetic field, the secondary magnetic field inducing eddy currents in at least one of the stator assembly and the rotor assembly to heat the ferrite permanent magnets.

Comparing de novo assemblers for 454 transcriptome data

PubMed Central

2010-01-01

Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible final product, and this strategy is recommended. PMID:20950480

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.

PubMed

Jayakumar, Vasanthan; Sakakibara, Yasubumi

2017-11-03

Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms. © The Author 2017. Published by Oxford University Press.

A fast sequence assembly method based on compressed data structures.

PubMed

Liang, Peifeng; Zhang, Yancong; Lin, Kui; Hu, Jinglu

2014-01-01

Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, a memory and time efficient assembler is presented from applying FM-index in JR-Assembler, called FMJ-Assembler, where FM stand for FMR-index derived from the FM-index and BWT and J for jumping extension. The FMJ-Assembler uses expanded FM-index and BWT to compress data of reads to save memory and jumping extension method make it faster in CPU time. An extensive comparison of the FMJ-Assembler with current assemblers shows that the FMJ-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less CPU time. All these advantages of the FMJ-Assembler indicate that the FMJ-Assembler will be an efficient assembly method in next generation sequencing technology.

Compensatory but not anticipatory adjustments are altered in older adults during lateral postural perturbations.

PubMed

Claudino, Renato; dos Santos, Eloá C C; Santos, Marcio J

2013-08-01

This study investigated anticipatory postural adjustments (APAs) and compensatory postural adjustments (CPAs) and their relationship in older adults during lateral postural perturbations. Unpredictable and predictable postural disturbances were induced by a swinging pendulum that impacted at the shoulder level of two groups of older adults, non-fallers (20) and fallers (20), and in a group of young control subjects (20). The electromyographic (EMG) activity of the postural muscles and the center of pressure (COP) displacement were recorded and quantified within the time intervals typical for APAs and CPAs. Both groups of older adults (non-fallers and fallers) showed higher magnitude of EMG activity in the lateral muscles and increased COP displacement, particularly, during the CPAs time interval when compared to the young group. Older adults, however, were able to change the electrical activity of the muscles during the predictable task by generating APAs with similar magnitudes of those found in young subjects. Compensatory but not anticipatory adjustments are altered in older adults during predictable lateral postural perturbations. These findings provide new data on the role of APAs and CPAs in their relationship in older adults during external lateral perturbations and may advance current rehabilitative management strategies to improve balance control in older individuals. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.

PubMed

Kleftogiannis, Dimitrios; Kalnis, Panos; Bajic, Vladimir B

2013-01-01

A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently. With recent improvements in DNA sequencing technologies, it is expected that the memory footprint required for the assembly process will increase dramatically and will emerge as a limiting factor in processing widely available NGS-generated reads. In this report, we compare current memory-efficient techniques for genome assembly with respect to quality, memory consumption and execution time. Our experiments prove that it is possible to generate draft assemblies of reasonable quality on conventional multi-purpose computers with very limited available memory by choosing suitable assembly methods. Our study reveals the minimum memory requirements for different assembly programs even when data volume exceeds memory capacity by orders of magnitude. By combining existing methodologies, we propose two general assembly strategies that can improve short-read assembly approaches and result in reduction of the memory footprint. Finally, we discuss the possibility of utilizing cloud infrastructures for genome assembly and we comment on some findings regarding suitable computational resources for assembly.

Industrial Technology Modernization Program. Project 32. Factory Vision. Phase 2

DTIC Science & Technology

1988-04-01

instructions for the PWA’s, generating the numerical control (NC) program instructions for factory assembly equipment, controlling the process... generating the numerical control (NC) program instructions for factory assembly equipment, controlling the production process instructions and NC... Assembly Operations the "Create Production Process Program" will automatically generate a sequence of graphics pages (in paper mode), or graphics screens

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

West, W.S.

Progress during the period includes completion of the SNAP 7C system tests, completion of safety analysis for the SNAP 7A and C systems, assembly and initial testing of SNAP 7A, assembly of a modified reliability model, and assembly of a 10-W generator. Other activities include completion of thermal and safety analyses for SNAP 7B and D generators and fuel processing for these generators. (J.R.D.)

Fixture for aligning motor assembly

DOEpatents

Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

2009-12-08

An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

Analysis of gene expression on anodic porous alumina microarrays

PubMed Central

Nicolini, Claudio; Singh, Manjul; Spera, Rosanna; Felli, Lamberto

2013-01-01

This paper investigates the application of anodic porous alumina as an advancement on chip laboratory for gene expressions. The surface was prepared by a suitable electrolytic process to obtain a regular distribution of deep micrometric holes and printed bypen robot tips under standard conditions. The gene expression within the Nucleic Acid Programmable Protein Array (NAPPA) is realized in a confined environment of 16 spots, containing circular DNA plasmids expressed using rabbit reticulocyte lysate. Authors demonstrated the usefulness of APA in withholding the protein expression by detecting with a CCD microscope the photoluminescence signal emitted from the complex secondary antibody anchored to Cy3 and confined in the pores. Friction experiments proved the mechanical resistance under external stresses by the robot tip pens printing. So far, no attempts have been made to directly compare APA with any other surface/substrate; the rationale for pursuing APA as a potential surface coating is that it provides advantages over the simple functionalization of a glass slide, overcoming concerns about printing and its ability to generate viable arrays. PMID:23783000

Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis.

PubMed

Shan, Lingjuan; Wu, Chan; Chen, Di; Hou, Lei; Li, Xin; Wang, Lixia; Chu, Xiao; Hou, Yifeng; Wang, Zhaohui

2017-02-20

In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear. Alternative polyadenylation (APA) is a highly conserved means of gene regulation and is achieved by the RNA 3'-processing machinery to generate diverse 3'UTR profiles. In Drosophila spermatogenesis, we observed distinct profiles of transcriptome-wide 3'UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 3'UTRs of hundreds of genes were consistently shifted. Remarkably, altering the levels of multiple 3'-processing factors disrupted germline's progression to meiosis, indicative of APA's active role in this transition. An RNA-binding protein (RBP) Tut could directly bind 3'UTRs of 3'-processing factors whose expressions were repressed in the presence of Tut-containing complex. Further, we demonstrated that this RBP complex could execute the repression post-transcriptionally by recruiting CCR4/Twin of deadenylation complex. Thus, we propose that an RBP complex regulates the dynamic APA profile to promote the mitosis-to-meiosis transition. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Wind turbine/generator set and method of making same

DOEpatents

Bevington, Christopher M.; Bywaters, Garrett L.; Coleman, Clint C.; Costin, Daniel P.; Danforth, William L.; Lynch, Jonathan A.; Rolland, Robert H.

2013-06-04

A wind turbine comprising an electrical generator that includes a rotor assembly. A wind rotor that includes a wind rotor hub is directly coupled to the rotor assembly via a simplified connection. The wind rotor and generator rotor assembly are rotatably mounted on a central spindle via a bearing assembly. The wind rotor hub includes an opening having a diameter larger than the outside diameter of the central spindle adjacent the bearing assembly so as to allow access to the bearing assembly from a cavity inside the wind rotor hub. The spindle is attached to a turret supported by a tower. Each of the spindle, turret and tower has an interior cavity that permits personnel to traverse therethrough to the cavity of the wind rotor hub. The wind turbine further includes a frictional braking system for slowing, stopping or keeping stopped the rotation of the wind rotor and rotor assembly.

Wind turbine/generator set having a stator cooling system located between stator frame and active coils

DOEpatents

Bevington, Christopher M.; Bywaters, Garrett L.; Coleman, Clint C.; Costin, Daniel P.; Danforth, William L.; Lynch, Jonathan A.; Rolland, Robert H.

2012-11-13

A wind turbine comprising an electrical generator that includes a rotor assembly. A wind rotor that includes a wind rotor hub is directly coupled to the rotor assembly via a simplified connection. The wind rotor and generator rotor assembly are rotatably mounted on a central spindle via a bearing assembly. The wind rotor hub includes an opening having a diameter larger than the outside diameter of the central spindle adjacent the bearing assembly so as to allow access to the bearing assembly from a cavity inside the wind rotor hub. The spindle is attached to a turret supported by a tower. Each of the spindle, turret and tower has an interior cavity that permits personnel to traverse therethrough to the cavity of the wind rotor hub. The wind turbine further includes a frictional braking system for slowing, stopping or keeping stopped the rotation of the wind rotor and rotor assembly.

Who Cares about APA Policy and Does it Have an Impact? 2006 Annual Report of the APA Policy and Planning Board

ERIC Educational Resources Information Center

American Psychologist, 2007

2007-01-01

What constitutes American Psychological Association (APA) policy? How does it affect the everyday and professional lives of APA members? How personally aware are psychologists of APA policies? In this report, the APA explores these questions and provide some intriguing findings on the fate of policies developed through the APA's complicated and…

Practicum in adapted physical activity: a Dewey-inspired action research project.

PubMed

Standal, Øyvind; Rugseth, Gro

2014-07-01

The purpose of this study was to investigate what adapted physical activity (APA) students learn from their practicum experiences. One cohort of APA students participated, and data were generated from an action research project that included observations, reflective journals, and a focus group interview. The theoretical framework for the study was Dewey's and Wackerhausen's theories of reflections. The findings show the objects of students' reflections, the kind of conceptual resources they draw on while reflecting, and their knowledge interests. In addition, two paradoxes are identified: the tension between reflecting from and on own values, and how practicum as a valued experience of reality can become too difficult to handle. In conclusion, we reflect on how practicum learning can be facilitated.

24 CFR 3280.304 - Materials.

Code of Federal Regulations, 2010 CFR

2010-04-01

... APA Trademarks)—PS 1-95. APA Design/Construction Guide, Residential and Commercial—APA E30-P-1996...-Plywood Beams—APA H-815E (PDS Supplement #5), 1995. Panel Design Specification—APA D410A, 2004. Design and Fabrication of Glued Plywood-Lumber Beams—APA-S 812Q, Suppl. 2-1992. Design and Fabrication of Plywood Curved...

SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.

PubMed

Barker, Michael S; Dlugosch, Katrina M; Reddy, A Chaitanya C; Amyotte, Sarah N; Rieseberg, Loren H

2009-02-15

Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences. SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html.

A unified convention for biological assemblies with helical symmetry

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

Tsai, Chung-Jung, E-mail: tsaic@mail.nih.gov; Nussinov, Ruth; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978

A new representation of helical structure by four parameters, [n{sub 1}, n{sub 2}, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam. Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems,more » respectively. The unification suggests that a new helical description with only four parameters [n{sub 1}, n{sub 2}, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.« less

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology.

PubMed

Judge, Kim; Hunt, Martin; Reuter, Sandra; Tracey, Alan; Quail, Michael A; Parkhill, Julian; Peacock, Sharon J

2016-09-01

Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug-resistant Enterobacter kobei isolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information. Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly. All four had a similar number of contigs and were more contiguous than the assembly using Illumina data alone, with SPAdes producing a single chromosomal contig. Evaluation of the four assemblies to represent the genome structure revealed a single large inversion in the SPAdes assembly, which also incorrectly integrated a plasmid into the chromosomal contig. Almost 50 %, 80 % and 90 % of MinION pass reads were generated in the first 6, 9 and 12 h, respectively. Using data from the first 6 h alone led to a less accurate, fragmented assembly, but data from the first 9 or 12 h generated similar assemblies to that from 48 h sequencing. Assemblies were generated in 2 h using Canu, indicating that going from isolate to assembled data is possible in less than 48 h. MinION data identified that genes responsible for resistance were carried by two plasmids encoding resistance to carbapenem and to sulphonamides, rifampicin and aminoglycosides, respectively.

Method of Liquifying a gas

DOEpatents

Zollinger, William T.; Bingham, Dennis N.; McKellar, Michael G.; Wilding, Bruce M.; Klingler, Kerry M.

2006-02-14

A method of liquefying a gas is disclosed and which includes the steps of pressurizing a liquid; mixing a reactant composition with the pressurized liquid to generate a high pressure gas; supplying the high pressure gas to an expansion engine which produces a gas having a reduced pressure and temperature, and which further generates a power and/or work output; coupling the expansion engine in fluid flowing relation relative to a refrigeration assembly, and wherein the gas having the reduced temperature is provided to the refrigeration assembly; and energizing and/or actuating the refrigeration assembly, at least in part, by supplying the power and/or work output generated by the expansion engine to the refrigeration assembly, the refrigeration assembly further reducing the temperature of the gas to liquefy same.

Electrode assemblies, plasma apparatuses and systems including electrode assemblies, and methods for generating plasma

DOEpatents

Kong, Peter C; Grandy, Jon D; Detering, Brent A; Zuck, Larry D

2013-09-17

Electrode assemblies for plasma reactors include a structure or device for constraining an arc endpoint to a selected area or region on an electrode. In some embodiments, the structure or device may comprise one or more insulating members covering a portion of an electrode. In additional embodiments, the structure or device may provide a magnetic field configured to control a location of an arc endpoint on the electrode. Plasma generating modules, apparatus, and systems include such electrode assemblies. Methods for generating a plasma include covering at least a portion of a surface of an electrode with an electrically insulating member to constrain a location of an arc endpoint on the electrode. Additional methods for generating a plasma include generating a magnetic field to constrain a location of an arc endpoint on an electrode.

Advanced Stirling Radioisotope Generator Engineering Unit 2 (ASRG EU2) Final Assembly

NASA Technical Reports Server (NTRS)

Oriti, Salvatore M.

2015-01-01

NASA Glenn Research Center (GRC) has recently completed the assembly of a unique Stirling generator test article for laboratory experimentation. Under the Advanced Stirling Radioisotope Generator (ASRG) flight development contract, NASA GRC initiated a task to design and fabricate a flight-like generator for in-house testing. This test article was given the name ASRG Engineering Unit 2 (EU2) as it was effectively the second engineering unit to be built within the ASRG project. The intent of the test article was to duplicate Lockheed Martin's qualification unit ASRG design as much as possible to enable system-level tests not previously possible at GRC. After the cancellation of the ASRG flight development project, the decision was made to continue the EU2 build, and make use of a portion of the hardware from the flight development project. GRC and Lockheed Martin engineers collaborated to develop assembly procedures, leveraging the valuable knowledge gathered by Lockheed Martin during the ASRG development contract. The ASRG EU2 was then assembled per these procedures at GRC with Lockheed Martin engineers on site. The assembly was completed in August 2014. This paper details the components that were used for the assembly, and the assembly process itself.

Analysis of Direct Solar Illumination on the Backside of Space Station Solar Cells

NASA Technical Reports Server (NTRS)

Delleur, Ann M.; Kerslake, Thomas W.; Scheiman, David A.

1999-01-01

The International Space Station (ISS) is a complex spacecraft that will take several years to assemble in orbit. During many of the assembly and maintenance procedures, the space station's large solar arrays must he locked, which can significantly reduce power generation. To date, power generation analyses have not included power generation from the backside of the solar cells in a desire to produce a conservative analysis. This paper describes the testing of ISS solar cell backside power generation, analytical modeling and analysis results on an ISS assembly mission.

Unexperienced mechanical effects of muscular fatigue can be predicted by the Central Nervous System as revealed by anticipatory postural adjustments.

PubMed

Monjo, Florian; Forestier, Nicolas

2014-09-01

Muscular fatigue effects have been shown to be compensated by the implementation of adaptive compensatory neuromuscular strategies, resulting in modifications of the initial motion coordination. However, no studies have focused on the efficiency of the feedforward motor commands when muscular fatigue occurs for the first time during a particular movement. This study included 18 healthy subjects who had to perform arm-raising movements in a standing posture at a maximal velocity before and after a fatiguing procedure involving focal muscles. The arm-raising task implies the generation of predictive processes of control, namely Anticipatory Postural Adjustments (APAs), whose temporal and quantitative features have been shown to be dependent on the kinematics of the upcoming arm-raising movement. By altering significantly the kinematic profile of the focal movement with a fatiguing procedure, we sought to find out whether APAs scaled to the lower mechanical disturbance. APAs were measured using surface electromyography. Following the fatiguing procedure, acceleration peaks of the arm movement decreased by ~27%. APAs scaled to this lower fatigue-related disturbance during the very first trial post-fatigue, suggesting that the Central Nervous System can predict unexperienced mechanical effects of muscle fatigue. It is suggested that these results are accounted for by prediction processes in which the central integration of the groups III and IV afferents leads to an update of the internal model by remapping the relationship between focal motor command magnitude and the actual mechanical output.

AutoAssemblyD: a graphical user interface system for several genome assemblers.

PubMed

Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

2013-01-01

Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

Combustion Stability of the Gas Generator Assembly from J-2X Engine E10001 and Powerpack Tests

NASA Technical Reports Server (NTRS)

Hulka, J. R.; Kenny, R. L.; Casiano, M. J.

2013-01-01

Testing of a powerpack configuration (turbomachinery and gas generator assembly) and the first complete engine system of the liquid oxygen/liquid hydrogen propellant J-2X rocket engine have been completed at the NASA Stennis Space Center. The combustion stability characteristics of the gas generator assemblies on these two systems are of interest for reporting since considerable effort was expended to eliminate combustion instability during early development of the gas generator assembly with workhorse hardware. Comparing the final workhorse gas generator assembly development test data to the powerpack and engine system test data provides an opportunity to investigate how the nearly identical configurations of gas generator assemblies operate with two very different propellant supply systems one the autonomous pressure-fed test configuration on the workhorse development test stand, the other the pump-fed configurations on the powerpack and engine systems. The development of the gas generator assembly and the elimination of the combustion instability on the pressure-fed workhorse test stand have been reported extensively in the two previous Liquid Propulsion Subcommittee meetings 1-7. The powerpack and engine system testing have been conducted from mid-2011 through 2012. All tests of the powerpack and engine system gas generator systems to date have been stable. However, measureable dynamic behavior, similar to that observed on the pressure-fed test stand and reported in Ref. [6] and attributed to an injection-coupled response, has appeared in both powerpack and engine system tests. As discussed in Ref. [6], these injection-coupled responses are influenced by the interaction of the combustion chamber with a branch pipe in the hot gas duct that supplies gaseous helium to pre-spin the turbine during the start transient. This paper presents the powerpack and engine system gas generator test data, compares these data to the development test data, and provides additional combustion stability analyses of the configurations.

Status of the International Space Station Regenerative ECLSS Water Recovery and Oxygen Generation Systems

NASA Technical Reports Server (NTRS)

Bagdigian, Robert M.; Cloud, Dale

2005-01-01

NASA is developing three racks containing regenerative water recovery and oxygen generation systems (WRS and OGS) for deployment on the International Space Station (ISS). The major assemblies included in these racks are the Water Processor Assembly (WPA), Urine Processor Assembly (UPA), Oxygen Generation Assembly (OGA), and the Power Supply Module (PSM) supporting the OGA. The WPA and OGA are provided by Hamilton Sundstrand Space Systems International (HSSSI), Inc., while the UPA and PSM are developed in- house by the Marshall Space Flight Center (MSFC). The assemblies have completed the manufacturing phase and are in various stages of testing and integration into the flight racks. This paper summarizes the status as of April 2005 and describes some of the technical challenges encountered and lessons learned over the past year.

Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and c-JUN to Bypass PUMILIO Posttranscriptional Regulation

PubMed Central

Miles, Wayne O.; Lembo, Antonio; Volorio, Angela; Brachtel, Elena; Tian, Bin; Sgroi, Dennis; Provero, Paolo; Dyson, Nicholas

2017-01-01

Alternative polyadenylation (APA) is a process that changes the posttranscriptional regulation and translation potential of mRNAs via addition or deletion of 3′ untranslated region (3′ UTR) sequences. To identify posttranscriptional-regulatory events affected by APA in breast tumors, tumor datasets were analyzed for recurrent APA events. Motif mapping of the changed 3′ UTR regions found that APA-mediated removal of Pumilio regulatory elements (PRE) was unusually common. Breast tumor subtype–specific APA profiling identified triple-negative breast tumors as having the highest levels of APA. To determine the frequency of these events, an independent cohort of triple-negative breast tumors and normal breast tissue was analyzed for APA. APA-mediated shortening of NRAS and c-JUN was seen frequently, and this correlated with changes in the expression of downstream targets. mRNA stability and luciferase assays demonstrated APA-dependent alterations in RNA and protein levels of affected candidate genes. Examination of clinical parameters of these tumors found those with APA of NRAS and c-JUN to be smaller and less proliferative, but more invasive than non-APA tumors. RT-PCR profiling identified elevated levels of polyadenylation factor CSTF3 in tumors with APA. Overexpression of CSTF3 was common in triple-negative breast cancer cell lines, and elevated CSTF3 levels were sufficient to induce APA of NRAS and c-JUN. Our results support the hypothesis that PRE-containing mRNAs are disproportionately affected by APA, primarily due to high sequence similarity in the motifs utilized by polyadenylation machinery and the PUM complex. PMID:27758885

Anticipatory postural adjustments during sitting reach movement in post-stroke subjects.

PubMed

Pereira, Soraia; Silva, Cláudia C; Ferreira, Sílvia; Silva, Cláudia; Oliveira, Nuno; Santos, Rubim; Vilas-Boas, John P; Correia, Miguel V

2014-02-01

The study assessed the effect of velocity of arm movement on anticipatory postural adjustments (APAs) generation in the contralateral and ipsilateral muscles of individuals with stroke in seating. Ten healthy and eight post-stroke subjects were studied in sitting. The task consisted in reaching an object placed at scapular plane and mid-sternum height at self-selected and fast velocities. Electromyography was recorded from anterior deltoid (AD), upper (UT) and lower trapezius (LT) and latissimus dorsi (LD). While kinematic analysis was used to assess peak velocity and trunk displacement. Differences were found between the timing of APAs on ipsi and contralateral LD and LT in both movement speeds and in ipsilateral UT during movement of the non-affected arm at a self-selected velocity. A delay on the contralateral LD to reach movement with the non-affected arm at fast velocity was also observed. The trunk displacement was greater in post-stroke subjects. Individuals with stroke demonstrated a delay of APAs in the muscles on both sides of the body compared to healthy subjects. The delay was observed during performance of the reaching task with the fast and self-selected velocity. Copyright © 2013 Elsevier Ltd. All rights reserved.

Electrically-induced muscle fatigue affects feedforward mechanisms of control.

PubMed

Monjo, F; Forestier, N

2015-08-01

To investigate the effects of focal muscle fatigue induced by electromyostimulation (EMS) on Anticipatory Postural Adjustments (APAs) during arm flexions performed at maximal velocity. Fifteen healthy subjects performed self-paced arm flexions at maximal velocity before and after the completion of fatiguing electromyostimulation programs involving the medial and anterior deltoids and aiming to degrade movement peak acceleration. APA timing and magnitude were measured using surface electromyography. Following muscle fatigue, despite a lower mechanical disturbance evidenced by significant decreased peak accelerations (-12%, p<.001), APAs remained unchanged as compared to control trials (p>.11 for all analyses). The fatigue signals evoked by externally-generated contractions seem to be gated by the Central Nervous System and result in postural strategy changes which aim to increase the postural safety margin. EMS is widely used in rehabilitation and training programs for its neuromuscular function-related benefits. However and from a motor control viewpoint, the present results show that the use of EMS can lead to acute inaccuracies in predictive motor control. We propose that clinicians should investigate the chronic and global effects of EMS on motor control. Copyright © 2014 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.

PubMed

Cerveau, Nicolas; Jackson, Daniel J

2016-12-09

Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data. This challenge becomes apparent when a variety of modern assembly tools (of which there is no shortage) are applied to the same raw NGS dataset. With the same assembly parameters these tools can generate markedly different assembly outputs. In this study we present an approach that generates an optimized consensus de novo assembly of eukaryotic coding transcriptomes. This approach does not represent a new assembler, rather it combines the outputs of a variety of established assembly packages, and removes redundancy via a series of clustering steps. We test and validate our approach using Illumina datasets from six phylogenetically diverse eukaryotes (three metazoans, two plants and a yeast) and two simulated datasets derived from metazoan reference genome annotations. All of these datasets were assembled using three currently popular assembly packages (CLC, Trinity and IDBA-tran). In addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. For all eight datasets our pipeline generates more concise transcriptomes that in fact possess more unique annotatable protein domains than any of the three individual assemblers we employed. Another measure of assembly completeness (using the purpose built BUSCO databases) also confirmed that our approach yields more information. Our approach yields coding transcriptome assemblies that are more likely to be closer to biological reality than any of the three individual assembly packages we investigated. This approach (freely available as a simple perl script) will be of use to researchers working with species for which there is little or no reference data against which the assembly of a transcriptome can be performed.

Generation and memory for contextual detail.

PubMed

Mulligan, Neil W

2004-07-01

Generation enhances item memory but may not enhance other aspects of memory. In 12 experiments, the author investigated the effect of generation on context memory, motivated in part by the hypothesis that generation produces a trade-off in encoding item and contextual information. Participants generated some study words (e.g., hot-c__) and read others (e.g., hot-cold). Generation consistently enhanced item memory but did not enhance context memory. More specifically, generation disrupted context memory for the color of the target word but did not affect context memory for location, background color, and cue-word color. The specificity of the negative generation effect in context memory argues against a general item-context trade-off. A processing account of generation meets greater success. In addition, the results provide no evidence that generation enhances recollection of contextual details. Copyright 2004 APA, all rights reserved

Simplifier: a web tool to eliminate redundant NGS contigs.

PubMed

Ramos, Rommel Thiago Jucá; Carneiro, Adriana Ribeiro; Azevedo, Vasco; Schneider, Maria Paula; Barh, Debmalya; Silva, Artur

2012-01-01

Modern genomic sequencing technologies produce a large amount of data with reduced cost per base; however, this data consists of short reads. This reduction in the size of the reads, compared to those obtained with previous methodologies, presents new challenges, including a need for efficient algorithms for the assembly of genomes from short reads and for resolving repetitions. Additionally after abinitio assembly, curation of the hundreds or thousands of contigs generated by assemblers demands considerable time and computational resources. We developed Simplifier, a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes. Application of Simplifier to data generated by assembly of the genome of Corynebacterium pseudotuberculosis strain 258 reduced the number of contigs generated by ab initio methods from 8,004 to 5,272, a reduction of 34.14%; in addition, N50 increased from 1 kb to 1.5 kb. Processing the contigs of Escherichia coli DH10B with Simplifier reduced the mate-paired library 17.47% and the fragment library 23.91%. Simplifier removed redundant sequences from datasets produced by assemblers, thereby reducing the effort required for finalization of genome assembly in tests with data from Prokaryotic organisms. Simplifier is available at http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtmlIt requires Sun jdk 6 or higher.

Membrane Assembly during the Infection Cycle of the Giant Mimivirus

PubMed Central

Mutsafi, Yael; Shimoni, Eyal; Shimon, Amir; Minsky, Abraham

2013-01-01

Although extensively studied, the structure, cellular origin and assembly mechanism of internal membranes during viral infection remain unclear. By combining diverse imaging techniques, including the novel Scanning-Transmission Electron Microscopy tomography, we elucidate the structural stages of membrane biogenesis during the assembly of the giant DNA virus Mimivirus. We show that this elaborate multistage process occurs at a well-defined zone localized at the periphery of large viral factories that are generated in the host cytoplasm. Membrane biogenesis is initiated by fusion of multiple vesicles, ∼70 nm in diameter, that apparently derive from the host ER network and enable continuous supply of lipid components to the membrane-assembly zone. The resulting multivesicular bodies subsequently rupture to form large open single-layered membrane sheets from which viral membranes are generated. Membrane generation is accompanied by the assembly of icosahedral viral capsids in a process involving the hypothetical major capsid protein L425 that acts as a scaffolding protein. The assembly model proposed here reveals how multiple Mimivirus progeny can be continuously and efficiently generated and underscores the similarity between the infection cycles of Mimivirus and Vaccinia virus. Moreover, the membrane biogenesis process indicated by our findings provides new insights into the pathways that might mediate assembly of internal viral membranes in general. PMID:23737745

PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants

PubMed Central

Wu, Xiaohui; Zhang, Yumin; Li, Qingshun Q.

2016-01-01

Alternative polyadenylation (APA) is an important layer of gene regulation that produces mRNAs that have different 3′ ends and/or encode diverse protein isoforms. Up to 70% of annotated genes in plants undergo APA. Increasing numbers of poly(A) sites collected in various plant species demand new methods and tools to access and mine these data. We have created an open-access web service called PlantAPA (http://bmi.xmu.edu.cn/plantapa) to visualize and analyze genome-wide poly(A) sites in plants. PlantAPA provides various interactive and dynamic graphics and seamlessly integrates a genome browser that can profile heterogeneous cleavage sites and quantify expression patterns of poly(A) sites across different conditions. Particularly, through PlantAPA, users can analyze poly(A) sites in extended 3′ UTR regions, intergenic regions, and ambiguous regions owing to alternative transcription or RNA processing. In addition, it also provides tools for analyzing poly(A) site selections, 3′ UTR lengthening or shortening, non-canonical APA site switching, and differential gene expression between conditions, making it more powerful for the study of APA-mediated gene expression regulation. More importantly, PlantAPA offers a bioinformatics pipeline that allows users to upload their own short reads or ESTs for poly(A) site extraction, enabling users to further explore poly(A) site selection using stored PlantAPA poly(A) sites together with their own poly(A) site datasets. To date, PlantAPA hosts the largest database of APA sites in plants, including Oryza sativa, Arabidopsis thaliana, Medicago truncatula, and Chlamydomonas reinhardtii. As a user-friendly web service, PlantAPA will be a valuable addition to the community of biologists studying APA mechanisms and gene expression regulation in plants. PMID:27446120

Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells

PubMed Central

Lin, Zhuoheng; Feng, Xuyang; Jiang, Xue; Songyang, Zhou; Huang, Junjiu

2015-01-01

A recently developed strategy of sequencing alternative polyadenylation (APA) sites (SAPAS) with second-generation sequencing technology can be used to explore complete genome-wide patterns of tandem APA sites and global gene expression profiles. spermatogonial stem cells (SSCs) maintain long-term reproductive abilities in male mammals. The detailed mechanisms by which SSCs self-renew and generate mature spermatozoa are not clear. To understand the specific alternative polyadenylation pattern and global gene expression profile of male germline stem cells (GSCs, mainly referred to SSCs here), we isolated and purified mouse Thy1+ cells from testis by magnetic-activated cell sorting (MACS) and then used the SAPAS method for analysis, using pluripotent embryonic stem cells (ESCs) and differentiated mouse embryonic fibroblast cells (MEFs) as controls. As a result, we obtained 99,944 poly(A) sites, approximately 40% of which were newly detected in our experiments. These poly(A) sites originated from three mouse cell types and covered 17,499 genes, including 831 long non-coding RNA (lncRNA) genes. We observed that GSCs tend to have shorter 3'UTR lengths while MEFs tend towards longer 3'UTR lengths. We also identified 1337 genes that were highly expressed in GSCs, and these genes were highly consistent with the functional characteristics of GSCs. Our detailed bioinformatics analysis identified APA site-switching events at 3'UTRs and many new specifically expressed genes in GSCs, which we experimentally confirmed. Furthermore, qRT-PCR was performed to validate several events of the 334 genes with distal-to-proximal poly(A) switch in GSCs. Consistently APA reporter assay confirmed the total 3'UTR shortening in GSCs compared to MEFs. We also analyzed the cis elements around the proximal poly(A) site preferentially used in GSCs and found C-rich elements may contribute to this regulation. Overall, our results identified the expression level and polyadenylation site profiles and these data provide new insights into the processes potentially involved in the GSC life cycle and spermatogenesis. PMID:26713853

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

PubMed

Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi

2017-04-26

The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.

Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly.

PubMed

Peichel, Catherine L; Sullivan, Shawn T; Liachko, Ivan; White, Michael A

2017-09-01

Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs. Using Hi-C based PGA, we generated complete chromosome assemblies from a distribution of short contigs (20-100 kb). We found that 96.40% of contigs were correctly assigned to linkage groups (LGs), with ordering nearly identical to the previous genome assembly. Using available bacterial artificial chromosome (BAC) end sequences, we provide evidence that some of the few discrepancies between the Hi-C assembly and the existing assembly are due to structural variation between the populations used for the 2 assemblies or errors in the existing assembly. This Hi-C assembly also allowed us to improve the existing assembly, assigning over 60% (13.35 Mb) of the previously unassigned (~21.7 Mb) contigs to LGs. Together, our results highlight the potential of the Hi-C based PGA method to be used in combination with short read data to perform relatively inexpensive de novo genome assemblies. This approach will be particularly useful in organisms in which it is difficult to perform linkage mapping or to obtain high molecular weight DNA required for other scaffolding methods. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.

PubMed

Lu, Fu-Hao; McKenzie, Neil; Kettleborough, George; Heavens, Darren; Clark, Matthew D; Bevan, Michael W

2018-05-01

The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics. Here we use a Fosill 38-kb jumping library to assess medium and longer-range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values. Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.

Status of the Node 3 Regenerative Environmental Cpntrol& Life Support System Water Recovery & Oxygen Generation Systems

NASA Technical Reports Server (NTRS)

Carrasquillo, Robyn L.

2003-01-01

NASA s Marshall Space Flight Center is providing three racks containing regenerative water recovery and oxygen generation systems (WRS and OGS) for flight on the lnternational Space Station s (ISS) Node 3 element. The major assemblies included in these racks are the Water Processor Assembly (WPA), Urine Processor Assembly (UPA), Oxygen Generation Assembly (OGA), and the Power Supply Module (PSM) supporting the OGA. The WPA and OGA are provided by Hamilton Sundstrand Space Systems lnternational (HSSSI), while the UPA and PSM are being designed and manufactured in-house by MSFC. The assemblies are currently in the manufacturing and test phase and are to be completed and integrated into flight racks this year. This paper gives an overview of the technologies and system designs, technical challenges encountered and solved, and the current status.

A new strategy for genome assembly using short sequence reads and reduced representation libraries.

PubMed

Young, Andrew L; Abaan, Hatice Ozel; Zerbino, Daniel; Mullikin, James C; Birney, Ewan; Margulies, Elliott H

2010-02-01

We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we applied this approach to sequence and assembled the majority of the 125-Mb Drosophila melanogaster genome. We subsequently demonstrate the accuracy of our assembly method with meaningful comparisons against the current available D. melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrificing quality.

Young adults in conflict: confident but struggling, networked but disconnected.

PubMed

McLeigh, Jill D; Boberiene, Liepa V

2014-11-01

This article discusses the conflict the cohort of adults known as the Millennials has been affected by. More specifically this article takes a look at how changes in the economy and society have influenced Millennials and what can be done to promote their well-being and that of future generations. (c) 2014 APA, all rights reserved.

Reflections on an Evolving View of Giftedness and Talent: An Interview with Rena Subotnik

ERIC Educational Resources Information Center

Henshon, Suzanna E.

2005-01-01

This article presents an interview with Dr. Rena F. Subotnik, a director of the Center for Gifted Education Policy at the American Psychological Association (APA). The Center's mission is to generate public awareness, advocacy, clinical applications, and cutting-edge research ideas that will enhance the achievement and performance of children and…

A modular assembling platform for manufacturing of microsystems by optical tweezers

NASA Astrophysics Data System (ADS)

Ksouri, Sarah Isabelle; Aumann, Andreas; Ghadiri, Reza; Prüfer, Michael; Baer, Sebastian; Ostendorf, Andreas

2013-09-01

Due to the increased complexity in terms of materials and geometries for microsystems new assembling techniques are required. Assembling techniques from the semiconductor industry are often very specific and cannot fulfill all specifications in more complex microsystems. Therefore, holographic optical tweezers are applied to manipulate structures in micrometer range with highest flexibility and precision. As is well known non-spherical assemblies can be trapped and controlled by laser light and assembled with an additional light modulator application, where the incident laser beam is rearranged into flexible light patterns in order to generate multiple spots. The complementary building blocks are generated by a two-photon-polymerization process. The possibilities of manufacturing arbitrary microstructures and the potential of optical tweezers lead to the idea of combining manufacturing techniques with manipulation processes to "microrobotic" processes. This work presents the manipulation of generated complex microstructures with optical tools as well as a storage solution for 2PP assemblies. A sample holder has been developed for the manual feeding of 2PP building blocks. Furthermore, a modular assembling platform has been constructed for an `all-in-one' 2PP manufacturing process as a dedicated storage system. The long-term objective is the automation process of feeding and storage of several different 2PP micro-assemblies to realize an automated assembly process.

APA Handbook of Industrial and Organizational Psychology. Three-Volume Set--Volume 1: Building and Developing the Organization. Volume 2: Selecting and Developing Members for the Organization. Volume 3: Maintaining, Expanding, and Contracting the Organization. APA Handbooks in Psychology Series. APA Reference Books Collection

ERIC Educational Resources Information Center

Zedeck, Sheldon, Ed.

2011-01-01

APA Books® announces the "APA Handbook of Industrial and Organizational Psychology"--the first offering in an new reference series covering core and emerging subdisciplines, the "APA Handbooks in Psychology." I/O Psychology is both a science/practice and an applied/basic research discipline. Appropriately, the "APA…

Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers

PubMed Central

Wajid, Bilal; Serpedin, Erchin

2012-01-01

In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity. PMID:22768980

Assembling short reads from jumping libraries with large insert sizes.

PubMed

Vasilinetc, Irina; Prjibelski, Andrey D; Gurevich, Alexey; Korobeynikov, Anton; Pevzner, Pavel A

2015-10-15

Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies. We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads. Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades. ap@bioinf.spbau.ru Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Expression and effect of inhibition of aminopeptidase-A during nephrogenesis.

PubMed

Dijkman, Henry B P M; Assmann, Karel J M; Steenbergen, Eric J; Wetzels, Jack F M

2006-02-01

Aminopeptidase-A (APA) is a metalloprotease that cleaves N-terminal aspartyl and glutamyl residues from peptides. Its best-known substrate is angiotensin II (Ang II), the most active compound of the renin-angiotensin system (RAS). The RAS is involved in renal development. Most components of the RAS system are expressed in the developing kidney. Thus far, APA has not been studied in detail. In the present study we have evaluated the expression of APA at the protein, mRNA, and enzyme activity (EA) level in the kidney during nephrogenesis. Furthermore, we have studied the effect of inhibiting APA EA by injection of anti-APA antibodies into 1-day-old mice. APA expression was observed from the comma stage onwards, predominantly in the developing podocytes and brush borders of proximal tubular cells. Notably, APA was absent in the medulla or the renal arterioles. Inhibition of APA EA caused temporary podocyte foot-process effacement, suggesting a minimum role for APA during nephrogenesis.

Variability of Anticipatory Postural Adjustments During Gait Initiation in Individuals With Parkinson Disease.

PubMed

Lin, Cheng-Chieh; Creath, Robert A; Rogers, Mark W

2016-01-01

In people with Parkinson disease (PD), difficulties with initiating stepping may be related to impairments of anticipatory postural adjustments (APAs). Increased variability in step length and step time has been observed in gait initiation in individuals with PD. In this study, we investigated whether the ability to generate consistent APAs during gait initiation is compromised in these individuals. Fifteen subjects with PD and 8 healthy control subjects were instructed to take rapid forward steps after a verbal cue. The changes in vertical force and ankle marker position were recorded via force platforms and a 3-dimensional motion capture system, respectively. Means, standard deviations, and coefficients of variation of both timing and magnitude of vertical force, as well as stepping variables, were calculated. During the postural phase of gait initiation the interval was longer and the force modulation was smaller in subjects with PD. Both the variability of timing and force modulation were larger in subjects with PD. Individuals with PD also had a longer time to complete the first step, but no significant differences were found for the variability of step time, length, and speed between groups. The increased variability of APAs during gait initiation in subjects with PD could affect posture-locomotion coupling, and lead to start hesitation, and even falls. Future studies are needed to investigate the effect of rehabilitation interventions on the variability of APAs during gait initiation in individuals with PD.Video abstract available for more insights from the authors (see Supplemental Digital Content 1, http://links.lww.com/JNPT/A119).

APADB: a database for alternative polyadenylation and microRNA regulation events

PubMed Central

Müller, Sören; Rycak, Lukas; Afonso-Grunz, Fabian; Winter, Peter; Zawada, Adam M.; Damrath, Ewa; Scheider, Jessica; Schmäh, Juliane; Koch, Ina; Kahl, Günter; Rotter, Björn

2014-01-01

Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3′ untranslated region (3′UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3′UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3′ end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3′ end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3′UTR lengths, especially for chicken, and APADB provides necessary information to close this gap. Database URL: http://tools.genxpro.net/apadb/ PMID:25052703

Molecular characteristics of the KCNJ5 mutated aldosterone-producing adenomas.

PubMed

Murakami, Masanori; Yoshimoto, Takanobu; Nakabayashi, Kazuhiko; Nakano, Yujiro; Fukaishi, Takahiro; Tsuchiya, Kyoichiro; Minami, Isao; Bouchi, Ryotaro; Okamura, Kohji; Fujii, Yasuhisa; Hashimoto, Koshi; Hata, Ken-Ichiro; Kihara, Kazunori; Ogawa, Yoshihiro

2017-10-01

The pathophysiology of aldosterone-producing adenomas (APAs) has been investigated via genetic approaches and the pathogenic significance of a series of somatic mutations, including KCNJ5 , has been uncovered. However, how the mutational status of an APA is associated with its molecular characteristics, including its transcriptome and methylome, has not been fully understood. This study was undertaken to explore the molecular characteristics of APAs, specifically focusing on APAs with KCNJ5 mutations as opposed to those without KCNJ5 mutations, by comparing their transcriptome and methylome status. Cortisol-producing adenomas (CPAs) were used as reference. We conducted transcriptome and methylome analyses of 29 APAs with KCNJ5 mutations, 8 APAs without KCNJ5 mutations and 5 CPAs. Genome-wide gene expression and CpG methylation profiles were obtained from RNA and DNA samples extracted from these 42 adrenal tumors. Cluster analysis of the transcriptome and methylome revealed molecular heterogeneity in APAs depending on their mutational status. DNA hypomethylation and gene expression changes in Wnt signaling and inflammatory response pathways were characteristic of APAs with KCNJ5 mutations. Comparisons between transcriptome data from our APAs and that from normal adrenal cortex obtained from the Gene Expression Omnibus suggested similarities between APAs with KCNJ5 mutations and zona glomerulosa. The present study, which is based on transcriptome and methylome analyses, indicates the molecular heterogeneity of APAs depends on their mutational status. Here, we report the unique characteristics of APAs with KCNJ5 mutations. © 2017 Society for Endocrinology.

A postmortem and future look at the personality disorders in DSM-5.

PubMed

Widiger, Thomas A

2013-10-01

It might seem difficult to describe the outcome of the proposals by the American Psychiatric Association's (APA) Personality and Personality Disorders Work Group (PPDWG) to be a success, given that all of the proposals were ultimately rejected. Nevertheless, one can interpret the result as a step forward, because the final outcome might not have been much different if a more conservative approach was adopted at the outset. The PPDWG did provide a significant contribution to the field through the provision of proposals that will likely generate a considerable body of informative research. The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) effort and suggestions for the future are discussed with respect to magnitude of change, documentation of empirical support, and addressing opposition. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Gonadotropin-Releasing Hormone Stimulate Aldosterone Production in a Subset of Aldosterone-Producing Adenoma

PubMed Central

Kishimoto, Rui; Oki, Kenji; Yoneda, Masayasu; Gomez-Sanchez, Celso E.; Ohno, Haruya; Kobuke, Kazuhiro; Itcho, Kiyotaka; Kohno, Nobuoki

2016-01-01

Abstract We aimed to detect novel genes associated with G protein-coupled receptors (GPCRs) in aldosterone-producing adenoma (APA) and elucidate the mechanisms underlying aldosterone production. Microarray analysis targeting GPCR-associated genes was conducted using APA without known mutations (APA-WT) samples (n = 3) and APA with the KCNJ5 mutation (APA-KCNJ5; n = 3). Since gonadotropin-releasing hormone receptor (GNRHR) was the highest expression in APA-WT by microarray analysis, we investigated the effect of gonadotropin-releasing hormone (GnRH) stimulation on aldosterone production. The quantitative polymerase chain reaction assay results revealed higher GNRHR expression levels in APA-WT samples those in APA-KCNJ5 samples (P < 0.05). LHCGR levels were also significantly elevated in APA-WT samples, and there was a significant and positive correlation between GNRHR and LHCGR expression in all APA samples (r = 0.476, P < 0.05). Patients with APA-WT (n = 9), which showed higher GNRHR and LHCGR levels, had significantly higher GnRH-stimulated aldosterone response than those with APA-KCNJ5 (n = 13) (P < 0.05). Multiple regression analysis revealed that the presence of the KCNJ5 mutation was linked to GNRHR mRNA expression (β = 0.94 and P < 0.01). HAC15 cells with KCNJ5 gene carrying T158A mutation exhibited a significantly lower GNRHR expression than that in control cells (P < 0.05). We clarified increased expression of GNRHR and LHCGR in APA-WT, and the molecular analysis including the receptor expression associated with clinical findings of GnRH stimulation. PMID:27196470

Bilateral aldosterone-producing adenomas: differentiation from bilateral adrenal hyperplasia.

PubMed

Wu, V C; Chueh, S C; Chang, H W; Lin, W C; Liu, K L; Li, H Y; Lin, Y H; Wu, K D; Hsieh, B S

2008-01-01

Primary aldosteronism (PA) is a common curable disease of secondary hypertension. Most such patients have either idiopathic bilateral adrenal hyperplasia (BAH) or unilateral aldosterone-producing adenoma (APA). Bilateral APAs are reportedly extremely rare. To compare the distinctive characteristics, clinical course, and outcomes of bilateral APA vs. BAH. Retrospective record review. From July 1994 to Jan 2007, 190 patients diagnosed with PA underwent surgical intervention at our hospital. Bilateral APA was diagnosed in 7/164 patients with histologically-proven APA. Twenty-one patients diagnosed as BAH, and 21 randomly selected of unilateral APA patients, matched by age and sex served as controls. Patients with bilateral APA had similar blood pressure, arterial blood gas analysis, spot urinary potassium to creatinine ratio and clinical symptoms to those with BAH, but lower serum potassium levels (p = 0.027), lower plasma renin activity (p = 0.037), and higher plasma aldosterone concentrations (p = 0.029). Aldosterone-renin ratio (ARR) after administration of 50 mg captopril was higher in bilateral APA than in BAH patients (p = 0.023), but not different between unilateral APA and BAH (p = 0.218). A cut-off of ARR >100 ng/dl per ng/ml/h and plasma aldosterone >20 ng/dl after captopril significantly differentiated bilateral APA from BAH. Bilateral subtotal adrenalectomy normalized blood pressure and biochemistry in all patients with bilateral APA. Bilateral APA, presenting simultaneously or sequentially, may not be a rare disease, accounting for 4.3% of APA in this sample. The clinical presentations of bilateral functional adenoma are not different from BAH, but patients with low serum potassium and ARR >100 after captopril should be carefully evaluated for bilateral adenoma.

The APA Style Converter: a Web-based interface for converting articles to APA style for publication.

PubMed

Li, Ping; Cunningham, Krystal

2005-05-01

The APA Style Converter is a Web-based tool with which authors may prepare their articles in APA style according to the APA Publication Manual (5th ed.). The Converter provides a user-friendly interface that allows authors to copy and paste text and upload figures through the Web, and it automatically converts all texts, references, and figures to a structured article in APA style. The output is saved in PDF or RTF format, ready for either electronic submission or hardcopy printing.

Analysis of Illumina Microbial Assemblies

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

Clum, Alicia; Foster, Brian; Froula, Jeff

2010-05-28

Since the emerging of second generation sequencing technologies, the evaluation of different sequencing approaches and their assembly strategies for different types of genomes has become an important undertaken. Next generation sequencing technologies dramatically increase sequence throughput while decreasing cost, making them an attractive tool for whole genome shotgun sequencing. To compare different approaches for de-novo whole genome assembly, appropriate tools and a solid understanding of both quantity and quality of the underlying sequence data are crucial. Here, we performed an in-depth analysis of short-read Illumina sequence assembly strategies for bacterial and archaeal genomes. Different types of Illumina libraries as wellmore » as different trim parameters and assemblers were evaluated. Results of the comparative analysis and sequencing platforms will be presented. The goal of this analysis is to develop a cost-effective approach for the increased throughput of the generation of high quality microbial genomes.« less

Removable bearing arrangement for a wind turbine generator

DOEpatents

Bagepalli, Bharat Sampathkumaran; Jansen, Patrick Lee; Gadre, Aniruddha Dattatraya

2010-06-15

A wind generator having removable change-out bearings includes a rotor and a stator, locking bolts configured to lock the rotor and stator, a removable bearing sub-assembly having at least one shrunk-on bearing installed, and removable mounting bolts configured to engage the bearing sub-assembly and to allow the removable bearing sub-assembly to be removed when the removable mounting bolts are removed.

Method for changing removable bearing for a wind turbine generator

DOEpatents

Bagepalli, Bharat Sampathkumaran [Niskayuna, NY; Jansen, Patrick Lee , Gadre; Dattatraya, Aniruddha [Rexford, NY

2008-04-22

A wind generator having removable change-out bearings includes a rotor and a stator, locking bolts configured to lock the rotor and stator, a removable bearing sub-assembly having at least one shrunk-on bearing installed, and removable mounting bolts configured to engage the bearing sub-assembly and to allow the removable bearing sub-assembly to be removed when the removable mounting bolts are removed.

Assembly and Testing of a Compact, Lightweight Homopolar Generator Power Supply

DTIC Science & Technology

1983-06-01

ASSEMBLY AND TESTING OF A COMPACT, LIGHTWEIGHT HOMOPOLAR GENERATOR POWER SUPPLY J. H. Gully Center for Electromechanics The University of Texas...portable systems. The initial step in developing the power supply was to design, fabricate and test a prototype homopolar generator, attempting to...levels. SUPPORT STRUCTURE HYDRAULIC Fig. 1. Section through compact homopolar generator ~1 l-oot!:__ __ 63.80 ----~ (25. 12) ~------ 85.88

In Situ Generation of Two-Dimensional Au–Pt Core–Shell Nanoparticle Assemblies

PubMed Central

2010-01-01

Two-dimensional assemblies of Au–Pt bimetallic nanoparticles are generated in situ on polyethyleneimmine (PEI) silane functionalized silicon and indium tin oxide (ITO) coated glass surfaces. Atomic force microscopy (AFM), UV–Visible spectroscopy, and electrochemical measurements reveal the formation of core–shell structure with Au as core and Pt as shell. The core–shell structure is further supported by comparing with the corresponding data of Au nanoparticle assemblies. Static contact angle measurements with water show an increase in hydrophilic character due to bimetallic nanoparticle generation on different surfaces. It is further observed that these Au–Pt core–shell bimetallic nanoparticle assemblies are catalytically active towards methanol electro-oxidation, which is the key reaction for direct methanol fuel cells (DMFCs). PMID:20651923

Aminopeptidase A initiates tumorigenesis and enhances tumor cell stemness via TWIST1 upregulation in colorectal cancer

PubMed Central

Chuang, Hui-Yu; Jiang, Jeng-Kae; Yang, Muh-Hwa; Wang, Hsei-Wei; Li, Ming-Chun; Tsai, Chan-Yen; Jhang, Yau-Yun; Huang, Jason C.

2017-01-01

Metastasis accounts for the high mortality rate associated with colorectal cancer (CRC), but metastasis regulators are not fully understood. To identify a novel gene involved in tumor metastasis, we used oligonucleotide microarrays, transcriptome distance analyses, and machine learning algorithms to determine links between primary and metastatic colorectal cancers. Aminopeptidase A (APA; also known as ENPEP) was selected as our focus because its relationship with colorectal cancer requires clarification. Higher APA mRNA levels were observed in patients in advanced stages of cancer, suggesting a correlation between ENPEP and degree of malignancy. Our data also indicate that APA overexpression in CRC cells induced cell migration, invasion, anchorage-independent capability, and mesenchyme-like characteristics (e.g., EMT markers). We also observed TWIST induction in APA-overexpressing SW480 cells and TWIST down-regulation in HT29 cells knocked down with APA. Both APA silencing and impaired APA activity were found to reduce migratory capacity, cancer anchorage, stemness properties, and drug resistance in vitro and in vivo. We therefore suggest that APA enzymatic activity affects tumor initiation and cancer malignancy in a TWIST-dependent manner. Results from RT-qPCR and the immunohistochemical staining of specimens taken from CRC patients indicate a significant correlation between APA and TWIST. According to data from SurvExpress analyses of TWIST1 and APA mRNA expression profiles, high APA and TWIST expression are positively correlated with poor CRC prognosis. APA may act as a prognostic factor and/or therapeutic target for CRC metastasis and recurrence. PMID:28177885

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

PubMed Central

Neve, Jonathan; Burger, Kaspar; Li, Wencheng; Hoque, Mainul; Patel, Radhika; Tian, Bin; Gullerova, Monika; Furger, Andre

2016-01-01

Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3′ UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type–specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3′ UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice. PMID:26546131

Analysis of 3-aminopropionamide: a potential precursor of acrylamide.

PubMed

Bagdonaite, Kristina; Viklund, Gunilla; Skog, Kerstin; Murkovic, Michael

2006-11-30

An analytical method for the analysis of 3-aminopropionamide (3-APA) based on derivatization with dansyl chloride and liquid chromatography/fluorescence detection was developed. We have analysed 3-APA formation in raw potatoes, grown and stored under different condition, green and roasted coffee beans and in freeze dried mixtures of asparagine with sucrose and glucose in molar ratio of 1:0.5, 1:1, and 1:1.5. In potatoes the 3-APA content varied depending on the potato variety. We detected 3-APA in potatoes up to 14 microg/g fresh weight. In the model experiment glucose had a stronger capacity to form 3-APA. The substance was formed at temperatures as low as 130 degrees C. However, in the model experiment with sucrose 3-APA was formed not below 150 degrees C. In heated mixtures with increasing molar ratio of sucrose at 170 degrees C we noticed a decrease of 3-APA and in the same mixtures at 150 degrees C we observed an increase of 3-APA. In coffee 3-APA was not formed, neither in green nor in roasted beans.

Low complexity adaptive equalizers for underwater acoustic communications

NASA Astrophysics Data System (ADS)

Soflaei, Masoumeh; Azmi, Paeiz

2014-08-01

Interference signals due to scattering from surface and reflecting from bottom is one of the most important problems of reliable communications in shallow water channels. To solve this problem, one of the best suggested ways is to use adaptive equalizers. Convergence rate and misadjustment error in adaptive algorithms play important roles in adaptive equalizer performance. In this paper, affine projection algorithm (APA), selective regressor APA(SR-APA), family of selective partial update (SPU) algorithms, family of set-membership (SM) algorithms and selective partial update selective regressor APA (SPU-SR-APA) are compared with conventional algorithms such as the least mean square (LMS) in underwater acoustic communications. We apply experimental data from the Strait of Hormuz for demonstrating the efficiency of the proposed methods over shallow water channel. We observe that the values of the steady-state mean square error (MSE) of SR-APA, SPU-APA, SPU-normalized least mean square (SPU-NLMS), SPU-SR-APA, SM-APA and SM-NLMS algorithms decrease in comparison with the LMS algorithm. Also these algorithms have better convergence rates than LMS type algorithm.

Significance of anti-phospholipid antibodies in patients with lupus nephritis.

PubMed

Frampton, G; Hicks, J; Cameron, J S

1991-06-01

Anti-phospholipid antibodies (APA) as markers or mediators of thrombosis in lupus could be of pathogenetic significance in nephritis, since glomerular capillary thrombi are an indicator of subsequent renal dysfunction. Isotype specific APA antibodies were measured, using cardiolipin as the antigen, in 76 patients with lupus nephritis. Twenty-nine percent of the patients had elevated IgG APA. Overall, 43% of patients showed raised levels of at least one isotype. In general, APA had specificity for anionic phospholipids. In vitro lupus anticoagulant activity was associated with all three isotypes of APA, but only the IgM isotype correlated with the biological false positive test for syphilis. APA were not associated with thromboses or neurological involvement, and only the IgA isotype correlated with thrombocytopenia. We confirmed an association between the presence of intraglomerular thrombi and serum IgG APA. However, we found no association between APA and renal histological pattern, or long-term renal function. Our data, therefore, do not support a major pathogenetic role for APA in the nephritis of lupus in treated patients.

Electrode assemblies, plasma generating apparatuses, and methods for generating plasma

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

Kong, Peter C.; Grandy, Jon D.; Detering, Brent A.

Electrode assemblies for plasma reactors include a structure or device for constraining an arc endpoint to a selected area or region on an electrode. In some embodiments, the structure or device may comprise one or more insulating members covering a portion of an electrode. In additional embodiments, the structure or device may provide a magnetic field configured to control a location of an arc endpoint on the electrode. Plasma generating modules, apparatus, and systems include such electrode assemblies. Methods for generating a plasma include covering at least a portion of a surface of an electrode with an electrically insulating membermore » to constrain a location of an arc endpoint on the electrode. Additional methods for generating a plasma include generating a magnetic field to constrain a location of an arc endpoint on an electrode.« less

Short-Term Effects of Thoracic Spine Manipulation on the Biomechanical Organisation of Gait Initiation: A Randomized Pilot Study

PubMed Central

Ditcharles, Sébastien; Yiou, Eric; Delafontaine, Arnaud; Hamaoui, Alain

2017-01-01

Speed performance during gait initiation is known to be dependent on the capacity of the central nervous system to generate efficient anticipatory postural adjustments (APA). According to the posturo-kinetic capacity (PKC) concept, any factor enhancing postural chain mobility and especially spine mobility, may facilitate the development of APA and thus speed performance. “Spinal Manipulative Therapy High-Velocity, Low-Amplitude” (SMT-HVLA) is a healing technique applied to the spine which is routinely used by healthcare practitioners to improve spine mobility. As such, it may have a positive effect on the PKC and therefore facilitate gait initiation. The present study aimed to investigate the short-term effect of thoracic SMT-HVLA on spine mobility, APA and speed performance during gait initiation. Healthy young adults (n = 22) performed a series of gait initiation trials on a force plate before (“pre-manipulation” condition) and after (“post-manipulation” condition) a sham manipulation or an HVLA manipulation applied to the ninth thoracic vertebrae (T9). Participants were randomly assigned to the sham (n = 11) or the HVLA group (n = 11).The spine range of motion (ROM) was assessed in each participant immediately after the sham or HVLA manipulations using inclinometers. The results showed that the maximal thoracic flexion increased in the HVLA group after the manipulation, which was not the case in the sham group. In the HVLA group, results further showed that each of the following gait initiation variables reached a significantly lower mean value in the post-manipulation condition as compared to the pre-manipulation condition: APA duration, peak of anticipatory backward center of pressure displacement, center of gravity velocity at foot-off, mechanical efficiency of APA, peak of center of gravity velocity and step length. In contrast, for the sham group, results showed that none of the gait initiation variables significantly differed between the pre- and post-manipulation conditions. It is concluded that HVLA manipulation applied to T9 has an immediate beneficial effect on spine mobility but a detrimental effect on APA development and speed performance during gait initiation. We suggest that a neural effect induced by SMT-HVLA, possibly mediated by a transient alteration in the early sensory-motor integration, might have masked the potential mechanical benefits associated with increased spine mobility. PMID:28713254

The Anti-Inflammatory Actions of Auricular Point Acupressure for Chronic Low Back Pain

PubMed Central

Lin, Wei-Chun; Morone, Natalia E.; Albers, Kathryn M.

2015-01-01

Background. Auricular point acupressure (APA) is a promising treatment for pain management. Few studies have investigated the physiological mechanisms of APA analgesics. Method. In this pilot randomized clinical trial (RCT), a 4-week APA treatment was used to manage chronic low back pain (CLBP). Sixty-one participants were randomized into a real APA group (n = 32) or a sham APA group (n = 29). Blood samples, pain intensity, and physical function were collected at baseline and after 4 weeks of treatment. Results. Subjects in the real APA group reported a 56% reduction of pain intensity and a 26% improvement in physical function. Serum blood samples showed (1) a decrease in IL-1β, IL-2, IL-6, and calcitonin gene-related peptide [CGRP] and (2) an increase in IL-4. In contrast, subjects in the sham APA group (1) reported a 9% reduction in pain and a 2% improvement in physical function and (2) exhibited minimal changes of inflammatory cytokines and neuropeptides. Statistically significant differences in IL-4 and CGRP expression between the real and sham APA groups were verified. Conclusion. These findings suggest that APA treatment affects pain intensity through modulation of the immune system, as reflected by APA-induced changes in serum inflammatory cytokine and neuropeptide levels. PMID:26170869

Transgene Delivery using Poly(amino ether)-Gold Nanorod Assemblies

PubMed Central

Ramos, James; Rege, Kaushal

2012-01-01

Gold nanorods (GNRs) have emerged as promising nanomaterials for biosensing, imaging, photothermal treatment and therapeutic delivery for several diseases, including cancer. We have generated poly(amino ether)-functionalized gold nanorods (PAE-GNRs) using a layer-by-layer deposition approach; polymers from a poly(amino ether) library recently synthesized in our laboratory were employed to generate the PAE-GNR assemblies. PAE-GNR assemblies demonstrate long-term colloidal stability as well as the capacity to bind plasmid DNA by means of electrostatic interactions. Sub-toxic concentrations of PAE-GNRs were employed to deliver plasmid DNA to prostate cancer cells in vitro. PAE-GNRs generated using 1,4C-1,4Bis, a cationic polymer from our laboratory demonstrated significantly higher transgene expression and exhibited lower cytotoxicities when compared to similar assemblies generated using 25 kDa poly(ethylene imine) (PEI25k-GNRs), a current standard for polymer-mediated gene delivery. The roles of polyelectrolyte chemistry and zeta-potential in determining transgene expression efficacies of PAE-GNR assemblies were investigated. Our results indicate that stable and effective PAE-GNR assemblies are a promising engineered platform for transgene delivery. PAE-GNRs also have the potential to be used simultaneously for photothermal ablation, photothermally enhanced drug and gene delivery, and biological imaging, thus making them a powerful theranostic platform. PMID:22170455

Aminopeptidase A is a functional target in angiogenic blood vessels.

PubMed

Marchiò, Serena; Lahdenranta, Johanna; Schlingemann, Reinier O; Valdembri, Donatella; Wesseling, Pieter; Arap, Marco A; Hajitou, Amin; Ozawa, Michael G; Trepel, Martin; Giordano, Ricardo J; Nanus, David M; Dijkman, Henri B P M; Oosterwijk, Egbert; Sidman, Richard L; Cooper, Max D; Bussolino, Federico; Pasqualini, Renata; Arap, Wadih

2004-02-01

We show that a membrane-associated protease, aminopeptidase A (APA), is upregulated and enzymatically active in blood vessels of human tumors. To gain mechanistic insight, we evaluated angiogenesis in APA null mice. We found that, although these mice develop normally, they fail to mount the expected angiogenic response to hypoxia or growth factors. We then isolated peptide inhibitors of APA from a peptide library and show that they specifically bind to and inhibit APA, suppress migration and proliferation of endothelial cells, inhibit angiogenesis, and home to tumor blood vessels. Finally, we successfully treated tumor-bearing mice with APA binding peptides or anti-APA blocking monoclonal antibodies. These data show that APA is a regulator of blood vessel formation, and can serve as a functional vascular target.

Improvement of anticipatory postural adjustments for balance control: effect of a single training session.

PubMed

Kanekar, Neeta; Aruin, Alexander S

2015-04-01

Humans use anticipatory and compensatory postural strategies to maintain and restore balance when perturbed. Inefficient generation and utilization of anticipatory postural adjustments (APAs) is one of the reasons for postural instability. The aim of the study was to investigate the role of training in improvement of APAs and its effect on subsequent control of posture. Thirteen healthy young adults were exposed to predictable external perturbations before and after a single training session consisting of catches of a medicine ball thrown at the shoulder level. 3-D body kinematics, EMG activity of thirteen trunk and lower limb muscles, and ground reaction forces were recorded before and immediately after a single training session. Muscle onsets, EMG integrals, center of pressure (COP), and center of mass (COM) displacements were analyzed during the anticipatory and compensatory phases of postural control. The effect of a single training session was seen as significantly early muscle onsets and larger anticipatory COP displacements. As a result, significantly smaller peak COM displacements were observed after the perturbation indicating greater postural stability. The outcome of this study provides a background for examining the role of training in improvement of APAs and its effect on postural stability in individuals in need. Copyright © 2014 Elsevier Ltd. All rights reserved.

Downscaling Alkaline Phosphatase Activity in a Subtropical Reservoir

NASA Astrophysics Data System (ADS)

Tseng, Y.

2011-12-01

This research was conducted by downscaling study to understand phosphorus (P)-deficient status of different plankton and the role of alkaline phosphatase activity (APA) in subtropical Feitsui Reservoir. Results from field survey showed that bulk APA (1.6~95.2 nM h-1) was widely observed in the epilimnion (0~20 m) with an apparent seasonal variations, suggesting that plankton in the system were subjected to P-deficient seasonally. Mixed layer depth (an index of phosphate availability) is the major factor influencing the variation of bulk APA and specific APA (124~1,253 nmol mg C-1 h-1), based on multiple linear regression analysis. Size-fractionated APA assays showed that picoplankton (size 0.2~3 um) contributed most of the bulk APA in the system. In addition, single-cell APA detected by enzyme-labeled fluorescence (ELF) assay indicated that heterotrophic bacteria are the major contributors of APA. Thus, we can infer that bacteria play an important role in accelerating P-cycle within P-deficient systems. Light/nutrient manipulation bioassays showed that bacterial growth was directly controlled by phosphate, while picocyanobacterial growth is controlled by light and can out-compete bacteria under P-limited condition with the aid of light. Further analysis revealed that the strength of summer typhoon is a factor responsible for the inter-annual variability of bulk and specific APA. APA study demonstrated the episodic events (e.g. strong typhoon and extreme precipitation) had significant influence on APA variability in sub-tropical to tropical aquatic ecosystems. Hence, the results herein will allow future studies on monitoring typhoon disturbance (intensity and frequency) as well as the APA of plankton during summer-to-autumn in subtropical systems.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

PubMed

Sim, Mikang; Kim, Jaebum

2015-02-01

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

Review of general algorithmic features for genome assemblers for next generation sequencers.

PubMed

Wajid, Bilal; Serpedin, Erchin

2012-04-01

In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity. Copyright © 2012 Beijing Institute of Genomics, Chinese Academy of Sciences. Published by Elsevier Ltd. All rights reserved.

Wind turbine having a direct-drive drivetrain

DOEpatents

Bevington, Christopher M.; Bywaters, Garrett L.; Coleman, Clint C.; Costin, Daniel P.; Danforth, William L.; Lynch, Jonathan A.; Rolland, Robert H.

2011-02-22

A wind turbine comprising an electrical generator that includes a rotor assembly. A wind rotor that includes a wind rotor hub is directly coupled to the rotor assembly via a simplified connection. The wind rotor and generator rotor assembly are rotatably mounted on a central spindle via a bearing assembly. The wind rotor hub includes an opening having a diameter larger than the outside diameter of the central spindle adjacent the bearing assembly so as to allow access to the bearing assembly from a cavity inside the wind rotor hub. The spindle is attached to a turret supported by a tower. Each of the spindle, turret and tower has an interior cavity that permits personnel to traverse therethrough to the cavity of the wind rotor hub. The wind turbine further includes a frictional braking system for slowing, stopping or keeping stopped the rotation of the wind rotor and rotor assembly.

Characterization of the Apa antigen from M. avium subsp. paratuberculosis: a conserved Mycobacterium antigen that elicits a strong humoral response in cattle.

PubMed

Gioffré, A; Echeverría-Valencia, G; Arese, A; Morsella, C; Garbaccio, S; Delgado, F; Zumárraga, M; Paolicchi, F; Cataldi, A; Romano, M I

2009-12-15

Johne's disease or paratuberculosis is widespread in almost all countries and remains difficult to eradicate. Nowadays, diagnosis of Mycobacterium avium subsp. paratuberculosis (MPTB) infection is one of the main concerns. In this work, we evaluated the expression, biochemical properties and antigenicity of the Apa antigen, encoded by the gene annotated as MAP1569, in the MPTB genome. We confirmed its expression in MPTB and its glycosylation by the ConA binding assay. Although the MPTB-Apa is not an immunodominant antigen, MPTB-infected cattle showed a strong humoral response to recombinant Apa by Western blot and ELISA. Milk was also a suitable sample to be tested by ELISA. We comparatively analysed the humoral cross-reactivity to the Apa from MPTB (MPTB-Apa) and the orthologue from Mycobacterium tuberculosis (MT-Apa, identical to that from Mycobacterium bovis) in both infected and control cows. Response of M. bovis- and MPTB-infected animals against MT-Apa was similar (P=0.6985) but the response of the M. bovis-infected ones to MPTB-Apa was differential, being significantly diminished (P<0.0001). Although 6 out 45 animals from MPTB-infected herds responded to MPTB-Apa stimulation in the IFNgamma release assay, we found no significant differences when compared infected herds with non-infected ones (P=0.34). This antigen, in contrast to bovine Purified Protein Derivative (PPDb), was strongly represented in avian PPD (PPDa), as shown by the recognition of BALB/c mice hyperimmune sera against MPTB-Apa by Dot-blot immunoassay. We therefore demonstrated the antigenicity of Apa in MPTB-infected animals and a differential response to the recombinant antigen when compared to M. bovis-infected animals. These traits herein described, added to the usefulness of milk samples to detect IgG anti-Apa, could be important for routine screening in dairy cattle, considering a multiantigenic approach to overcome the lack of immunodominance.

Sacrifice of accessory pudendal arteries in normally potent men during robot-assisted radical prostatectomy does not impact potency.

PubMed

Box, Geoffrey N; Kaplan, Adam G; Rodriguez, Esequiel; Skarecky, Douglas W; Osann, Kathryn E; Finley, David S; Ahlering, Thomas E

2010-01-01

Whether or not sacrificing accessory pudendal arteries (APAs) during radical prostatectomy affects potency has been an ongoing source of concern. Herein, we present our potency results relative to sacrificing APAs in normally pre-potent men following robot-assisted radical prostatectomy (RARP). The distribution of APAs and clinical characteristics were prospectively recorded in 200 consecutive patients undergoing RARP with a cautery-free technique. Sexual function was assessed using the International Index of Erectile Function 5-item questionnaire (IIEF-5). All APAs were sacrificed due to stapling the dorsal vein complex. Postoperatively, potency was defined by an affirmative answer to the following two questions: "Were erections adequate for penetration?" and "were the erections satisfactory?" Postoperative IIEF-5 scores and quality of erections (% of preoperative firmness: 0%, 25%, 50%, 75%, 100%) were also obtained. Subgroup analysis of patients age < or =65 years with IIEF-5 score of 22-25 was performed. Eighty patients (40%) had APAs. Preoperatively, there was no association with having an APA and normal/abnormal sexual function. Preoperatively, 58/200 were < or =65 years with self-administered IIEF-5 scores of 22-25. Postoperatively, 53/58 (91%) were potent at 24 months follow-up. Nineteen of 58 patients had a sacrificed APA; 39 patients had no APA. Eighteen of 19 (95%) patients with sacrificed APAs were potent vs. 35/39 (90%) with no APA present (P = 0.53). Multivariate analysis showed no significant correlation between sacrificing an APA and time of potency recovery, quality of postoperative erections (94% vs. 90% P = 0.80) or mean IIEF-5 score (22.4 vs. 20.8, P = 0.13). We found no correlation between the presence or absence of APAs and preoperative sexual function. Furthermore, after sacrificing all APAs, we found no correlation with potency return, time to return of potency, quality of erections, or mean IIEF-5 scores at 24 months.

NEFM (Neurofilament Medium) Polypeptide, a Marker for Zona Glomerulosa Cells in Human Adrenal, Inhibits D1R (Dopamine D1 Receptor)-Mediated Secretion of Aldosterone.

PubMed

Maniero, Carmela; Garg, Sumedha; Zhao, Wanfeng; Johnson, Timothy Isaac; Zhou, Junhua; Gurnell, Mark; Brown, Morris J

2017-08-01

Heterogeneity among aldosterone-producing adenomas (APAs) has been highlighted by the discovery of somatic mutations. KCNJ5 mutations predominate in large zona fasciculata (ZF)-like APAs; mutations in CACNA1D , ATP1A1, ATP2B3 , and CTNNB1 are more likely to be found in small zona glomerulosa (ZG)-like APAs. Microarray comparison of KCNJ5 mutant versus wild-type APAs revealed significant differences in transcriptomes. NEFM , encoding a neurofilament subunit which is a D1R (dopamine D1 receptor)-interacting protein, was 4-fold upregulated in ZG-like versus ZF-like APAs and 14-fold more highly expressed in normal ZG versus ZF. Immunohistochemistry confirmed selective expression of NEFM (neurofilament medium) polypeptide in ZG and in ZG-like APAs. Silencing NEFM in adrenocortical H295R cells increased basal aldosterone secretion and cell proliferation; silencing also amplified aldosterone stimulation by the D1R agonist, fenoldopam, and inhibition by the D1R antagonist, SCH23390. NEFM coimmunoprecipitated with D1R, and its expression was stimulated by fenoldopam. Immunohistochemistry for D1R was mainly intracellular in ZG-like APAs but membranous in ZF-like APAs. Aldosterone secretion in response to fenoldopam in primary cells from ZF-like APAs was higher than in cells from ZG-like APAs. Transfection of mutant KCNJ5 caused a large reduction in NEFM expression in H295R cells. We conclude that NEFM is a negative regulator of aldosterone production and cell proliferation, in part by facilitating D1R internalization from the plasma membrane. Downregulation of NEFM in ZF-like APAs may contribute to a D1R/D2R imbalance underlying variable pharmacological responses to dopaminergic drugs among patients with APAs. Finally, taken together, our data point to the possibility that ZF-like APAs are in fact ZG in origin. © 2017 American Heart Association, Inc.

Mini-Brayton heat source assembly development

NASA Technical Reports Server (NTRS)

Wein, D.; Zimmerman, W. F.

1978-01-01

The work accomplished on the Mini-Brayton Heat Source Assembly program is summarized. Required technologies to design, fabricate and assemble components for a high temperature Heat Source Assembly (HSA) which would generate and transfer the thermal energy for a spaceborne Brayton Isotope Power System (BIPS) were developed.

Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways

PubMed Central

Kaushik, Abhinav; Ali, Shakir; Gupta, Dinesh

2017-01-01

Gene connection rewiring is an essential feature of gene network dynamics. Apart from its normal functional role, it may also lead to dysregulated functional states by disturbing pathway homeostasis. Very few computational tools measure rewiring within gene co-expression and its corresponding regulatory networks in order to identify and prioritize altered pathways which may or may not be differentially regulated. We have developed Altered Pathway Analyzer (APA), a microarray dataset analysis tool for identification and prioritization of altered pathways, including those which are differentially regulated by TFs, by quantifying rewired sub-network topology. Moreover, APA also helps in re-prioritization of APA shortlisted altered pathways enriched with context-specific genes. We performed APA analysis of simulated datasets and p53 status NCI-60 cell line microarray data to demonstrate potential of APA for identification of several case-specific altered pathways. APA analysis reveals several altered pathways not detected by other tools evaluated by us. APA analysis of unrelated prostate cancer datasets identifies sample-specific as well as conserved altered biological processes, mainly associated with lipid metabolism, cellular differentiation and proliferation. APA is designed as a cross platform tool which may be transparently customized to perform pathway analysis in different gene expression datasets. APA is freely available at http://bioinfo.icgeb.res.in/APA. PMID:28084397

Pelvic magnetic resonance imaging angioanatomy of the arterial blood supply to the penis in suspected prostate cancer patients.

PubMed

Thai, Cao Tan; Karam, Ibrahim Michel; Nguyen-Thi, Phi Linh; Lefèvre, Frédéric; Hubert, Jacques; Felblinger, Jacques; Eschwège, Pascal

2015-05-01

To describe the internal pudendal artery (IPA) and accessory pudendal artery (APA) detected by magnetic resonance (MR) angiography to help surgeons to find and preserve them during radical prostatectomy (RP). Constrast-enhanced MR 3.0 T angiography of the pelvis were performed in 111 male patients suspected diagnosis of prostate cancer (PCa), and describe the penile arterial blood supply. There are three patterns of the arterial blood supply to the penis (IPA and/or APA) accounting for 51.4%, 46.8% and 1.8% of cases, respectively. About the accessory pudendal artery (APA): 54/111 (48.6%) patients had APA with five different branching patterns, they were type I (APA bilateral symmetry): 17 (31.5%); type II (APA bilateral asymmetry): 1 (1.9%); type III (APA unilateral lateral): 13 (24%); type IV (APA unilateral apical): 21 (38.9%); type V (APA unilateral mix): 2 (3.7%). APA origin were from inferior epigastric artery (IEA): 7 (9.5%); from inferior vesical artery (IVA): 32 (43.2%); from obturator artery (OA): 35 (47.3%). A precise angioanatomic evalutation of arteries destined to the penis by MR angiography pre-operation for male pelvic organs will help surgeons to preserve them and contributes to reduce the erectile dysfunction after these procedures. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A parallel algorithm for generation and assembly of finite element stiffness and mass matrices

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Carmona, E. A.; Nguyen, D. T.; Baddourah, M. A.

1991-01-01

A new algorithm is proposed for parallel generation and assembly of the finite element stiffness and mass matrices. The proposed assembly algorithm is based on a node-by-node approach rather than the more conventional element-by-element approach. The new algorithm's generality and computation speed-up when using multiple processors are demonstrated for several practical applications on multi-processor Cray Y-MP and Cray 2 supercomputers.

Treatment of Pituitary Carcinomas and Atypical Pituitary Adenomas: A Review

PubMed Central

HIROHATA, Toshio; ISHII, Yudo; MATSUNO, Akira

2014-01-01

Atypical pituitary adenomas (APAs) are aggressive tumors, harboring a Ki-67 (MIB-1) staining index of 3% or more, and positive immunohistochemical staining for p53 protein, according to the World Health Organization (WHO) classification in 2004. Pituitary carcinomas (PC) usually develop from progressive APAs and predominantly consist of hormone-generating tumors, defined by the presence of disseminations in the cerebrospinal system or systemic metastases. Most of the cases with these malignant pituitary adenomas underwent surgeries, irradiations and adjuvant medical treatments, nevertheless, the therapies are mainly palliative. Recently, the efficacy of temozolomide (TMZ), an orally administered alkylating agent, has been reported as an alternative medical treatment. However, some recent studies have demonstrated a significant recurrence rate after effective response to TMZ. Further clinical and pathological researches of malignant pituitary adenomas will be required to improve the outcome of patients with these tumors. PMID:25446382

Arthur C. Graesser: Award for Distinguished Contributions of Applications of Psychology to Education and Training.

PubMed

2011-11-01

Presents Arthur C. Graesser as the 2011 winner of the American Psychological Association Award for Distinguished Contributions of Applications of Psychology to Education and Training. "As a multifaceted psychologist, cognitive engineer of useful education and training technologies, and mentor of new talent for the world of applied and translational cognitive science, Arthur C. Graesser is the perfect role model, showing how a strong scholar and intellect can shape both research and practice. His work is a mix of top-tier scholarship in psychology, education, intelligent systems, and computational linguistics. He combines cognitive science excellence with bold use of psychological knowledge and intelligent systems to design new generations of learning opportunities and to help lay the foundation for a translational science of learning." (PsycINFO Database Record (c) 2011 APA, all rights reserved). 2011 APA, all rights reserved

From print to digital (1985-2015): APA's evolving role in psychological publishing.

PubMed

VandenBos, Gary R

2017-11-01

Knowledge dissemination plays an important role in all scientific fields. The American Psychological Association's (APA) journal publication program was established in 1927. During the 1960s, the Psychological Abstracts publication was computerized. In the mid-1980s, a reenergizing of APA Publishing began, with the establishment of the APA Books Program, as well as the movement of abstracts to CD-ROMs. This article describes the 30-year program of expansion of APA Publishing, covering the period from 1985 through 2015. This period saw the journals program grow from 15 journals to 89 journals, the abstract program grow into an Internet-based delivery system, the creation of the APA's own PsycNET delivery platform, the creation of 6 addition databases, and the establishment of dictionaries and handbooks of psychology. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Aldosterone-stimulating somatic gene mutations are common in normal adrenal glands

PubMed Central

Nishimoto, Koshiro; Tomlins, Scott A.; Kuick, Rork; Cani, Andi K.; Giordano, Thomas J.; Hovelson, Daniel H.; Liu, Chia-Jen; Sanjanwala, Aalok R.; Edwards, Michael A.; Gomez-Sanchez, Celso E.; Nanba, Kazutaka; Rainey, William E.

2015-01-01

Primary aldosteronism (PA) represents the most common cause of secondary hypertension, but little is known regarding its adrenal cellular origins. Recently, aldosterone-producing cell clusters (APCCs) with high expression of aldosterone synthase (CYP11B2) were found in both normal and PA adrenal tissue. PA-causing aldosterone-producing adenomas (APAs) harbor mutations in genes encoding ion channels/pumps that alter intracellular calcium homeostasis and cause renin-independent aldosterone production through increased CYP11B2 expression. Herein, we hypothesized that APCCs have APA-related aldosterone-stimulating somatic gene mutations. APCCs were studied in 42 normal adrenals from kidney donors. To clarify APCC molecular characteristics, we used microarrays to compare the APCC transcriptome with conventional adrenocortical zones [zona glomerulosa (ZG), zona fasciculata, and zona reticularis]. The APCC transcriptome was most similar to ZG but with an enhanced capacity to produce aldosterone. To determine if APCCs harbored APA-related mutations, we performed targeted next generation sequencing of DNA from 23 APCCs and adjacent normal adrenal tissue isolated from both formalin-fixed, paraffin-embedded, and frozen tissues. Known aldosterone driver mutations were identified in 8 of 23 (35%) APCCs, including mutations in calcium channel, voltage-dependent, L-type, α1D-subunit (CACNA1D; 6 of 23 APCCs) and ATPase, Na+/K+ transporting, α1-polypeptide (ATP1A1; 2 of 23 APCCs), which were not observed in the adjacent normal adrenal tissue. Overall, we show three major findings: (i) APCCs are common in normal adrenals, (ii) APCCs harbor somatic mutations known to cause excess aldosterone production, and (iii) the mutation spectrum of aldosterone-driving mutations is different in APCCs from that seen in APA. These results provide molecular support for APCC as a precursor of PA. PMID:26240369

[Physical exercise for people with cerebral palsy: effects, recommendations and barriers].

PubMed

Barak, Sharon; Hutzler, Yeshayahu; Dubnov-Raz, Gal

2014-05-01

The management goal of cerebral palsy (CP) is improving functionality, locomotion and independence. Treatment programs commonly encompass adapted physical activity (APA). This review summarizes the knowledge regarding the effects and recommendations for APA in persons with CP. In addition, barriers to APA in this population are reviewed. The available literature on benefits of APA to persons with CP has focused mainly on youth. The components of the APA programs generally consist of strength, aerobic and flexibility training. There is no empirical evidence that strength-training increases spasticity in people with CP. Furthermore, strength-training may increase strength and the ability to perform daily activities. Aerobic-training is especially important as persons with CP typically have low cardiorespiratory fitness and high prevalence of cardiac disease. However, limited published evidence exists on aerobic-training effects in this population. Nonetheless, the evidence suggests that aerobic-training in persons with CP can improve physiological outcomes, yet the influence of these changes on participation has not been investigated sufficiently. Stretching exercise is a common treatment for spasticity. Surprisingly, there is inconclusive evidence for the effectiveness of stretching exercise for persons with CP. Despite the importance attributed to APA for people with CP, low levels of physical activity have been reported in this population. However, when caregivers perceive greater benefits of exercise, individuals with CP are more likely to be active. In contrast, barriers to APA include costs of APA programs, limited means of transportation to APA facilities, lack of information regarding APA facilities and limited appropriate exercising equipment in the APA facilities.

Resolving a Conflict between APA Learning Goals and APA Ethical Principles

ERIC Educational Resources Information Center

Corty, Eric W.

2008-01-01

Although American Psychological Association (APA) Ethical Standards make it clear that instructors cannot require students to disclose personal information in class-related activities, an APA learning goal for undergraduate psychology students is that they reflect on their experiences to develop insight into their behavior and mental processes.…

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

PubMed

Desai, Aarti; Marwah, Veer Singh; Yadav, Akshay; Jha, Vineet; Dhaygude, Kishor; Bangar, Ujwala; Kulkarni, Vivek; Jere, Abhay

2013-01-01

Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

PubMed

Moll, Karen M; Zhou, Peng; Ramaraj, Thiruvarangan; Fajardo, Diego; Devitt, Nicholas P; Sadowsky, Michael J; Stupar, Robert M; Tiffin, Peter; Miller, Jason R; Young, Nevin D; Silverstein, Kevin A T; Mudge, Joann

2017-08-04

Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies.

Progress toward a low budget reference grade genome assembly

USDA-ARS?s Scientific Manuscript database

Reference quality de novo genome assemblies were once solely the domain of large, well-funded genome projects. While next-generation short read technology removed some of the cost barriers, accurate chromosome-scale assembly remains a real challenge. Here we present efforts to de novo assemble the...

Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs

DOE PAGES

Scholz, Matthew; Lo, Chien -Chi; Chain, Patrick S. G.

2014-10-01

Assembly of metagenomic samples is a very complex process, with algorithms designed to address sequencing platform-specific issues, (read length, data volume, and/or community complexity), while also faced with genomes that differ greatly in nucleotide compositional biases and in abundance. To address these issues, we have developed a post-assembly process: MetaGenomic Assembly by Merging (MeGAMerge). We compare this process to the performance of several assemblers, using both real, and in-silico generated samples of different community composition and complexity. MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. MeGAMerge contigs aremore » supported by read mapping and contig alignment data, when using synthetically-derived and real metagenomic data, as well as by gene prediction analyses and similarity searches. Ultimately, MeGAMerge is a flexible method that generates improved metagenome assemblies, with the ability to accommodate upcoming sequencing platforms, as well as present and future assembly algorithms.« less

ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling

PubMed Central

Torigoe, Sharon E; Patel, Ashok; Khuong, Mai T; Bowman, Gregory D; Kadonaga, James T

2013-01-01

Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI: http://dx.doi.org/10.7554/eLife.00863.001 PMID:23986862

Compression of next-generation sequencing reads aided by highly efficient de novo assembly

PubMed Central

Jones, Daniel C.; Ruzzo, Walter L.; Peng, Xinxia

2012-01-01

We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based compressor, using a novel de novo assembly algorithm. A probabilistic data structure is used to dramatically reduce the memory required by traditional de Bruijn graph assemblers, allowing millions of reads to be assembled very efficiently. Read sequences are then stored as positions within the assembled contigs. This is combined with statistical compression of read identifiers, quality scores, alignment information and sequences, effectively collapsing very large data sets to <15% of their original size with no loss of information. Availability: Quip is freely available under the 3-clause BSD license from http://cs.washington.edu/homes/dcjones/quip. PMID:22904078

Towards automatic planning for manufacturing generative processes

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

CALTON,TERRI L.

2000-05-24

Generative process planning describes methods process engineers use to modify manufacturing/process plans after designs are complete. A completed design may be the result from the introduction of a new product based on an old design, an assembly upgrade, or modified product designs used for a family of similar products. An engineer designs an assembly and then creates plans capturing manufacturing processes, including assembly sequences, component joining methods, part costs, labor costs, etc. When new products originate as a result of an upgrade, component geometry may change, and/or additional components and subassemblies may be added to or are omitted from themore » original design. As a result process engineers are forced to create new plans. This is further complicated by the fact that the process engineer is forced to manually generate these plans for each product upgrade. To generate new assembly plans for product upgrades, engineers must manually re-specify the manufacturing plan selection criteria and re-run the planners. To remedy this problem, special-purpose assembly planning algorithms have been developed to automatically recognize design modifications and automatically apply previously defined manufacturing plan selection criteria and constraints.« less

A Hybrid Approach for the Automated Finishing of Bacterial Genomes

PubMed Central

Robins, William P.; Chin, Chen-Shan; Webster, Dale; Paxinos, Ellen; Hsu, David; Ashby, Meredith; Wang, Susana; Peluso, Paul; Sebra, Robert; Sorenson, Jon; Bullard, James; Yen, Jackie; Valdovino, Marie; Mollova, Emilia; Luong, Khai; Lin, Steven; LaMay, Brianna; Joshi, Amruta; Rowe, Lori; Frace, Michael; Tarr, Cheryl L.; Turnsek, Maryann; Davis, Brigid M; Kasarskis, Andrew; Mekalanos, John J.; Waldor, Matthew K.; Schadt, Eric E.

2013-01-01

Dramatic improvements in DNA sequencing technology have revolutionized our ability to characterize most genomic diversity. However, accurate resolution of large structural events has remained challenging due to the comparatively shorter read lengths of second-generation technologies. Emerging third-generation sequencing technologies, which yield markedly increased read length on rapid time scales and for low cost, have the potential to address assembly limitations. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at > 99.9% accuracy. Complex regions with clinically significant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 reference we obtain 14 and 8 scaffolds greater than 1kb, respectively, correcting several errors in the underlying source data. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. PMID:22750883

Optical harmonic generator

DOEpatents

Summers, M.A.; Eimerl, D.; Boyd, R.D.

1982-06-10

A pair of uniaxial birefringent crystal elements are fixed together to form a serially arranged, integral assembly which, alternatively, provides either a linearly or elliptically polarized second-harmonic output wave or a linearly polarized third-harmonic output wave. The extraordinary or e directions of the crystal elements are oriented in the integral assembly to be in quadrature (90/sup 0/). For a second-harmonic generation in the Type-II-Type-II angle tuned case, the input fundamental wave has equal amplitude o and e components. For a third-harmonic generation, the input fundamental wave has o and e components whose amplitudes are in a ratio of 2:1 (o:e reference first crystal). In the typical case of a linearly polarized input fundamental wave this can be accomplished by simply rotating the crystal assembly about the input beam direction by 10/sup 0/. For both second and third harmonic generation input precise phase-matching is achieved by tilting the crystal assembly about its two sensitive axeses (o).

Optical harmonic generator

DOEpatents

Summers, Mark A.; Eimerl, David; Boyd, Robert D.

1985-01-01

A pair of uniaxial birefringent crystal elements are fixed together to form a serially arranged, integral assembly which, alternatively, provides either a linearly or elliptically polarized second-harmonic output wave or a linearly polarized third-harmonic output wave. The "extraordinary" or "e" directions of the crystal elements are oriented in the integral assembly to be in quadrature (90.degree.). For a second-harmonic generation in the Type-II-Type-II angle tuned case, the input fundamental wave has equal amplitude "o" and "e" components. For a third-harmonic generation, the input fundamental wave has "o" and "e" components whose amplitudes are in a ratio of 2:1 ("o":"e" reference first crystal). In the typical case of a linearly polarized input fundamental wave this can be accomplished by simply rotating the crystal assembly about the input beam direction by 10.degree.. For both second and third harmonic generation input precise phase-matching is achieved by tilting the crystal assembly about its two sensitive axes ("o").

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.

PubMed

Xu, Jiajia; Li, Yuanyuan; Ma, Xiuling; Ding, Jianfeng; Wang, Kai; Wang, Sisi; Tian, Ye; Zhang, Hui; Zhu, Xin-Guang

2013-09-01

Setaria viridis is an emerging model species for genetic studies of C4 photosynthesis. Many basic molecular resources need to be developed to support for this species. In this paper, we performed a comprehensive transcriptome analysis from multiple developmental stages and tissues of S. viridis using next-generation sequencing technologies. Sequencing of the transcriptome from multiple tissues across three developmental stages (seed germination, vegetative growth, and reproduction) yielded a total of 71 million single end 100 bp long reads. Reference-based assembly using Setaria italica genome as a reference generated 42,754 transcripts. De novo assembly generated 60,751 transcripts. In addition, 9,576 and 7,056 potential simple sequence repeats (SSRs) covering S. viridis genome were identified when using the reference based assembled transcripts and the de novo assembled transcripts, respectively. This identified transcripts and SSR provided by this study can be used for both reverse and forward genetic studies based on S. viridis.

76 FR 30232 - Hours of Service (HOS) of Drivers; Application of American Pyrotechnics Association (APA) for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

...-28043] Hours of Service (HOS) of Drivers; Application of American Pyrotechnics Association (APA) for... American Pyrotechnics Association (APA) has applied for a limited exemption from FMCSA's regulation that... exemption would apply solely to the operation of CMVs by 9 designated APA-member motor carriers in...

76 FR 37880 - Hours of Service (HOS) of Drivers; Granting of Exemption; American Pyrotechnics Association (APA)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

...-28043] Hours of Service (HOS) of Drivers; Granting of Exemption; American Pyrotechnics Association (APA... exemption from the American Pyrotechnics Association (APA) on behalf of 9 member motor carriers seeking... such exemption'' (49 U.S.C. 31315(b)(1)). The initial APA application for waiver or exemption relief...

76 FR 37876 - Hours of Service (HOS) of Drivers; Renewal of American Pyrotechnics Association (APA) Exemption...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

...-28043] Hours of Service (HOS) of Drivers; Renewal of American Pyrotechnics Association (APA) Exemption... announces the renewal of the exemption of specified members of the American Pyrotechnics Association (APA... of this exemption in effect, designated APA-member motor carriers will maintain a level of safety...

77 FR 55695 - Approval and Promulgation of Implementation Plans; Virginia; Revisions to the State...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

... Administrative Procedure Act (APA). This exemption in the APA authorizes agencies to dispense with public... otherwise provided for in the APA. DATES: This action is effective September 11, 2012. ADDRESSES: EPA has...'' exemption in section 553(b)(3)(B) of the Administrative Procedure Act (APA). This exemption authorizes...

77 FR 38378 - Hours of Service (HOS) of Drivers; Revision of Exemption; American Pyrotechnics Association (APA)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-27

...-28043] Hours of Service (HOS) of Drivers; Revision of Exemption; American Pyrotechnics Association (APA... Pyrotechnics Association (APA) that were granted an exemption from FMCSA's prohibition on driving commercial...-July 8, inclusive, in 2011 and 2012. The exemption covered renewal of 53 APA-member motor carriers and...

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

PubMed Central

Lackford, Brad; Yao, Chengguo; Charles, Georgette M; Weng, Lingjie; Zheng, Xiaofeng; Choi, Eun-A; Xie, Xiaohui; Wan, Ji; Xing, Yi; Freudenberg, Johannes M; Yang, Pengyi; Jothi, Raja; Hu, Guang; Shi, Yongsheng

2014-01-01

mRNA alternative polyadenylation (APA) plays a critical role in post-transcriptional gene control and is highly regulated during development and disease. However, the regulatory mechanisms and functional consequences of APA remain poorly understood. Here, we show that an mRNA 3′ processing factor, Fip1, is essential for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Fip1 promotes stem cell maintenance, in part, by activating the ESC-specific APA profiles to ensure the optimal expression of a specific set of genes, including critical self-renewal factors. Fip1 expression and the Fip1-dependent APA program change during ESC differentiation and are restored to an ESC-like state during somatic reprogramming. Mechanistically, we provide evidence that the specificity of Fip1-mediated APA regulation depends on multiple factors, including Fip1-RNA interactions and the distance between APA sites. Together, our data highlight the role for post-transcriptional control in stem cell self-renewal, provide mechanistic insight on APA regulation in development, and establish an important function for APA in cell fate specification. PMID:24596251

Scaffolding of long read assemblies using long range contact information

USDA-ARS?s Scientific Manuscript database

Long read technologies have made a revolution in de novo genome assembly by generating long contigs. Although the assembly contiguity has increased, it may not span a chromosome, resulting in an unfinished chromosome level assembly. To address this problem, we develop a scaffolding method that can b...

Model-based guiding pattern synthesis for robust assembly of contact layers using directed self-assembly

NASA Astrophysics Data System (ADS)

Mitra, Joydeep; Torres, Andres; Ma, Yuansheng; Pan, David Z.

2018-01-01

Directed self-assembly (DSA) has emerged as one of the most compelling next-generation patterning techniques for sub 7 nm via or contact layers. A key issue in enabling DSA as a mainstream patterning technique is the generation of grapho-epitaxy-based guiding pattern (GP) shapes to assemble the contact patterns on target with high fidelity and resolution. Current GP generation is mostly empirical, and limited to a very small number of via configurations. We propose the first model-based GP synthesis algorithm and methodology for on-target and robust DSA, on general via pattern configurations. The final postoptical proximity correction-printed GPs derived from our original synthesized GPs are resilient to process variations and continue to maintain the same DSA fidelity in terms of placement error and target shape.

Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

PubMed Central

Thomas, Laurent F.; Sætrom, Pål

2012-01-01

Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3′ untranslated region (UTR) lengths. Different 3′UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells' natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3′UTR length, miRNA regulation, and mRNA expression—both between homozygote individuals and within heterozygote individuals. Furthermore, we show that a significant fraction of the alleles that cause APA are strongly and positively linked with alleles found by genome-wide studies to be associated with disease. Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease. PMID:22915998

Apa is a trimeric autotransporter adhesin of Actinobacillus pleuropneumoniae responsible for autoagglutination and host cell adherence.

PubMed

Xiao, Longwen; Zhou, Liang; Sun, Changjiang; Feng, Xin; Du, ChongTao; Gao, Yu; Ji, Qun; Yang, Shuxin; Wang, Yu; Han, Wenyu; Langford, P R; Lei, Liancheng

2012-10-01

Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia, and adherence to host cells is a key step in the pathogenic process. Although trimeric autotransporter adhesins (TAAs) were identified in many pathogenic bacteria in recent years, none in A. pleuropneumoniae have been characterized. In this study, we identified a TAA from A. pleuropneumoniae, Apa, and characterized the contribution of its amino acid residues to the adhesion process. Sequence analysis of the C-terminal amino acid residues of Apa revealed the presence of a putative translocator domain and six conserved HsfBD1-like or HsfBD2-like binding domains. Western blot analysis revealed that the 126 C-terminal amino acids of Apa could form trimeric molecules. By confocal laser scanning microscopy, one of these six domains (ApaBD3) was determined to mediate adherence to epithelial cells. Adherence assays and adherence inhibition assays using a recombinant E. coli- ApaBD3 strain which expressed ApaBD3 on the surface of E. coli confirmed that this domain was responsible for the adhesion activity. Moreover, cellular enzyme-linked immunosorbent assays demonstrated that ApaBD3 mediated high-level adherence to epithelial cell lines. Intriguingly, autoagglutination was observed with the E. coli- ApaBD3 strain, and this phenomenon was dependent upon the association of the expressed ApaBD3 with the C-terminal translocator domain. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

1. MISSILE TEST AND ASSEMBLY BUILDING, FRONT, LOOKING SOUTH. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. MISSILE TEST AND ASSEMBLY BUILDING, FRONT, LOOKING SOUTH. - NIKE Missile Base SL-40, Missile Test & Assembly Building, South end of launch area, northeast of Generator Building No. 3, Hecker, Monroe County, IL

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

PubMed

Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

2013-01-01

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

Antiphospholipid antibodies and antiphospholipid syndrome in patients presenting with immune thrombocytopenic purpura: a prospective cohort study.

PubMed

Diz-Küçükkaya, R; Hacihanefioğlu, A; Yenerel, M; Turgut, M; Keskin, H; Nalçaci, M; Inanç, M

2001-09-15

The pathogenetic role and the clinical importance of the presence of antiphospholipid antibodies (APAs) in patients with immune thrombocytopenic purpura (ITP) are not clear. In this study, the prevalence and clinical significance of APAs were investigated in patients with ITP. Eighty-two newly diagnosed ITP patients were prospectively studied. They were evaluated for the presence of lupus anticoagulant (LA) and immunoglobulin G/M anticardiolipin antibodies (ACAs). Thirty-one patients (37.8%) were APA positive at diagnosis. No statistically significant differences were found between the APA-positive and APA-negative groups regarding gender, initial platelet counts, or response to methylprednisolone therapy. After 5 years of follow-up, cumulative thrombosis-free survival of APA-positive (n = 31) and APA-negative (n = 51) ITP patients was 39% and 97.7%, respectively. A significant difference was found between these groups by log-rank test (P =.0004). In addition, LA was an important risk marker for the development of thrombosis in ITP patients. After a median follow-up of 38 months, 14 ITP patients (45%) who had APA positivity developed clinical features (thrombosis or fetal losses) of antiphospholipid syndrome (APS). There were no differences between the APA-positive patients with and without APS regarding the initial platelet counts, response to the therapy, or ACA positivity. The positivity rate for LA was significantly higher in those patients with ITP who developed APS (chi(2): P =.0036; relative risk 7.15; 95% confidence interval, 1.7-47). In conclusion, this study indicates that a significant proportion of patients initially presenting with ITP and APA positivity developed APS. In patients with ITP, the persistent presence of APAs is an important risk factor for the development of APS.

The Organization and Control of Intra-Limb Anticipatory Postural Adjustments and Their Role in Movement Performance

PubMed Central

Cavallari, Paolo; Bolzoni, Francesco; Bruttini, Carlo; Esposti, Roberto

2016-01-01

Anticipatory Postural Adjustments (APAs) are commonly described as unconscious muscular activities aimed to counterbalance the perturbation caused by the primary movement, so as to ensure the whole-body balance, as well as contributing to initiate the displacement of the body center of mass when starting gait or whole-body reaching movements. These activities usually create one or more fixation chains which spread over several muscles of different limbs, and may be thus called inter-limb APAs. However, it has been reported that APAs also precede voluntary movements involving tiny masses, like a flexion/extension of the wrist or even a brisk flexion of the index-finger. In particular, such movements are preceded by an intra-limb APA chain, that involves muscles acting on the proximal joints. Considering the small mass of the moving segments, it is unlikely that the ensuing perturbation could threaten the whole-body balance, so that it is interesting to enquire the physiological role of intra-limb APAs and their organization and control compared to inter-limb APAs. This review is focused on intra-limb APAs and highlights a strict correspondence in their behavior and temporal/spatial organization with respect to inter-limb APAs. Hence it is suggested that both are manifestations of the same phenomenon. Particular emphasis is given to intra-limb APAs preceding index-finger flexion, because their relatively simple biomechanics and the fact that muscular actions were limited to a single arm allowed peculiar investigations, leading to important conclusions. Indeed, such paradigm provided evidence that by granting a proper fixation of those body segments proximal to the moving one APAs are involved in refining movement precision, and also that APAs and prime mover activation are driven by a shared motor command. PMID:27807411

A new building block for DNA network formation by self-assembly and polymerase chain reaction.

PubMed

Bußkamp, Holger; Keller, Sascha; Robotta, Marta; Drescher, Malte; Marx, Andreas

2014-01-01

The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.

Independence of scientific publishing. Reaffirming the principle.

PubMed

Bjork, R A

2000-09-01

Historically, the American Psychological Association (APA), as part of its contract with the editors of APA journals, has granted to the editors sole responsibility to accept or reject manuscripts for publication, without such actions being open for review by APA. Such a policy fosters the freedom of inquiry and expression so necessary for a healthy science. It also serves to protect the Association because publication of an article in an APA journal does not represent endorsement by APA itself. The lessons of history are clear: When political or other pressures interfere with the autonomy of science, the societal and scientific consequences are grim. APA should reaffirm the principle that a healthy science of psychology requires an open exchange of ideas and findings.

Planning Assembly Of Large Truss Structures In Outer Space

NASA Technical Reports Server (NTRS)

De Mello, Luiz S. Homem; Desai, Rajiv S.

1992-01-01

Report dicusses developmental algorithm used in systematic planning of sequences of operations in which large truss structures assembled in outer space. Assembly sequence represented by directed graph called "assembly graph", in which each arc represents joining of two parts or subassemblies. Algorithm generates assembly graph, working backward from state of complete assembly to initial state, in which all parts disassembled. Working backward more efficient than working forward because it avoids intermediate dead ends.

4. MISSILE TEST AND ASSEMBLY BUILDING, LEFT SIDE, LOOKING NORTH. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. MISSILE TEST AND ASSEMBLY BUILDING, LEFT SIDE, LOOKING NORTH. - NIKE Missile Base SL-40, Missile Test & Assembly Building, South end of launch area, northeast of Generator Building No. 3, Hecker, Monroe County, IL

2. MISSILE TEST AND ASSEMBLY BUILDING, RIGHT SIDE, LOOKING WEST. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. MISSILE TEST AND ASSEMBLY BUILDING, RIGHT SIDE, LOOKING WEST. - NIKE Missile Base SL-40, Missile Test & Assembly Building, South end of launch area, northeast of Generator Building No. 3, Hecker, Monroe County, IL

3. MISSILE TEST AND ASSEMBLY BUILDING, REAR SIDE, LOOKING NORTH. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

3. MISSILE TEST AND ASSEMBLY BUILDING, REAR SIDE, LOOKING NORTH. - NIKE Missile Base SL-40, Missile Test & Assembly Building, South end of launch area, northeast of Generator Building No. 3, Hecker, Monroe County, IL

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

PubMed

Rando, Halie M; Farré, Marta; Robson, Michael P; Won, Naomi B; Johnson, Jennifer L; Buch, Ronak; Bastounes, Estelle R; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N; Larkin, Denis M; Kukekova, Anna V

2018-06-20

The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Wind turbine having a direct-drive drivetrain

DOEpatents

Bevington, Christopher M.; Bywaters, Garrett L.; Coleman, Clint C.; Costin, Daniel P.; Danforth, William L.; Lynch, Jonathan A.; Rolland, Robert H.

2008-10-07

A wind turbine (100) comprising an electrical generator (108) that includes a rotor assembly (112). A wind rotor (104) that includes a wind rotor hub (124) is directly coupled to the rotor assembly via a simplified connection. The wind rotor and generator rotor assembly are rotatably mounted on a central spindle (160) via a bearing assembly (180). The wind rotor hub includes an opening (244) having a diameter larger than the outside diameter of the central spindle adjacent the bearing assembly so as to allow access to the bearing assembly from a cavity (380) inside the wind rotor hub. The spindle is attached to a turret (140) supported by a tower (136). Each of the spindle, turret and tower has an interior cavity (172, 176, 368) that permits personnel to traverse therethrough to the cavity of the wind rotor hub. The wind turbine further includes a frictional braking system (276) for slowing, stopping or keeping stopped the rotation of the wind rotor and rotor assembly.

Investigation into the High Voltage Shutdown of the Oxygen Generator System in the International Space Station

NASA Technical Reports Server (NTRS)

Carpenter, Joyce E.; Gentry, Gregory J.; Diderich, Greg S.; Roy, Robert J.; Golden, John L.; VanKeuren, Steve; Steele, John W.; Rector, Tony J.; Varsik, Jerome D.; Montefusco, Daniel J.;

Starter for inductively coupled plasma tube

DOEpatents

Hull, Donald E.; Bieniewski, Thomas M.

1988-01-01

A starter assembly is provided for use with an inductively coupled plasma (ICP) tube to reliably initate a plasma at internal pressures above about 30 microns. A conductive probe is inserted within the inductor coil about the tube and insulated from the tube shield assembly. A capacitive circuit is arranged for momentarily connecting a high voltage radio-frequency generator to the probe while simultaneously energizing the coil. When the plasma is initiated the probe is disconnected from the generator and electrically connected to the shield assembly for operation.

78 FR 64162 - Airworthiness Directives; Airbus Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-28

... container assembly. We are issuing this AD to prevent a high temperature oxygen generator and mask from... oxygen generators installed on a certain batch of passenger emergency oxygen container assemblies might become detached by extreme pulling of the mask tube at the end of the oxygen supply causing a high...

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo) genome assembly and analysis

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing technologies were used to rapidly and efficiently sequence the genome of the domestic turkey (Meleagris gallopavo). The current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to chromosomes. Innate heterozygosity of the sequenced bird allowed discovery of...

21 CFR 892.1760 - Diagnostic x-ray tube housing assembly.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Diagnostic x-ray tube housing assembly. 892.1760... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1760 Diagnostic x-ray tube housing assembly. (a) Identification. A diagnostic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.1760 - Diagnostic x-ray tube housing assembly.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Diagnostic x-ray tube housing assembly. 892.1760... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1760 Diagnostic x-ray tube housing assembly. (a) Identification. A diagnostic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.1760 - Diagnostic x-ray tube housing assembly.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Diagnostic x-ray tube housing assembly. 892.1760... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1760 Diagnostic x-ray tube housing assembly. (a) Identification. A diagnostic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.5930 - Therapeutic x-ray tube housing assembly.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Therapeutic x-ray tube housing assembly. 892.5930... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Therapeutic Devices § 892.5930 Therapeutic x-ray tube housing assembly. (a) Identification. A therapeutic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.5930 - Therapeutic x-ray tube housing assembly.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Therapeutic x-ray tube housing assembly. 892.5930... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Therapeutic Devices § 892.5930 Therapeutic x-ray tube housing assembly. (a) Identification. A therapeutic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.5930 - Therapeutic x-ray tube housing assembly.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Therapeutic x-ray tube housing assembly. 892.5930... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Therapeutic Devices § 892.5930 Therapeutic x-ray tube housing assembly. (a) Identification. A therapeutic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.5930 - Therapeutic x-ray tube housing assembly.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Therapeutic x-ray tube housing assembly. 892.5930... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Therapeutic Devices § 892.5930 Therapeutic x-ray tube housing assembly. (a) Identification. A therapeutic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.5930 - Therapeutic x-ray tube housing assembly.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Therapeutic x-ray tube housing assembly. 892.5930... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Therapeutic Devices § 892.5930 Therapeutic x-ray tube housing assembly. (a) Identification. A therapeutic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.1760 - Diagnostic x-ray tube housing assembly.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Diagnostic x-ray tube housing assembly. 892.1760... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1760 Diagnostic x-ray tube housing assembly. (a) Identification. A diagnostic x-ray tube housing assembly is an x-ray generating tube encased...

21 CFR 892.1760 - Diagnostic x-ray tube housing assembly.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Diagnostic x-ray tube housing assembly. 892.1760... (CONTINUED) MEDICAL DEVICES RADIOLOGY DEVICES Diagnostic Devices § 892.1760 Diagnostic x-ray tube housing assembly. (a) Identification. A diagnostic x-ray tube housing assembly is an x-ray generating tube encased...

An efficient approach to BAC based assembly of complex genomes.

PubMed

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

2016-01-01

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

Excess of Aminopeptidase A in the Brain Elevates Blood Pressure via the Angiotensin II Type 1 and Bradykinin B2 Receptors without Dipsogenic Effect

PubMed Central

Ishida, Akio; Ohya, Yusuke

2017-01-01

Aminopeptidase A (APA) cleaves angiotensin (Ang) II, kallidin, and other related peptides. In the brain, it activates the renin angiotensin system and causes hypertension. Limited data are available on the dipsogenic effect of APA and pressor effect of degraded peptides of APA such as bradykinin. Wistar-Kyoto rats received intracerebroventricular (icv) APA in a conscious, unrestrained state after pretreatment with (i) vehicle, (ii) 80 μg of telmisartan, an Ang II type-1 (AT1) receptor blocker, (iii) 800 nmol of amastatin, an aminopeptidase inhibitor, and (iv) 1 nmol of HOE-140, a bradykinin B2 receptor blocker. Icv administration of 400 and 800 ng of APA increased blood pressure by 12.6 ± 3.0 and 19.0 ± 3.1 mmHg, respectively. APA did not evoke drinking behavior. Pressor response to APA was attenuated on pretreatment with telmisartan (vehicle: 22.1 ± 2.2 mmHg versus telmisartan: 10.4 ± 3.2 mmHg). Pressor response to APA was also attenuated with amastatin and HOE-140 (vehicle: 26.5 ± 1.1 mmHg, amastatin: 14.4 ± 4.2 mmHg, HOE-140: 16.4 ± 2.2 mmHg). In conclusion, APA increase in the brain evokes a pressor response via enzymatic activity without dipsogenic effect. AT1 receptors and B2 receptors in the brain may contribute to the APA-induced pressor response. PMID:28421141

Antiphospholipid antibodies and recurrent thrombosis after a first unprovoked venous thromboembolism.

PubMed

Kearon, Clive; Parpia, Sameer; Spencer, Frederick A; Baglin, Trevor; Stevens, Scott M; Bauer, Kenneth A; Lentz, Steven R; Kessler, Craig M; Douketis, James D; Moll, Stephan; Kaatz, Scott; Schulman, Sam; Connors, Jean M; Ginsberg, Jeffrey S; Spadafora, Luciana; Bhagirath, Vinai; Liaw, Patricia C; Weitz, Jeffrey I; Julian, Jim A

2018-05-10

It is uncertain whether antiphospholipid antibodies (APAs) increase the risk of recurrence after a first unprovoked venous thromboembolism (VTE). We tested for anticardiolipin antibodies, anti-β2 glycoprotein 1 antibodies, and lupus anticoagulant on 2 occasions ∼6 months apart in 307 patients with a first unprovoked VTE who were part of a prospective cohort study. We then determined if APAs were associated with recurrent thrombosis in the 290 patients who stopped anticoagulant therapy in response to negative D-dimer results. Compared with those without an APA, the hazard ratios for recurrent VTE were 1.8 (95% confidence interval [CI], 0.9-3.7; P = .09) in the 25.9% of patients with an APA on ≥1 occasions, 2.7 (95% CI, 1.1-.7; P = .03) in the 9.0% of patients with the same APA on 2 occasions, and 4.5 (95% CI, 1.5-13.0; P = .006) in the 3.8% of patients with 2 or 3 different APA types on either the same or different occasions. There was no association between having an APA and D-dimer levels. We conclude that having the same type of APA on 2 occasions or having >1 type of APA on the same or different occasions is associated with recurrent thrombosis in patients with a first unprovoked VTE who stop anticoagulant therapy in response to negative D-dimer tests. APA and D-dimer levels seem to be independent predictors of recurrence in patients with an unprovoked VTE. This trial was registered at www.clinicaltrials.gov as #NCT00720915. © 2018 by The American Society of Hematology.

DHEA, DHEAS and PCOS.

PubMed

Goodarzi, Mark O; Carmina, Enrico; Azziz, Ricardo

2015-01-01

Approximately 20-30% of PCOS women demonstrate excess adrenal precursor androgen (APA) production, primarily using DHEAS as a marker of APA in general and more specifically DHEA, synthesis. The role of APA excess in determining or causing PCOS is unclear, although observations in patients with inherited APA excess (e.g., patients with 21-hydroxylase deficient congenital classic or non-classic adrenal hyperplasia) demonstrate that APA excess can result in a PCOS-like phenotype. Inherited defects of the enzymes responsible for steroid biosynthesis, or defects in cortisol metabolism, account for only a very small fraction of women suffering from hyperandrogenism or APA excess. Rather, women with PCOS and APA excess appear to have a generalized exaggeration in adrenal steroidogenesis in response to ACTH stimulation, although they do not have an overt hypothalamic-pituitary-adrenal axis dysfunction. In general, extra-adrenal factors, including obesity, insulin and glucose levels, and ovarian secretions, play a limited role in the increased APA production observed in PCOS. Substantial heritabilities of APAs, particularly DHEAS, have been found in the general population and in women with PCOS; however, the handful of SNPs discovered to date account only for a small portion of the inheritance of these traits. Paradoxically, and as in men, elevated levels of DHEAS appear to be protective against cardiovascular risk in women, although the role of DHEAS in modulating this risk in women with PCOS remains unknown. In summary, the exact cause of APA excess in PCOS remains unclear, although it may reflect a generalized and inherited exaggeration in androgen biosynthesis of an inherited nature. Copyright © 2014 Elsevier Ltd. All rights reserved.

Immunohistochemical characteristics of atypical polypoid adenomyoma with special reference to h-caldesmon.

PubMed

Horita, Ayako; Kurata, Atsushi; Maeda, Daichi; Fukayama, Masashi; Sakamoto, Atsuhiko

2011-01-01

Atypical polypoid adenomyoma (APA) is a relatively rare benign uterine tumor, histologically characterized by proliferation of irregular endometrioid glands accompanied by stromal cells of smooth muscle origin. As the epithelial components of APA usually show cytological atypia, a differential diagnosis between this tumor and endometrioid carcinoma invading myometrium is often difficult, especially in curettage material. This distinction is clinically very important to avoid unnecessary hysterectomy. However, only a few immunohistochemical studies of APA that differentiate it from malignancy have been published. Therefore, we have investigated the expression of several antigens in APA and compared them with those present in myoinvasive carcinoma. Six specimens of APA were studied, along with controls of endometrioid carcinoma invading myometrium. Antibodies to p53, Ki-67, CD10, and h-caldesmon reacted positively using immunohistochemistry. Variable positive expressions of p53 and Ki-67 were observed in both epithelial and stromal components of APA, and in myoinvasive endometrioid carcinoma. CD10 was negative or partially and weakly positive whereas h-caldesmon was completely negative in the stromal cells of all 6 specimens of APA. However, in the myometrium in which endometrioid carcinoma invaded, a fringe-like positive staining pattern was occasionally observed for CD10, whereas a diffuse positive signal was obtained for h-caldesmon. The results of this study indicate that immunohistochemically, p53, and Ki-67 are not reliable markers but that h-caldesmon is useful in distinguishing APA from myoinvasive endometrioid carcinoma. Further, our data suggest that the stromal cells of APA are mainly immature smooth muscle cells, and thus APA may be a mixed tumor.

Consensus generation and variant detection by Celera Assembler.

PubMed

Denisov, Gennady; Walenz, Brian; Halpern, Aaron L; Miller, Jason; Axelrod, Nelson; Levy, Samuel; Sutton, Granger

2008-04-15

We present an algorithm to identify allelic variation given a Whole Genome Shotgun (WGS) assembly of haploid sequences, and to produce a set of haploid consensus sequences rather than a single consensus sequence. Existing WGS assemblers take a column-by-column approach to consensus generation, and produce a single consensus sequence which can be inconsistent with the underlying haploid alleles, and inconsistent with any of the aligned sequence reads. Our new algorithm uses a dynamic windowing approach. It detects alleles by simultaneously processing the portions of aligned reads spanning a region of sequence variation, assigns reads to their respective alleles, phases adjacent variant alleles and generates a consensus sequence corresponding to each confirmed allele. This algorithm was used to produce the first diploid genome sequence of an individual human. It can also be applied to assemblies of multiple diploid individuals and hybrid assemblies of multiple haploid organisms. Being applied to the individual human genome assembly, the new algorithm detects exactly two confirmed alleles and reports two consensus sequences in 98.98% of the total number 2,033311 detected regions of sequence variation. In 33,269 out of 460,373 detected regions of size >1 bp, it fixes the constructed errors of a mosaic haploid representation of a diploid locus as produced by the original Celera Assembler consensus algorithm. Using an optimized procedure calibrated against 1 506 344 known SNPs, it detects 438 814 new heterozygous SNPs with false positive rate 12%. The open source code is available at: http://wgs-assembler.cvs.sourceforge.net/wgs-assembler/

Collusion, torture, and inequality: Understanding the actions of the American Psychological Association as institutional betrayal.

PubMed

Gómez, Jennifer M; Smith, Carly P; Gobin, Robyn L; Tang, Shin Shin; Freyd, Jennifer J

2016-01-01

The Hoffman Report (Hoffman et al., 2015) documented devastating information about the American Psychological Association (APA) and the profession of psychology in the United States, prompting a public apology and a formal commitment by APA to correct its mistakes (APA, 2015). In the current article, we utilize betrayal trauma theory (Freyd, 1997), including betrayal blindness (e.g., Freyd, 1996; Tang, 2015) and institutional betrayal (Smith & Freyd, 2014b), to understand and learn from APA's behaviors. We further situate this discussion in the context of inequality, both within APA and in American society generally. We detail how the impact of APA's institutional betrayals extended beyond the organization, its members, and the psychology profession, highlighting the potential for disproportionate harm to minorities, including those who were tortured; Muslims, Middle Easterners, Afghans, and non-Americans who were not tortured; and other minority individuals (Gómez, 2015d). Acknowledging, understanding, and addressing its institutional betrayals offers APA the opportunity to take meaningful corrective and preventive measures. We propose several institutional reparations, including making concrete changes with transparency and conducting self-assessments to inform further needed changes (Freyd & Birrell, 2013). By engaging in institutional courage, APA has the potential to grow into an ethical governing body that fulfills its mission to "advance the creation, communication and application of psychological knowledge to benefit society and improve people's lives" (APA, 2016).

Automated ensemble assembly and validation of microbial genomes.

PubMed

Koren, Sergey; Treangen, Todd J; Hill, Christopher M; Pop, Mihai; Phillippy, Adam M

2014-05-03

The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.

42 CFR 137.309 - How are NEPA and NHPA obligations typically enforced?

Code of Federal Regulations, 2010 CFR

2010-10-01

... may only be filed in Federal court under the provisions of the APA, 5 U.S.C. 701-706. Under the APA, a... the court's views for those of the agency. Jury trials and civil discovery are not permitted in APA... injunctive relief to the interested party. No money damages or fines are permitted in APA proceedings. ...

78 FR 73698 - Prevention of Significant Deterioration for Particulate Matter Less Than 2.5 Micrometers...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-09

... Administrative Procedure Act (APA) good cause exemption applies here. In general, the APA requires that general... opportunity for public participation in the rulemaking process. However, the APA does provide an avenue for an... of the APA, 5 U.S.C. 553(b)(B). Therefore, the requirements of CAA section 307(d), including the...

The sequence and de novo assembly of the giant panda genome

PubMed Central

Li, Ruiqiang; Fan, Wei; Tian, Geng; Zhu, Hongmei; He, Lin; Cai, Jing; Huang, Quanfei; Cai, Qingle; Li, Bo; Bai, Yinqi; Zhang, Zhihe; Zhang, Yaping; Wang, Wen; Li, Jun; Wei, Fuwen; Li, Heng; Jian, Min; Li, Jianwen; Zhang, Zhaolei; Nielsen, Rasmus; Li, Dawei; Gu, Wanjun; Yang, Zhentao; Xuan, Zhaoling; Ryder, Oliver A.; Leung, Frederick Chi-Ching; Zhou, Yan; Cao, Jianjun; Sun, Xiao; Fu, Yonggui; Fang, Xiaodong; Guo, Xiaosen; Wang, Bo; Hou, Rong; Shen, Fujun; Mu, Bo; Ni, Peixiang; Lin, Runmao; Qian, Wubin; Wang, Guodong; Yu, Chang; Nie, Wenhui; Wang, Jinhuan; Wu, Zhigang; Liang, Huiqing; Min, Jiumeng; Wu, Qi; Cheng, Shifeng; Ruan, Jue; Wang, Mingwei; Shi, Zhongbin; Wen, Ming; Liu, Binghang; Ren, Xiaoli; Zheng, Huisong; Dong, Dong; Cook, Kathleen; Shan, Gao; Zhang, Hao; Kosiol, Carolin; Xie, Xueying; Lu, Zuhong; Zheng, Hancheng; Li, Yingrui; Steiner, Cynthia C.; Lam, Tommy Tsan-Yuk; Lin, Siyuan; Zhang, Qinghui; Li, Guoqing; Tian, Jing; Gong, Timing; Liu, Hongde; Zhang, Dejin; Fang, Lin; Ye, Chen; Zhang, Juanbin; Hu, Wenbo; Xu, Anlong; Ren, Yuanyuan; Zhang, Guojie; Bruford, Michael W.; Li, Qibin; Ma, Lijia; Guo, Yiran; An, Na; Hu, Yujie; Zheng, Yang; Shi, Yongyong; Li, Zhiqiang; Liu, Qing; Chen, Yanling; Zhao, Jing; Qu, Ning; Zhao, Shancen; Tian, Feng; Wang, Xiaoling; Wang, Haiyin; Xu, Lizhi; Liu, Xiao; Vinar, Tomas; Wang, Yajun; Lam, Tak-Wah; Yiu, Siu-Ming; Liu, Shiping; Zhang, Hemin; Li, Desheng; Huang, Yan; Wang, Xia; Yang, Guohua; Jiang, Zhi; Wang, Junyi; Qin, Nan; Li, Li; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Wong, Gane Ka-Shu; Olson, Maynard; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

2013-01-01

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. PMID:20010809

Genome Sequencing and Assembly by Long Reads in Plants

PubMed Central

Li, Changsheng; Lin, Feng; An, Dong; Huang, Ruidong

2017-01-01

Plant genomes generated by Sanger and Next Generation Sequencing (NGS) have provided insight into species diversity and evolution. However, Sanger sequencing is limited in its applications due to high cost, labor intensity, and low throughput, while NGS reads are too short to resolve abundant repeats and polyploidy, leading to incomplete or ambiguous assemblies. The advent and improvement of long-read sequencing by Third Generation Sequencing (TGS) methods such as PacBio and Nanopore have shown promise in producing high-quality assemblies for complex genomes. Here, we review the development of sequencing, introducing the application as well as considerations of experimental design in TGS of plant genomes. We also introduce recent revolutionary scaffolding technologies including BioNano, Hi-C, and 10× Genomics. We expect that the informative guidance for genome sequencing and assembly by long reads will benefit the initiation of scientists’ projects. PMID:29283420

Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape Across 7 Tumor Types

PubMed Central

Xia, Zheng; Donehower, Lawrence A; Cooper, Thomas A.; Neilson, Joel R.; Wheeler, David A.; Wagner, Eric J.; Li, Wei

2015-01-01

Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted, global cancer APA studies are very limited. Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq. When applied to 358 TCGA Pan-Cancer tumor/normal pairs across 7 tumor types, DaPars reveals 1,346 genes with recurrent and tumor-specific APAs. Most APA genes (91%) have shorter 3′ UTRs in tumors that can avoid miRNA-mediated repression, including glutaminase (GLS), a key metabolic enzyme for tumor proliferation. Interestingly, selected APA events add strong prognostic power beyond common clinical and molecular variables, suggesting their potential as novel prognostic biomarkers. Finally, our results implicate CstF64, an essential polyadenylation factor, as a master regulator of 3′ UTR shortening across multiple tumor types. PMID:25409906

Variation of alkaline phosphatase activity in sediments of shrimp culture ponds and its relationship with the contents of C, N and P

NASA Astrophysics Data System (ADS)

Su, Yuepeng; Ma, Shen; Dong, Shuanglin

2005-01-01

Nine enclosures (5 m × 5 m) were built in a Fenneropenaeus chinensis culture pond of Rushan Gulf in April, 2001. The probiotics and BIO ENERGIZER solution were applied for disparate treatments. Variations of alkaline phosphatase activity (APA) and its relationship with the contents of C, N and P in sediments were studied. Results show that APA of sediments increases from 3.096 nmol g-1min-1 to 5.407nmol g-1min-1 in culture period; the bacteria biomass is not the only factor to determine APA; the contents of total P and total organic carbon have a significant positive correlation with APA, while that of total nitrogen has a negative correlation. In addition, the contents of inorganic P and organic P are not regular with APA. By comparison, TOC shows a more significant coherence with APA, meaning that organic pollution in sediments affects APA remarkably.

5. MISSILE TEST AND ASSEMBLY BUILDING, FRONT AND RIGHT SIDES, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. MISSILE TEST AND ASSEMBLY BUILDING, FRONT AND RIGHT SIDES, LOOKING SOUTHEAST. - NIKE Missile Base SL-40, Missile Test & Assembly Building, South end of launch area, northeast of Generator Building No. 3, Hecker, Monroe County, IL

6. MISSILE TEST AND ASSEMBLY BUILDING, REAR AND LEFT SIDES, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

6. MISSILE TEST AND ASSEMBLY BUILDING, REAR AND LEFT SIDES, LOOKING NORTHWEST. - NIKE Missile Base SL-40, Missile Test & Assembly Building, South end of launch area, northeast of Generator Building No. 3, Hecker, Monroe County, IL

De novo assembly and phasing of a Korean human genome.

PubMed

Seo, Jeong-Sun; Rhie, Arang; Kim, Junsoo; Lee, Sangjin; Sohn, Min-Hwan; Kim, Chang-Uk; Hastie, Alex; Cao, Han; Yun, Ji-Young; Kim, Jihye; Kuk, Junho; Park, Gun Hwa; Kim, Juhyeok; Ryu, Hanna; Kim, Jongbum; Roh, Mira; Baek, Jeonghun; Hunkapiller, Michael W; Korlach, Jonas; Shin, Jong-Yeon; Kim, Changhoon

2016-10-13

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Active turbulence in a gas of self-assembled spinners

PubMed Central

Kokot, Gašper; Das, Shibananda; Winkler, Roland G.; Aranson, Igor S.; Snezhko, Alexey

2017-01-01

Colloidal particles subject to an external periodic forcing exhibit complex collective behavior and self-assembled patterns. A dispersion of magnetic microparticles confined at the air–liquid interface and energized by a uniform uniaxial alternating magnetic field exhibits dynamic arrays of self-assembled spinners rotating in either direction. Here, we report on experimental and simulation studies of active turbulence and transport in a gas of self-assembled spinners. We show that the spinners, emerging as a result of spontaneous symmetry breaking of clock/counterclockwise rotation of self-assembled particle chains, generate vigorous vortical flows at the interface. An ensemble of spinners exhibits chaotic dynamics due to self-generated advection flows. The same-chirality spinners (clockwise or counterclockwise) show a tendency to aggregate and form dynamic clusters. Emergent self-induced interface currents promote active diffusion that could be tuned by the parameters of the external excitation field. Furthermore, the erratic motion of spinners at the interface generates chaotic fluid flow reminiscent of 2D turbulence. Our work provides insight into fundamental aspects of collective transport in active spinner materials and yields rules for particle manipulation at the microscale. PMID:29158382

Protein Self-Assemblies That Can Generate, Hold, and Discharge Electric Potential in Response to Changes in Relative Humidity.

PubMed

Carter, Nathan A; Grove, Tijana Z

2018-05-30

Generation of electric potential upon external stimulus has attracted much attention for the development of highly functional sensors and devices. Herein, we report large-displacement, fast actuation in the self-assembled engineered repeat protein Consensus Tetratricopeptide Repeat protein (CTPR18) materials. The ionic nature of the CTPR18 protein coupled to the long-range alignment upon self-assembly results in the measured conductivity of 7.1 × 10 -2 S cm -1 , one of the highest reported for protein materials. The change of through-thickness morphological gradient in the self-assembled materials provides the means to select between faster, highly water-sensitive actuation or vastly increased mechanical strength. Tuning of the mode of motion, e.g., bending, twisting, and folding, is achieved by changing the morphological director. We further show that the highly ionic character of CTPR18 gives rise to piezo-like behavior in these materials, exemplified by low-voltage, ionically driven actuation and mechanically driven generation/discharge of voltage. This work contributes to our understanding of the emergence of stimuli-responsiveness in biopolymer assemblies.

Hierarchical Self-Organization of Perylene Bisimides into Supramolecular Spheres and Periodic Arrays Thereof.

PubMed

Sahoo, Dipankar; Peterca, Mihai; Aqad, Emad; Partridge, Benjamin E; Heiney, Paul A; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Percec, Virgil

2016-11-09

Perylene bisimide derivatives (PBIs) are known to form only columnar or lamellar assemblies. There is no known example of a PBI self-assembling into a supramolecular sphere. Therefore, periodic and quasiperiodic arrays generated from spherical assemblies produced from PBIs are also not known. Here, a PBI functionalized at its imide groups with a second generation self-assembling dendron is reported to self-assemble into supramolecular spheres. These spheres self-organize in a body-centered cubic (BCC) periodic array, rarely encountered for self-assembling dendrons but often encountered in block copolymers. These supramolecular spheres also assemble into a columnar hexagonal array in which the supramolecular columns are unexpectedly and unprecedentedly made from spheres. At lower temperature, two additional columnar hexagonal phases consisting of symmetric and asymmetric tetrameric crowns of PBI are observed. Structural and retrostructural analysis via X-ray diffraction (XRD), molecular modeling, molecular simulation, and solid state NMR suggests that inversion of the symmetric tetrameric crowns at high temperature mediates their transformation into supramolecular spheres. The tetrameric crowns of PBIs are able to form an isotropic sphere in the cubic phase due to rapid molecular motion at high temperature, unobservable by XRD but demonstrated by solid state NMR studies. This mechanism of hierarchical self-organization of PBI into supramolecular spheres is most probably general and can be applied to other related planar molecules to generate new functions.

Recognition of psychotherapy effectiveness: the APA resolution.

PubMed

Campbell, Linda F; Norcross, John C; Vasquez, Melba J T; Kaslow, Nadine J

2013-03-01

In August 2012, the American Psychological Association (APA) Council of Representatives voted overwhelmingly to adopt as APA policy a Resolution on the Recognition of Psychotherapy Effectiveness. This invited article traces the origins and intentions of that resolution and its protracted journey through the APA governance labyrinth. We summarize the planned dissemination and projected results of the resolution and identify several lessons learned through the entire process.

75 FR 37730 - National Emission Standards for Hazardous Air Pollutants From Petroleum Refineries

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-30

... reference. Section 553 of the Administrative Procedure Act (APA), 5 U.S.C. 553(b)(B), provides that, when an... 553(b)(B) of the APA, the procedures in section 307(d) in subsection 553(b) of the APA, the procedures... subject to notice and comment requirements under the APA or any other statute (see Section I of this...

75 FR 39633 - Extension of Deadline for Action on Section 126 Petition From New Jersey

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-12

... Procedures Act (APA) C. Effective Date Under the APA III. Statutory and Executive Order Reviews A. Executive... Procedures Act (APA) This document is a final agency action, but may not be subject to the notice-and-comment requirements of the APA, 5 U.S.C. 553(b). The EPA believes that, because of the limited time provided to make a...

75 FR 69889 - Extension of Deadline for Action on the Second Section 126 Petition From New Jersey

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-16

... Act (APA) C. Effective Date Under the APA III. Statutory and Executive Order Reviews A. Executive... Administrative Procedures Act (APA) This document is a final agency action, but may not be subject to the notice-and-comment requirements of the APA, 5 U.S.C. 553(b). The EPA believes that, because of the limited...

Perceptions of Co-Curricular Involvement and Counseling Use among Incoming Asian and Pacific and Latino American College Students. Report No. 7-96.

ERIC Educational Resources Information Center

Liu, William M.; Sedlacek, William E.

Latinos and Asian Pacific Americans (APAs) are increasing in numbers throughout the United States. This study reports on a survey administered to 350 APA and 119 Latino American students entering a large east coast university. Significant differences between APA and Latino students emerged: (1) APA students were less likely than Latino students to…

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission.

PubMed

Geib, Scott M; Hall, Brian; Derego, Theodore; Bremer, Forest T; Cannoles, Kyle; Sim, Sheina B

2018-04-01

One of the most overlooked, yet critical, components of a whole genome sequencing (WGS) project is the submission and curation of the data to a genomic repository, most commonly the National Center for Biotechnology Information (NCBI). While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into the NCBI's annotation table format, these tools typically require back-end setup and connection to an Structured Query Language (SQL) database and/or some knowledge of programming (Perl, Python) to implement. With WGS becoming commonplace, genome sequencing projects are moving away from the genome centers and into the ecology or biology lab, where fewer resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, and transfer annotation and convert a draft genome assembly and annotation set into the NCBI annotation table (.tbl) format, facilitating submission to the NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms, and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks. The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline. The Genome Annotation Generator achieves the goal of providing a publicly available tool that will facilitate the submission of annotated genome assemblies to the NCBI. It is useful for any individual researcher or research group that wishes to submit a genome assembly of their study system to the NCBI.

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission

PubMed Central

Hall, Brian; Derego, Theodore; Bremer, Forest T; Cannoles, Kyle

2018-01-01

Abstract Background One of the most overlooked, yet critical, components of a whole genome sequencing (WGS) project is the submission and curation of the data to a genomic repository, most commonly the National Center for Biotechnology Information (NCBI). While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into the NCBI’s annotation table format, these tools typically require back-end setup and connection to an Structured Query Language (SQL) database and/or some knowledge of programming (Perl, Python) to implement. With WGS becoming commonplace, genome sequencing projects are moving away from the genome centers and into the ecology or biology lab, where fewer resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, and transfer annotation and convert a draft genome assembly and annotation set into the NCBI annotation table (.tbl) format, facilitating submission to the NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms, and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks. Findings The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline Conclusions The Genome Annotation Generator achieves the goal of providing a publicly available tool that will facilitate the submission of annotated genome assemblies to the NCBI. It is useful for any individual researcher or research group that wishes to submit a genome assembly of their study system to the NCBI. PMID:29635297

A mannequin study of intubation with the AP advance and GlideScope Ranger videolaryngoscopes and the Macintosh laryngoscope.

PubMed

Hodd, Jack A R; Doyle, D John; Gupta, Shipra; Dalton, Jarrod E; Cata, Juan P; Brewer, Edward J; James, Monyulona; Sessler, Daniel I

2011-10-01

The AP Advance (APA) is a videolaryngoscope with interchangeable blades: intubators can choose standard Macintosh blades or a difficult-airway blade with increased curvature and a channel to guide the tube to the larynx. The APA may therefore be comparably effective in both normal and difficult airways. We tested the hypotheses that intubation with the APA is no slower than Macintosh laryngoscopy for normal mannequin airways, and that it is no slower than videolaryngoscopy using a GlideScope Ranger in difficult mannequin airways. Medical professionals whose roles potentially include tracheal intubation were trained with each device. Participants intubated simulated (Laerdal SimMan) normal and difficult airways with the APA, GlideScope, and a conventional Macintosh blade. Speed of intubation was compared using Cox proportional hazards regression, with a hazard ratio >0.8 considered noninferior. We also compared laryngeal visualization, failures, and participant preferences. Unadjusted intubation times in the normal airway with the APA and Macintosh were virtually identical (median, 22 vs 23 seconds); after adjustment for effects of experience, order, and period, the hazard ratio (95% confidence interval) comparing APA with Macintosh laryngoscopy was 0.87 (0.65, 1.17), which was not significantly more than our predefined noninferiority boundary of 0.8 (P = 0.26). Intubation with the APA was faster than with the GlideScope in difficult airways (hazard ratio = 7.6 [5.0, 11.3], P < 0.001; median, 20 vs 59 seconds). All participants intubated the difficult airway mannequin with the APA, whereas 33% and 37% failed with the GlideScope and Macintosh, respectively. In the difficult airway, 99% of participants achieved a Cormack and Lehane grade I to II view with the APA, versus 85% and 33% with the GlideScope and Macintosh, respectively. When asked to choose 1 device overall, 82% chose the APA. Intubation times were similar with the APA and Macintosh laryngoscopes in mannequins with normal airways. However, intubation with the APA was significantly faster than with the GlideScope in the difficult mannequin simulation.

CHEMO/mechanical energy conversiona via supramolecular self-assembly

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

Lynn, David G.; Conticello, Vincent

With the assembly codes for protein/peptide self-assembly sufficiently developed to control these phases, we are positioned to address critical requirements for generating unique self-propagating functional assemblies such as chemical batteries and engines that can be used to extend the capability of living cells. These integrative functional assemblies can then be used within cells to create new functions that will address the world’s energy challenges.

The present and future of de novo whole-genome assembly.

PubMed

Sohn, Jang-Il; Nam, Jin-Wu

2018-01-01

As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Are Hypometric Anticipatory Postural Adjustments Contributing to Freezing of Gait in Parkinson’s Disease?

PubMed Central

Schlenstedt, Christian; Mancini, Martina; Nutt, Jay; Hiller, Amie P.; Maetzler, Walter; Deuschl, Günther; Horak, Fay

2018-01-01

Introduction: This study aims at investigating whether impaired anticipatory postural adjustments (APA) during gait initiation contribute to the occurrence of freezing of gait (FOG) or whether altered APAs compensate for FOG in Parkinson’s disease (PD). Methods: Gait initiation after 30 s quiet stance was analyzed without and with a cognitive dual task (DT) in 33 PD subjects with FOG (PD+FOG), 30 PD subjects without FOG (PD-FOG), and 32 healthy controls (HC). APAs were characterized with inertial sensors and muscle activity of the tensor fasciae latae (TFL), gastrocnemius, and tibialis anterior was captured with electromyography recordings. Nine trials (of 190) were associated with start hesitation/FOG and analyzed separately. Results: PD+FOG and PD-FOG did not differ in disease duration, disease severity, age, or gender. PD+FOG had significantly smaller medio-lateral (ML) and anterio-posterior APAs compared to PD-FOG (DT, p < 0.05). PD+FOG had more co-contraction of left and right TFL during APAs compared to PD-FOG (p < 0.01). Within the PD+FOG, the ML size of APA (DT) was positively correlated with the severity of FOG history (NFOG-Q), with larger APAs associated with worse FOG (rho = 0.477, p = 0.025). ML APAs were larger during trials with observed FOG compared to trials of PD+FOG without FOG. Conclusions: People with PD who have a history of FOG have smaller ML APAs (weight shifting) during gait initiation compared to PD-FOG and HC. However, start hesitation (FOG) is not caused by an inability to sufficiently displace the center of mass toward the stance leg because APAs were larger during trials with observed FOG. We speculate that reducing the acceleration of the body center of mass with hip abductor co-contraction for APAs might be a compensatory strategy in PD+FOG, to address postural control deficits and enable step initiation. PMID:29497374

Use of an Automatic Problem Generator to Teach Basic Skills in a First Course in Assembly Language.

ERIC Educational Resources Information Center

Benander, Alan; And Others

1989-01-01

Discussion of the use of computer aided instruction (CAI) and instructional software in college level courses highlights an automatic problem generator, AUTOGEN, that was written for computer science students learning assembly language. Design of the software is explained, and student responses are reported. (nine references) (LRW)

Analyses of the Integration of Carbon Dioxide Removal Assembly, Compressor, Accumulator and Sabatier Carbon Dioxide Reduction Assembly

NASA Technical Reports Server (NTRS)

Jeng, Frank F.; Lafuse, Sharon; Smith, Frederick D.; Lu, Sao-Dung; Knox, James C.; Campbell, Mellssa L.; Scull, Timothy D.; Green Steve

2010-01-01

A tool has been developed by the Sabatier Team for analyzing/optimizing CO2 removal assembly, CO2 compressor size, its operation logic, water generation from Sabatier, utilization of CO2 from crew metabolic output, and Hz from oxygen generation assembly. Tests had been conducted using CDRA/Simulation compressor set-up at MSFC in 2003. Analysis of test data has validated CO2 desorption rate profile, CO2 compressor performance, CO2 recovery and CO2 vacuum vent in CDRA desorption. Optimizing the compressor size and compressor operation logic for an integrated closed air revitalization system Is being conducted by the Sabatier Team.

Genome assembly reborn: recent computational challenges

PubMed Central

2009-01-01

Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, leading to new computational challenges. In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain. PMID:19482960

Tablet—next generation sequence assembly visualization

PubMed Central

Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David

2010-01-01

Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions. Contact: tablet@scri.ac.uk PMID:19965881

Characterization of pituitary cells targeted by antipituitary antibodies in patients with isolated autoimmune diseases without pituitary insufficiency may help to foresee the kind of future hypopituitarism.

PubMed

De Bellis, A; Dello Iacovo, A; Bellastella, G; Savoia, A; Cozzolino, D; Sinisi, A A; Bizzarro, A; Bellastella, A; Giugliano, D

2014-10-01

Detection of antipituitary antibodies (APA) at high levels and with a particular immunofluorescence pattern in patients with autoimmune polyendocrine syndromes may indicate a possible future autoimmune pituitary involvement. This longitudinal study was aimed at characterizing in patients with a single organ-specific autoimmune disease the pituitary cells targeted by APA at start, verifying whether this characterization allows to foresee the kind of possible subsequent hypopituitarism. Thirty-six APA positive and 40 APA negative patients with isolated autoimmune diseases participated in the study. None of them had pituitary dysfunction at entry. Characterization by four-layer immunofluorescence of pituitary cells targeted by APA in APA positive patients at entry and study of pituitary function in all patients were performed every 6 months during a 5 year follow-up. Antipituitary antibodies immunostained selectively one type of pituitary-secreting cells in 21 patients (58.3 %, group 1), and several types of pituitary cells in the remaining 15 (41.7 %, group 2). All patients in group 1 showed subsequently a pituitary insufficiency, corresponding to the type of cells targeted by APA in 18 of them (85.7 %). Only 8 out of 15 patients in group 2 (53.3 %) showed a hypopituitarism, isolated in 7 and combined in the other one. None of APA negative patients showed hypopituitarism. The characterization of pituitary cells targeted by APA in patients with isolated autoimmune diseases, when the pituitary function is still normal, may help to foresee the kind of subsequent hypopituitarism, especially when APA immunostained selectively only one type of pituitary cells. A careful follow-up of pituitary function in these patients is advisable to allow an early diagnosis of hypopituitarism, even in subclinical phase and a consequent timely replacement therapy.

Effect of KCNJ5 Mutations on Gene Expression in Aldosterone-Producing Adenomas and Adrenocortical Cells

PubMed Central

Monticone, Silvia; Hattangady, Namita G.; Nishimoto, Koshiro; Mantero, Franco; Rubin, Beatrice; Cicala, Maria Verena; Pezzani, Raffaele; Auchus, Richard J.; Ghayee, Hans K.; Shibata, Hirotaka; Kurihara, Isao; Williams, Tracy A.; Giri, Judith G.; Bollag, Roni J.; Edwards, Michael A.; Isales, Carlos M.

2012-01-01

Context: Primary aldosteronism is a heterogeneous disease that includes both sporadic and familial forms. A point mutation in the KCNJ5 gene is responsible for familial hyperaldosteronism type III. Somatic mutations in KCNJ5 also occur in sporadic aldosterone producing adenomas (APA). Objective: The objective of the study was to define the effect of the KCNJ5 mutations on gene expression and aldosterone production using APA tissue and human adrenocortical cells. Methods: A microarray analysis was used to compare the transcriptome profiles of female-derived APA samples with and without KCNJ5 mutations and HAC15 adrenal cells overexpressing either mutated or wild-type KCNJ5. Real-time PCR validated a set of differentially expressed genes. Immunohistochemical staining localized the KCNJ5 expression in normal adrenals and APA. Results: We report a 38% (18 of 47) prevalence of KCNJ5 mutations in APA. KCNJ5 immunostaining was highest in the zona glomerulosa of NA and heterogeneous in APA tissue, and KCNJ5 mRNA was 4-fold higher in APA compared with normal adrenals (P < 0.05). APA with and without KCNJ5 mutations displayed slightly different gene expression patterns, notably the aldosterone synthase gene (CYP11B2) was more highly expressed in APA with KCNJ5 mutations. Overexpression of KCNJ5 mutations in HAC15 increased aldosterone production and altered expression of 36 genes by greater than 2.5-fold (P < 0.05). Real-time PCR confirmed increases in CYP11B2 and its transcriptional regulator, NR4A2. Conclusions: KCNJ5 mutations are prevalent in APA, and our data suggest that these mutations increase expression of CYP11B2 and NR4A2, thus increasing aldosterone production. PMID:22628608

Temozolomide treatment of pituitary carcinomas and atypical adenomas: systematic review of case reports

PubMed Central

Ji, Yan; Vogel, Rachel Isaksson; Lou, Emil

2016-01-01

Background Pituitary carcinomas (PC) and atypical pituitary adenomas (APA) are rare variants of pituitary tumors for which no evidence-based treatment currently exists. We sought to determine whether temozolomide represents an effective chemotherapeutic option for patients with PC and APA. Methods A systematic review was performed using all published cases of PC and APA treated with temozolomide, and for which information on treatment regimen, clinical response, and survival could be identified. The primary goal of this analysis was to describe overall survival and progression-free survival among PC and APA patients after temozolomide treatment. Secondary goals included assessment of response rate and biomarkers of response. Results We identified 57 cases and obtained follow-up data on 54 patients (31 APA and 23 PC) for analysis. Estimates of 5-year progression-free survival and overall survival were 21.9% and 57.4% for patients with APA and 36.1% and 56.2% for patients with PC. Among those who responded to temozolomide, overall survival was marginally statistically significantly greater for patients on long-term temozolomide therapy compared with those who were not (5-year overall survival 91.7% vs 54.1%, P = .08); Progression-free survival results were similar but not statistically significant. The objective response rate was 48.4% for patients with APA and 65.2% for patients with PC. Stable disease occurred in 29% of APA and 17.4% of PC patients. Neither histology nor expression of Ki-67 correlated with response; however, negative O6-methylguanine-DNA methyltransferase staining was strongly related to response to temozolomide in patients with APA (P < .001). Conclusions Temozolomide is an effective treatment of both PC and APA, and long-term treatment can be considered for particularly aggressive cases. PMID:27551432

Trapped field internal dipole superconducting motor generator

DOEpatents

Hull, John R.

2001-01-01

A motor generator including a high temperature superconductor rotor and an internally disposed coil assembly. The motor generator superconductor rotor is constructed of a plurality of superconductor elements magnetized to produce a dipole field. The coil assembly can be either a conventional conductor or a high temperature superconductor. The superconductor rotor elements include a magnetization direction and c-axis for the crystals of the elements and which is oriented along the magnetization direction.

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod.

PubMed

Tørresen, Ole K; Star, Bastiaan; Jentoft, Sissel; Reinar, William B; Grove, Harald; Miller, Jason R; Walenz, Brian P; Knight, James; Ekholm, Jenny M; Peluso, Paul; Edvardsen, Rolf B; Tooming-Klunderud, Ave; Skage, Morten; Lien, Sigbjørn; Jakobsen, Kjetill S; Nederbragt, Alexander J

2017-01-18

The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual. The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

Comparative performance tests on the Mod-2, 2.5-mW wind turbine with and without vortex generators

NASA Technical Reports Server (NTRS)

Miller, G. E.

1995-01-01

A test program was conducted on the third Mod-2 unit at Goldendale, Washington, to systematically study the effect of vortex generators (VG's) on power performance. The subject unit was first tested without VG's to obtain baseline data. Vortex generators were then installed on the mid-blade assemblies, and the resulting 70% VG configuration was tested. Finally, vortex generators were mounted on the tip assemblies, and data was recorded for the 100% VG configuration. This test program and its results are discussed in this paper. The development of vortex generators is also presented.

Oxygen Generation Assembly Technology Development

NASA Technical Reports Server (NTRS)

Bagdigian, Robert; Cloud, Dale

1999-01-01

Hamilton Standard Space Systems International (HSSI) is under contract to NASA Marshall Space Flight Center (MSFC) to develop an Oxygen Generation Assembly (OGA) for the International Space Station (ISS). The International Space Station Oxygen Generation Assembly (OGA) electrolyzes potable water from the Water Recovery System (WRS) to provide gaseous oxygen to the Space Station module atmosphere. The OGA produces oxygen for metabolic consumption by crew and biological specimens. The OGA also replenishes oxygen lost by experiment ingestion, airlock depressurization, CO2 venting, and leakage. As a byproduct, gaseous hydrogen is generated. The hydrogen will be supplied at a specified pressure range above ambient to support future utilization. Initially, the hydrogen will be vented overboard to space vacuum. This paper describes the OGA integration into the ISS Node 3. It details the development history supporting the design and describes the OGA System characteristics and its physical layout.

28 CFR 42.208 - Notice of noncompliance.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Act (APA) if: (1) The agency gives all interested parties opportunity for— (i) The submission and... consistent with the APA, it shall presume the APA procedures were applied, and send notification under § 42...

Alternative Polyadenylation in Glioblastoma Multiforme and Changes in Predicted RNA Binding Protein Profiles

PubMed Central

Shao, Jiaofang; Zhang, Jing; Zhang, Zengming; Jiang, Huawei; Lou, Xiaoyan; Foltz, Gregory; Lan, Qing; Huang, Qiang

2013-01-01

Abstract Alternative polyadenylation (APA) is widely present in the human genome and plays a key role in carcinogenesis. We conducted a comprehensive analysis of the APA products in glioblastoma multiforme (GBM, one of the most lethal brain tumors) and normal brain tissues and further developed a computational pipeline, RNAelements (http://sysbio.zju.edu.cn/RNAelements/), using covariance model from known RNA binding protein (RBP) targets acquired by RNA Immunoprecipitation (RIP) analysis. We identified 4530 APA isoforms for 2733 genes in GBM, and found that 182 APA isoforms from 148 genes showed significant differential expression between normal and GBM brain tissues. We then focused on three genes with long and short APA isoforms that show inconsistent expression changes between normal and GBM brain tissues. These were myocyte enhancer factor 2D, heat shock factor binding protein 1, and polyhomeotic homolog 1 (Drosophila). Using the RNAelements program, we found that RBP binding sites were enriched in the alternative regions between the first and the last polyadenylation sites, which would result in the short APA forms escaping regulation from those RNA binding proteins. To the best of our knowledge, this report is the first comprehensive APA isoform dataset for GBM and normal brain tissues. Additionally, we demonstrated a putative novel APA-mediated mechanism for controlling RNA stability and translation for APA isoforms. These observations collectively lay a foundation for novel diagnostics and molecular mechanisms that can inform future therapeutic interventions for GBM. PMID:23421905

Impact of presence of antiphospholipid antibodies on in vitro fertilization outcome

PubMed Central

Hong, Yeon Hee; Kim, Se Jeong; Moon, Kyoung Yong; Kim, Seul Ki; Lee, Won Don; Kim, Seok Hyun

2018-01-01

Objective To investigate prevalence of antiphospholipid antibody (APA) in Korean infertile women undergoing the first in vitro fertilization (IVF) treatment and to evaluate the influence of APA on the subsequent IVF outcomes. Method Two hundred nineteen infertile women who destined the first IVF were prospectively enrolled in 2 infertility centers. Male factor or uterine factor infertility and women with past or current endocrine or immunologic disorders were completely excluded. Plasma concentration of lupus anticoagulant was measured by clot-based method, and anticardiolipin antibody (IgG/IgM), and anti-β2-glycoprotein 1 antibody (IgG/IgM) was measured by enzyme-linked immunosorbent assay method before starting ovarian stimulation for IVF. Results APA was positive in 13 women (5.9%). Lupus anticoagulant was positive in 2 women (0.9%), anticardiolipin antibody was positive in 7 women (3.2%), and anti-β2-glycoprotein 1 antibody was positive in 4 women (1.8%). In 193 women entering embryo transfer, clinical characteristics and stimulation outcomes were comparable between APA-positive (n=12) and APA-negative group (n=181). The clinical pregnancy rate (66.7% vs. 45.9%), ongoing pregnancy rate (58.3% vs. 37.0%), and miscarriage rate (12.5% vs. 19.3%) were all similar between APA-positive and APA-negative group. Conclusion The prevalence of APA is low in Korean infertile women undergoing the first IVF cycle, and the presence of APA appears to neither decrease their first IVF success nor increase abortion rate. PMID:29780778

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.

PubMed

Ashrafi, Hamid; Hill, Theresa; Stoffel, Kevin; Kozik, Alexander; Yao, Jiqiang; Chin-Wo, Sebastian Reyes; Van Deynze, Allen

2012-10-30

Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80-120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were designed for the identified markers. The assembly was annotated by Blast2GO and 14,740 (12%) of annotated contigs were associated with functional proteins. Before availability of pepper genome sequence, assembling transcriptomes of this economically important crop was required to generate thousands of high-quality molecular markers that could be used in breeding programs. In order to have a better understanding of the assembled sequences and to identify candidate genes underlying QTLs, we annotated the contigs of Sanger-EST and Illumina transcriptome assemblies. These and other information have been curated in a database that we have dedicated for pepper project.

Use of the ventricular propagated excitation model in the magnetocardiographic inverse problem for reconstruction of electrophysiological properties.

PubMed

Ohyu, Shigeharu; Okamoto, Yoshiwo; Kuriki, Shinya

2002-06-01

A novel magnetocardiographic inverse method for reconstructing the action potential amplitude (APA) and the activation time (AT) on the ventricular myocardium is proposed. This method is based on the propagated excitation model, in which the excitation is propagated through the ventricle with nonuniform height of action potential. Assumption of stepwise waveform on the transmembrane potential was introduced in the model. Spatial gradient of transmembrane potential, which is defined by APA and AT distributed in the ventricular wall, is used for the computation of a current source distribution. Based on this source model, the distributions of APA and AT are inversely reconstructed from the QRS interval of magnetocardiogram (MCG) utilizing a maximum a posteriori approach. The proposed reconstruction method was tested through computer simulations. Stability of the methods with respect to measurement noise was demonstrated. When reference APA was provided as a uniform distribution, root-mean-square errors of estimated APA were below 10 mV for MCG signal-to-noise ratios greater than, or equal to, 20 dB. Low-amplitude regions located at several sites in reference APA distributions were correctly reproduced in reconstructed APA distributions. The goal of our study is to develop a method for detecting myocardial ischemia through the depression of reconstructed APA distributions.

Sambot II: A self-assembly modular swarm robot

NASA Astrophysics Data System (ADS)

Zhang, Yuchao; Wei, Hongxing; Yang, Bo; Jiang, Cancan

2018-04-01

The new generation of self-assembly modular swarm robot Sambot II, based on the original generation of self-assembly modular swarm robot Sambot, adopting laser and camera module for information collecting, is introduced in this manuscript. The visual control algorithm of Sambot II is detailed and feasibility of the algorithm is verified by the laser and camera experiments. At the end of this manuscript, autonomous docking experiments of two Sambot II robots are presented. The results of experiments are showed and analyzed to verify the feasibility of whole scheme of Sambot II.

Starter for inductively coupled plasma tube

DOEpatents

Hull, D.E.; Bieniewski, T.M.

1988-08-23

A starter assembly is provided for use with an inductively coupled plasma (ICP) tube to reliably initiate a plasma at internal pressures above about 30 microns. A conductive probe is inserted within the inductor coil about the tube and insulated from the tube shield assembly. A capacitive circuit is arranged for momentarily connecting a high voltage radio-frequency generator to the probe while simultaneously energizing the coil. When the plasma is initiated the probe is disconnected from the generator and electrically connected to the shield assembly for operation. 1 fig.

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

PubMed

Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

2012-01-01

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

Journal article reporting standards for quantitative research in psychology: The APA Publications and Communications Board task force report.

PubMed

Appelbaum, Mark; Cooper, Harris; Kline, Rex B; Mayo-Wilson, Evan; Nezu, Arthur M; Rao, Stephen M

2018-01-01

Following a review of extant reporting standards for scientific publication, and reviewing 10 years of experience since publication of the first set of reporting standards by the American Psychological Association (APA; APA Publications and Communications Board Working Group on Journal Article Reporting Standards, 2008), the APA Working Group on Quantitative Research Reporting Standards recommended some modifications to the original standards. Examples of modifications include division of hypotheses, analyses, and conclusions into 3 groupings (primary, secondary, and exploratory) and some changes to the section on meta-analysis. Several new modules are included that report standards for observational studies, clinical trials, longitudinal studies, replication studies, and N-of-1 studies. In addition, standards for analytic methods with unique characteristics and output (structural equation modeling and Bayesian analysis) are included. These proposals were accepted by the Publications and Communications Board of APA and supersede the standards included in the 6th edition of the Publication Manual of the American Psychological Association (APA, 2010). (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Enzymatic characteristics of an ApaH-like phosphatase, PrpA, and a diadenosine tetraphosphate hydrolase, ApaH, from Myxococcus xanthus.

PubMed

Sasaki, Masashi; Takegawa, Kaoru; Kimura, Yoshio

2014-09-17

We characterized the activities of the Myxococcus xanthus ApaH-like phosphatases PrpA and ApaH, which share homologies with both phosphoprotein phosphatases and diadenosine tetraphosphate (Ap4A) hydrolases. PrpA exhibited a phosphatase activity towards p-nitrophenyl phosphate (pNPP), tyrosine phosphopeptide and tyrosine-phosphorylated protein, and a weak hydrolase activity towards ApnA and ATP. In the presence of Mn(2+), PrpA hydrolyzed Ap4A into AMP and ATP, whereas in the presence of Co(2+) PrpA hydrolyzed Ap4A into two molecules of ADP. ApaH exhibited high phosphatase activity towards pNPP, and hydrolase activity towards ApnA and ATP. Mn(2+) was required for ApaH-mediated pNPP dephosphorylation and ATP hydrolysis, whereas Co(2+) was required for ApnA hydrolysis. Thus, PrpA and ApaH may function mainly as a tyrosine protein phosphatase and an ApnA hydrolase, respectively. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Expression of inflammation-related genes in aldosterone-producing adenomas with KCNJ5 mutation.

PubMed

Murakami, Masanori; Yoshimoto, Takanobu; Nakano, Yujiro; Tsuchiya, Kyoichiro; Minami, Isao; Bouchi, Ryotaro; Fujii, Yasuhisa; Nakabayashi, Kazuhiko; Hashimoto, Koshi; Hata, Ken-Ichiro; Kihara, Kazunori; Ogawa, Yoshihiro

2016-08-05

The adrenocortical cells have been shown to produce various inflammatory cytokines such as TNFα and IL-6, which could modulate steroidogenesis. However, the role of inflammatory cytokines in aldosterone-producing adenomas (APAs) is not fully understood. In the present study, we examined the relationships between mRNA expression levels of the inflammation-related genes and somatic mutations in APA tissues. We evaluated mRNA expression levels of TNFA, IL6, and NFKB1 in APA tissues obtained from 44 Japanese APA patients. We revealed that mRNA expression patterns of the inflammation-related genes depended on a KCNJ5 somatic mutation. In addition, we showed that mRNA expression levels of the inflammation-related genes correlated with those of the steroidogenic enzyme CYP11B1 in the patients with APAs. The present study documented for the first time the expression of inflammation-related genes in APAs and the correlation of their expression levels with the KCNJ5 mutation status and mRNA expression levels of steroidogenic enzymes, indicating the pathophysiological relevance of inflammation-related genes in APAs. Copyright © 2016 Elsevier Inc. All rights reserved.

Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

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

Matsui, Hiroshi

Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide filmsmore » reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.« less

Dovetail spoke internal permanent magnet machine

DOEpatents

Alexander, James Pellegrino [Ballston Lake, NY; EL-Refaie, Ayman Mohamed Fawzi [Niskayuna, NY; Lokhandwalla, Murtuza [Clifton Park, NY; Shah, Manoj Ramprasad [Latham, NY; VanDam, Jeremy Daniel [West Coxsackie, NY

2011-08-23

An internal permanent magnet (IPM) machine is provided. The IPM machine includes a stator assembly and a stator core. The stator core also includes multiple stator teeth. The stator assembly is further configured with stator windings to generate a stator magnetic field when excited with alternating currents and extends along a longitudinal axis with an inner surface defining a cavity. The IPM machine also includes a rotor assembly and a rotor core. The rotor core is disposed inside the cavity and configured to rotate about the longitudinal axis. The rotor assembly further includes a shaft. The shaft further includes multiple protrusions alternately arranged relative to multiple bottom structures provided on the shaft. The rotor assembly also includes multiple stacks of laminations disposed on the protrusions and dovetailed circumferentially around the shaft. The rotor assembly further includes multiple pair of permanent magnets for generating a magnetic field, which magnetic field interacts with the stator magnetic field to produce a torque. The multiple pair of permanent magnets are disposed between the stacks. The rotor assembly also includes multiple middle wedges mounted between each pair of the multiple permanent magnets.

Flow-oriented dynamic assembly algorithm in TCP over OBS networks

NASA Astrophysics Data System (ADS)

Peng, Shuping; Li, Zhengbin; He, Yongqi; Xu, Anshi

2008-11-01

OBS is envisioned as a promising infrastructure for the next generation optical network, and TCP is likely to be the dominant transport protocol in the next generation network. Therefore, it is necessary to evaluate the performance of TCP over OBS networks. The assembly at the ingress edge nodes will impact the network performance. There have been several Fixed Assembly Period (FAP) algorithms proposed. However, the assembly period in FAP is fixed, and it can not be adjusted according to the network condition. Moreover, in FAP, the packets from different TCP sources are assembled into one burst. In that case, if such a burst is dropped, the TCP windows of the corresponding sources will shrink and the throughput will be reduced. In this paper, we introduced a flow-oriented Dynamic Assembly Period (DAP) algorithm for TCP over OBS networks. Through comparing the previous and current burst lengths, DAP can track the variation of TCP window, and update the assembly period dynamically for the next assembly. The performance of DAP is evaluated over a single TCP connection and multiple connections, respectively. The simulation results show that DAP performs better than FAP at almost the whole range of burst dropping probability.

Reducing assembly complexity of microbial genomes with single-molecule sequencing

USDA-ARS?s Scientific Manuscript database

Genome assembly algorithms cannot fully reconstruct microbial chromosomes from the DNA reads output by first or second-generation sequencing instruments. Therefore, most genomes are left unfinished due to the significant resources required to manually close gaps left in the draft assemblies. Single-...

Guide to APA-Based Models

NASA Technical Reports Server (NTRS)

Robins, Robert E.; Delisi, Donald P.

2008-01-01

In Robins and Delisi (2008), a linear decay model, a new IGE model by Sarpkaya (2006), and a series of APA-Based models were scored using data from three airports. This report is a guide to the APA-based models.

Psi Chi/APA Edwin B. Newman Graduate Research Award.

PubMed

2016-11-01

The Edwin B. Newman Graduate Research Award is sponsored jointly by Psi Chi, the national honor society in psychology, and the APA. The award is presented annually to the psychology graduate student who submits the best research paper that was published or presented at a national, regional, or state psychological association conference during the past calendar year. The Edwin B. Newman Graduate Research Award is given jointly by Psi Chi and APA. Members of the 2016 Edwin B. Newman Award Committee were Shawn Carlton, PhD, Psi Chi representative; Christina Frederick-Recascino, PhD; John Norcross, PhD, APA representative; Karenna Malavanti, PhD, Psi Chi representative; Steven Kohn, PhD, Psi Chi representative; Warren Fass, PhD, Psi Chi representative; Chris Lovelace, PhD, Psi Chi representative; and Cathy Epkins, PhD, APA representative. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Violations of exhibiting and FDA rules at an American Psychiatric Association annual meeting.

PubMed

Lurie, Peter; Tran, Tung; Wolfe, Sidney Manuel; Goodman, Robert

2005-12-01

We conducted a cross-sectional study of all exhibit booths for the 24 pharmaceutical companies at the 2002 American Psychiatric Association (APA) convention. We collected and categorized one of each item distributed by the companies at each booth. A total of 268 items were collected from 24 companies (median=8). The most common categories of items were "reprints or pamphlets" (37%) and "noneducational gifts" (27%), including music CDs and invitations to dinners and museums. There were a total of 16 violations of the APA's own exhibit rules: eight companies had one violation and two companies had four violations. Four companies engaged in FDA-prohibited off-label promotion; one also violated the APA code. Over half of all companies (54%) were in violation of either APA rules or FDA regulations. The APA's voluntary code has failed to adequately reduce inappropriate promotional activity at the annual APA meeting.

Layer-by-layer assembled biopolymer microcapsule with separate layer cavities generated by gas-liquid microfluidic approach.

PubMed

Wang, Yifeng; Zhou, Jing; Guo, Xuecheng; Hu, Qian; Qin, Chaoran; Liu, Hui; Dong, Meng; Chen, Yanjun

2017-12-01

In this work, a layer-by-layer (LbL) assembled biopolymer microcapsule with separate layer cavities is generated by a novel and convenient gas-liquid microfluidic approach. This approach exhibits combined advantages of microfluidic approach and LbL assembly method, and it can straightforwardly build LbL-assembled capsules in mild aqueous environments at room temperature. In particular, using this approach we can build the polyelectrolyte multilayer capsule with favorable cavities in each layer, and without the need for organic solvent, emulsifying agent, or sacrificial template. Various components (e.g., drugs, proteins, fluorescent dyes, and nanoparticles) can be respectively encapsulated in the separate layer cavities of the LbL-assembled capsules. Moreover, the encapsulated capsules present the ability as colorimetric sensors, and they also exhibit the interesting release behavior. Therefore, the LbL-assembled biopolymer capsule is a promising candidate for biomedical applications in targeted delivery, controlled release, and bio-detection. Copyright © 2017 Elsevier B.V. All rights reserved.

Hierarchical self-assembly of a bow-shaped molecule bearing self-complementary hydrogen bonding sites into extended supramolecular assemblies.

PubMed

Ikeda, Masato; Nobori, Tadahito; Schmutz, Marc; Lehn, Jean-Marie

2005-01-07

The bow-shaped molecule 1 bearing a self-complementary DAAD-ADDA (D=donor A=acceptor) hydrogen-bonding array generates, in hydrocarbon solvents, highly ordered supramolecular sheet aggregates that subsequently give rise to gels by formation of an entangled network. The process of hierarchical self-assembly of compound 1 was investigated by the concentration and temperature dependence of UV-visible and (1)H NMR spectra, fluorescence spectra, and electron microscopy data. The temperature dependence of the UV-visible spectra indicates a highly cooperative process for the self-assembly of compound 1 in decaline. The electron micrograph of the decaline solution of compound 1 (1.0 mM) revealed supramolecular sheet aggregates forming an entangled network. The selected area electronic diffraction patterns of the supramolecular sheet aggregates were typical for single crystals, indicative of a highly ordered assembly. The results exemplify the generation, by hierarchical self-assembly, of highly organized supramolecular materials presenting novel collective properties at each level of organization.

Hybrid error correction and de novo assembly of single-molecule sequencing reads

PubMed Central

Koren, Sergey; Schatz, Michael C.; Walenz, Brian P.; Martin, Jeffrey; Howard, Jason; Ganapathy, Ganeshkumar; Wang, Zhong; Rasko, David A.; McCombie, W. Richard; Jarvis, Erich D.; Phillippy, Adam M.

2012-01-01

Emerging single-molecule sequencing instruments can generate multi-kilobase sequences with the potential to dramatically improve genome and transcriptome assembly. However, the high error rate of single-molecule reads is challenging, and has limited their use to resequencing bacteria. To address this limitation, we introduce a novel correction algorithm and assembly strategy that utilizes shorter, high-identity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on Pacbio RS reads of phage, prokaryotic, and eukaryotic whole genomes, including the novel genome of the parrot Melopsittacus undulatus, as well as for RNA-seq reads of the corn (Zea mays) transcriptome. Our approach achieves over 99.9% read correction accuracy and produces substantially better assemblies than current sequencing strategies: in the best example, quintupling the median contig size relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly. PMID:22750884

Complete mitochondrial genome of Helicoverpa zea (Boddie) and expression profiles of mitochondrial-encoded genes in early and late embryos

USDA-ARS?s Scientific Manuscript database

The mitochondrial genome of the bollworm, Helicoverpa zea, was assembled using paired-end nucleotide sequence reads generated with a next-generation sequencing platform. Assembly resulted in a mitogenome of 15,348 bp with greater than 17,000-fold average coverage. Organization of the H. zea mitogen...

Whole-genome sequencing for comparative genomics and de novo genome assembly.

PubMed

Benjak, Andrej; Sala, Claudia; Hartkoorn, Ruben C

2015-01-01

Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes. Next-generation sequencing however generates a vast quantity of data that can only be transformed into a usable and comprehensible form using bioinformatics. Here we describe the methodology one would use to prepare libraries for whole-genome sequencing, and the basic bioinformatics to identify mutations in a genome following Illumina HiSeq or MiSeq sequencing, as well as de novo genome assembly following sequencing using Pacific Biosciences (PacBio).

New branched DNA constructs.

PubMed

Chandra, Madhavaiah; Keller, Sascha; Gloeckner, Christian; Bornemann, Benjamin; Marx, Andreas

2007-01-01

The Watson-Crick base pairing of DNA is an advantageous phenomenon that can be exploited when using DNA as a scaffold for directed self-organization of nanometer-sized objects. Several reports have appeared in the literature that describe the generation of branched DNA (bDNA) with variable numbers of arms that self-assembles into predesigned architectures. These bDNA units are generated by using cleverly designed rigid crossover DNA molecules. Alternatively, bDNA can be generated by using synthetic branch points derived from either nucleoside or non-nucleoside building blocks. Branched DNA has scarcely been explored for use in nanotechnology or from self-assembling perspectives. Herein, we wish to report our results for the synthesis, characterization, and assembling properties of asymmetrical bDNA molecules that are able to generate linear and circular bDNA constructs. Our strategy for the generation of bDNA is based on a branching point that makes use of a novel protecting-group strategy. The bDNA units were generated by means of automated DNA synthesis methods and were used to generate novel objects by employing chemical and biological techniques. The entities generated might be useful building blocks for DNA-based nanobiotechnology.

Army Posture Statement: A Statement on the Posture of the United States Army, 2009

DTIC Science & Technology

2009-05-07

Research Institute Army Physical Readiness Training (FM 3-22.02) Army Preparatory School Army Prepositioned Stocks (APS) Army Reserve Employer Relations...ARFORGEN Army Force Generation AFRICOM Africa Command AMAP Army Medical Action Plan AMC Army Material Command APA Army Prepositioned Stocks AR Army...Ordnance Disposal ES2 Every Soldier a Sensor ETF Enterprise Task Force FCS Future Combat Systems FM Field Manual FORSCOM Forces Command FY Fiscal Year

In vivo antibody-mediated modulation of aminopeptidase A in mouse proximal tubular epithelial cells.

PubMed

Mentzel, S; Dijkman, H B; van Son, J P; Wetzels, J F; Assmann, K J

1999-07-01

Aminopeptidase A (APA) is one of the many renal hydrolases. In mouse kidney, APA is predominantly expressed on the brush borders and sparsely on the basolateral membranes of proximal tubular epithelial cells. However, when large amounts of monoclonal antibodies (MAbs) against APA were injected into mice, we observed strong binding of the MAbs to the basolateral membranes, whereas the MAbs bound only transiently to the brush borders of the proximal tubular epithelial cells. In parallel, APA itself disappeared from the brush borders by both endocytosis and shedding, whereas it was increasingly expressed on the basolateral sides. Using ultrastructural immunohistology, we found no evidence for transcellular transport of endocytosed APA to the basolateral side of the proximal tubular epithelial cells. The absence of transcellular transport was confirmed by experiments in which we used a low dose of the MAbs. Such a low dose did not result in binding of the MAbs to the brush borders and had no effect on the presence of APA in the brush borders of the proximal tubular epithelial cells. In these experiments we still could observe binding of the MAbs to the basolateral membranes in parallel with the local appearance of APA. In addition, treatment of mice with chlorpromazine, a calmodulin antagonist that interferes with cytoskeletal function, largely inhibited the MAb-induced modulation of APA. Our studies suggest that injection of MAbs to APA specifically interrupts the normal intracellular traffic of this enzyme in proximal tubular epithelial cells. This intracellular transport is dependent on the action of cytoskeletal proteins.

Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors.

PubMed

Rehfeld, Anders; Plass, Mireya; Døssing, Kristina; Knigge, Ulrich; Kjær, Andreas; Krogh, Anders; Friis-Hansen, Lennart

2014-01-01

The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3' untranslated regions. Additionally, APA can also produce mRNAs containing different 3'-terminal coding regions. Therefore, APA alters both the repertoire and the expression level of proteins. Here, we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three SI-NETs and a reference sample. In the tumors, 16 genes showed significant changes of APA pattern, which lead to either the 3' truncation of mRNA coding regions or 3' untranslated regions. Among these, 11 genes had been previously associated with cancer, with 4 genes being known tumor suppressors: DCC, PDZD2, MAGI1, and DACT2. We validated the APA in three out of three cases with quantitative real-time-PCR. Our findings suggest that changes of APA pattern in these 16 genes could be involved in the tumorigenesis of SI-NETs. Furthermore, they also point to APA as a new target for both diagnostic and treatment of SI-NETs. The identified genes with APA specific to the SI-NETs could be further tested as diagnostic markers and drug targets for disease prevention and treatment.

Alternative Polyadenylation of Tumor Suppressor Genes in Small Intestinal Neuroendocrine Tumors

PubMed Central

Rehfeld, Anders; Plass, Mireya; Døssing, Kristina; Knigge, Ulrich; Kjær, Andreas; Krogh, Anders; Friis-Hansen, Lennart

2014-01-01

The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3′ untranslated regions. Additionally, APA can also produce mRNAs containing different 3′-terminal coding regions. Therefore, APA alters both the repertoire and the expression level of proteins. Here, we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three SI-NETs and a reference sample. In the tumors, 16 genes showed significant changes of APA pattern, which lead to either the 3′ truncation of mRNA coding regions or 3′ untranslated regions. Among these, 11 genes had been previously associated with cancer, with 4 genes being known tumor suppressors: DCC, PDZD2, MAGI1, and DACT2. We validated the APA in three out of three cases with quantitative real-time-PCR. Our findings suggest that changes of APA pattern in these 16 genes could be involved in the tumorigenesis of SI-NETs. Furthermore, they also point to APA as a new target for both diagnostic and treatment of SI-NETs. The identified genes with APA specific to the SI-NETs could be further tested as diagnostic markers and drug targets for disease prevention and treatment. PMID:24782827

PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.

PubMed

Gao, Yubang; Wang, Huiyuan; Zhang, Hangxiao; Wang, Yongsheng; Chen, Jinfeng; Gu, Lianfeng

2018-05-01

The single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) based on Pacific Bioscience (PacBio) platform has received increasing attention for its ability to explore full-length isoforms. Thus, comprehensive tools for Iso-Seq bioinformatics analysis are extremely useful. Here, we present a one-stop solution for Iso-Seq analysis, called PRAPI to analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively. PRAPI is capable of combining Iso-Seq full-length isoforms with short read data, such as RNA-Seq or polyadenylation site sequencing (PAS-seq) for differential expression analysis of NAT, AS, APA and circRNAs. Furthermore, PRAPI can annotate new genes and correct mis-annotated genes when gene annotation is available. Finally, PRAPI generates high-quality vector graphics to visualize and highlight the Iso-Seq results. The Dockerfile of PRAPI is available at http://www.bioinfor.org/tool/PRAPI. lfgu@fafu.edu.cn.

LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.

PubMed

El-Metwally, Sara; Zakaria, Magdi; Hamza, Taher

2016-11-01

The deluge of current sequenced data has exceeded Moore's Law, more than doubling every 2 years since the next-generation sequencing (NGS) technologies were invented. Accordingly, we will able to generate more and more data with high speed at fixed cost, but lack the computational resources to store, process and analyze it. With error prone high throughput NGS reads and genomic repeats, the assembly graph contains massive amount of redundant nodes and branching edges. Most assembly pipelines require this large graph to reside in memory to start their workflows, which is intractable for mammalian genomes. Resource-efficient genome assemblers combine both the power of advanced computing techniques and innovative data structures to encode the assembly graph efficiently in a computer memory. LightAssembler is a lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of [Formula: see text]-spaced sequenced [Formula: see text]-mers and the other holding [Formula: see text]-mers classified as likely correct, using a simple statistical test. LightAssembler contains a light implementation of the graph traversal and simplification modules that achieves comparable assembly accuracy and contiguity to other competing tools. Our method reduces the memory usage by [Formula: see text] compared to the resource-efficient assemblers using benchmark datasets from GAGE and Assemblathon projects. While LightAssembler can be considered as a gap-based sequence assembler, different gap sizes result in an almost constant assembly size and genome coverage. https://github.com/SaraEl-Metwally/LightAssembler CONTACT: sarah_almetwally4@mans.edu.egSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The use of ethnic minority populations in published psychological research, 1990-1999.

PubMed

Imada, Toshie; Schiavo, R Steven

2005-09-01

For this study, the authors analyzed the contents of 16 psychology journals for the presence of empirical articles on African Americans, Latinos, Asians, and Native Americans during the period ranging from 1990 to 1999. In 6 APA journals, there was a low percentage (4.7%) of such articles. African Americans were the most studied ethnic group. Data collected for this study also indicated that minority research has been increasing more in non-APA journals than in APA journals. In both APA and non-APA journals, counseling-oriented journals had higher percentages of minority articles than did journals of other subdisciplines. Possible explanations, consequences, and suggestions for future research are discussed.

The polyadenylation code: a unified model for the regulation of mRNA alternative polyadenylation*

PubMed Central

Davis, Ryan; Shi, Yongsheng

2014-01-01

The majority of eukaryotic genes produce multiple mRNA isoforms with distinct 3′ ends through a process called mRNA alternative polyadenylation (APA). Recent studies have demonstrated that APA is dynamically regulated during development and in response to environmental stimuli. A number of mechanisms have been described for APA regulation. In this review, we attempt to integrate all the known mechanisms into a unified model. This model not only explains most of previous results, but also provides testable predictions that will improve our understanding of the mechanistic details of APA regulation. Finally, we briefly discuss the known and putative functions of APA regulation. PMID:24793760

De novo assembly of a haplotype-resolved human genome.

PubMed

Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C A M; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun

2015-06-01

The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

The recovery and analysis of mitochondrial DNA from exploded pipe bombs.

PubMed

Foran, David R; Gehring, Michael E; Stallworth, Shawn E

2009-01-01

Improvised explosive devices (IEDs) represent one of the most common modes of arbitrarily injuring or killing human beings. Because of the heat generated by, and destruction to, an IED postconflagration, most methods for identifying who assembled the device are ineffective. In the research presented, steel pipe bombs were mock-assembled by volunteers, and the bombs detonated under controlled conditions. The resultant shrapnel was collected and swabbed for residual cellular material. Mitochondrial DNA profiles were generated and compared blind to the pool of individuals who assembled the bombs. Assemblers were correctly identified 50% of the time, while another 19% could be placed into a group of three individuals with shared haplotypes. Only one bomb was assigned incorrectly. In some instances a contaminating profile (mixture) was also observed. Taken together, the results speak to the extreme sensitivity the methods have for identifying those who assemble IEDs, along with precautions needed when collecting and processing such evidence.

Unaligned instruction relocation

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

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

In-vitro analysis of APA microcapsules for oral delivery of live bacterial cells.

PubMed

Chen, H; Ouyang, W; Jones, M; Haque, T; Lawuyi, B; Prakash, S

2005-08-01

Oral administration of microcapsules containing live bacterial cells has potential as an alternative therapy for several diseases. This article evaluates the suitability of the alginate-poly-L-lysine-alginate (APA) microcapsules for oral delivery of live bacterial cells, in-vitro, using a dynamic simulated human gastro-intestinal (GI) model. Results showed that the APA microcapsules were morphologically stable in the simulated stomach conditions, but did not retain their structural integrity after a 3-day exposure in simulated human GI media. The microbial populations of the tested bacterial cells and the activities of the tested enzymes in the simulated human GI suspension were not substantially altered by the presence of the APA microcapsules, suggesting that there were no significant adverse effects of oral administration of the APA microcapsules on the flora of the human gastrointestinal tract. When the APA microcapsules containing Lactobacillus plantarum 80 (LP80) were challenged in the simulated gastric medium (pH = 2.0), 80.0% of the encapsulated cells remained viable after a 5-min incubation; however, the viability decreased considerably (8.3%) after 15 min and dropped to 2.6% after 30 min and lower than 0.2% after 60 min, indicating the limitations of the currently obtainable APA membrane for oral delivery of live bacteria. Further in-vivo studies are required before conclusions can be made concerning the inadequacy of APA microcapsules for oral delivery of live bacterial cells.

Boosting BCG-primed responses with a subunit Apa vaccine during the waning phase improves immunity and imparts protection against Mycobacterium tuberculosis.

PubMed

Nandakumar, Subhadra; Kannanganat, Sunil; Dobos, Karen M; Lucas, Megan; Spencer, John S; Amara, Rama Rao; Plikaytis, Bonnie B; Posey, James E; Sable, Suraj B

2016-05-13

Heterologous prime-boosting has emerged as a powerful vaccination approach against tuberculosis. However, optimal timing to boost BCG-immunity using subunit vaccines remains unclear in clinical trials. Here, we followed the adhesin Apa-specific T-cell responses in BCG-primed mice and investigated its BCG-booster potential. The Apa-specific T-cell response peaked 32-52 weeks after parenteral or mucosal BCG-priming but waned significantly by 78 weeks. A subunit-Apa-boost during the contraction-phase of BCG-response had a greater effect on the magnitude and functional quality of specific cellular and humoral responses compared to a boost at the peak of BCG-response. The cellular response increased following mucosal BCG-prime-Apa-subunit-boost strategy compared to Apa-subunit-prime-BCG-boost approach. However, parenteral BCG-prime-Apa-subunit-boost by a homologous route was the most effective strategy in-terms of enhancing specific T-cell responses during waning in the lung and spleen. Two Apa-boosters markedly improved waning BCG-immunity and significantly reduced Mycobacterium tuberculosis burdens post-challenge. Our results highlight the challenges of optimization of prime-boost regimens in mice where BCG drives persistent immune-activation and suggest that boosting with a heterologous vaccine may be ideal once the specific persisting effector responses are contracted. Our results have important implications for design of prime-boost regimens against tuberculosis in humans.

Joint effect of freshwater plume and coastal upwelling on phytoplankton growth off the Changjiang River

NASA Astrophysics Data System (ADS)

Tseng, Y.-F.; Lin, J.; Dai, M.; Kao, S.-J.

2013-06-01

Changjiang River discharges vast amount of unbalanced nutrients (dissolved inorganic nitrogen (N) and phosphorus (P) with N / P > 80 in general) into the East China Sea during summertime. To explore nutrient dynamics and P stress potential for phytoplankton, a cruise was conducted in the Changjiang plume during summer 2011. With 3-D observations of nutrients, chlorophyll a (Chl a), and bulk alkaline phosphatase activity (APA), we concluded that the Changjiang Diluted Water (CDW) and coastal upwelling significantly influenced the horizontal and vertical heterogeneities of phytoplankton P-deficiency in the plume. Allochthonous APA was detected at nutrient-enriched freshwater end. Excessive N (~10 to 112 µM) was obserevd throughout the entire plume surface. In the plume fringe where featured by stratification and excess N, diapycnal phosphate supply was blocked to stimulate APA for phytoplankton growth. We observed upwelling outcrops just attaching the turbidity front at seaward side, where Chl a peaked yet much less APA was detected. An external phosphate supply from subsurface, which stimulated phytoplankton growth but inhibited APA, was suggested and the supply was likely sourced from the Nearshore Kuroshio Branch Current. In such hydrographically complicated Changjiang plume, phosphate supply instead of its concentration was more important determining the expression of APA. Meanwhile, allochthounous APA may also alter the usefulness of APA as a P-stress indicator.

Joint effect of freshwater plume and coastal upwelling on phytoplankton growth off the Changjiang River

NASA Astrophysics Data System (ADS)

Tseng, Y.-F.; Lin, J.; Dai, M.; Kao, S.-J.

2014-01-01

The Changjiang (Yangtze) River discharges vast amount of unbalanced nutrients (dissolved inorganic nitrogen and phosphorus with N / P ratio > 80 in general) into the East China Sea in summer. To study nutrient dynamics and P-stress potential for phytoplankton, a cruise was conducted in the Changjiang plume during summer 2011. With 3-D observations of nutrients, chlorophyll a (Chl a), and bulk alkaline phosphatase activity (APA), we concluded that the Changjiang Diluted Water and coastal upwelling significantly influenced the horizontal and vertical heterogeneities of phytoplankton P deficiency in the Changjiang plume. Allochthonous APA was detected at nutrient-enriched freshwater end. Excessive N (~ 10 to 112 μM) was observed throughout the entire plume surface. In the plume fringe featuring stratification and excess N, diapycnal phosphate supply was blocked and phytoplankton APA was stimulated for growth. We observed an upwelling just attaching to the turbidity front at seaward side where Chl a peaked yet much less APA was detected. An external phosphate supply from subsurface, which promoted phytoplankton growth but inhibited APA, was suggested to be sourced from the Nearshore Kuroshio Branch Current. In the so hydrographically complicated Changjiang plume, phosphate supply instead of its concentration may be more important in determining the expression of APA. Meanwhile, allochthonous APA may also alter the usefulness of APA as a P-stress indicator.

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

PubMed Central

You, Leiming; Wu, Jiexin; Feng, Yuchao; Fu, Yonggui; Guo, Yanan; Long, Liyuan; Zhang, Hui; Luan, Yijie; Tian, Peng; Chen, Liangfu; Huang, Guangrui; Huang, Shengfeng; Li, Yuxin; Li, Jie; Chen, Chengyong; Zhang, Yaqing; Chen, Shangwu; Xu, Anlong

2015-01-01

Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3′-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3′-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3′-untranslated regions (3′-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish. PMID:25378337

Templated assembly of BiFeO3 nanocrystals into 3D mesoporous networks for catalytic applications

NASA Astrophysics Data System (ADS)

Papadas, I. T.; Subrahmanyam, K. S.; Kanatzidis, M. G.; Armatas, G. S.

2015-03-01

The self-assembly of uniform nanocrystals into large porous architectures is currently of immense interest for nanochemistry and nanotechnology. These materials combine the respective advantages of discrete nanoparticles and mesoporous structures. In this article, we demonstrate a facile nanoparticle templating process to synthesize a three-dimensional mesoporous BiFeO3 material. This approach involves the polymer-assisted aggregating assembly of 3-aminopropanoic acid-stabilized bismuth ferrite (BiFeO3) nanocrystals followed by thermal decomposition of the surfactant. The resulting material consists of a network of tightly connected BiFeO3 nanoparticles (~6-7 nm in diameter) and has a moderately high surface area (62 m2 g-1) and uniform pores (ca. 6.3 nm). As a result of the unique mesostructure, the porous assemblies of BiFeO3 nanoparticles show an excellent catalytic activity and chemical stability for the reduction of p-nitrophenol to p-aminophenol with NaBH4.The self-assembly of uniform nanocrystals into large porous architectures is currently of immense interest for nanochemistry and nanotechnology. These materials combine the respective advantages of discrete nanoparticles and mesoporous structures. In this article, we demonstrate a facile nanoparticle templating process to synthesize a three-dimensional mesoporous BiFeO3 material. This approach involves the polymer-assisted aggregating assembly of 3-aminopropanoic acid-stabilized bismuth ferrite (BiFeO3) nanocrystals followed by thermal decomposition of the surfactant. The resulting material consists of a network of tightly connected BiFeO3 nanoparticles (~6-7 nm in diameter) and has a moderately high surface area (62 m2 g-1) and uniform pores (ca. 6.3 nm). As a result of the unique mesostructure, the porous assemblies of BiFeO3 nanoparticles show an excellent catalytic activity and chemical stability for the reduction of p-nitrophenol to p-aminophenol with NaBH4. Electronic supplementary information (ESI) available: IR spectra and TG profiles of as-made BiFeO3 NPs and MBFA samples, TEM images of 3-APA-capped BiFeO3 NPs, EDS spectrum of MBFAs, N2 adsorption-desorption isotherms of randomly aggregated BiFeO3 NPs and catalytic data for 4-NP reduction by MBFAs and other nanostructured catalysts. See DOI: 10.1039/c5nr00185d

Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.).

PubMed

Blair, Matthew W; Prieto, Sergio; Díaz, Lucy M; Buendía, Héctor F; Cardona, César

2010-04-29

An interesting seed protein family with a role in preventing insect herbivory is the multi-gene, APA family encoding the alpha-amylase inhibitor, phytohemagglutinin and arcelin proteins of common bean (Phaseolus vulgaris). Variability for this gene family exists and has been exploited to breed for insect resistance. For example, the arcelin locus has been successfully transferred from wild to cultivated common bean genotypes to provide resistance against the bruchid species Zabrotes subfasciatus although the process has been hampered by a lack of genetic tools for and understanding about the locus. In this study, we analyzed linkage disequilibrium (LD) between microsatellite markers at the APA locus and bruchid resistance in a germplasm survey of 105 resistant and susceptible genotypes and compared this with LD in other parts of the genome. Microsatellite allele diversity was found to vary with each of the eight APA-linked markers analyzed, and two markers within the APA locus were found to be diagnostic for bruchid resistance or susceptibility and for the different arcelin alleles inherited from the wild accessions. Arc1 was found to provide higher levels of resistance than Arc5 and the markers in the APA locus were highly associated with resistance showing that introgression of this gene-family from wild beans provides resistance in cultivated beans. LD around the APA locus was found to be intermediate compared to other regions of the genome and the highest LD was found within the APA locus itself for example between the markers PV-atct001 and PV-ag004. We found the APA locus to be an important genetic determinant of bruchid resistance and also found that LD existed mostly within the APA locus but not beyond it. Moderate LD was also found for some other regions of the genome perhaps related to domestication genes. The LD pattern may reflect the introgression of arcelin from the wild into the cultivated background through breeding. LD and association studies for the arcelin gene, linked genes and other members of the APA family are essential for breaking linkage drag while maintaining high levels of bruchid resistance in common bean.

Genovo: De Novo Assembly for Metagenomes

NASA Astrophysics Data System (ADS)

Laserson, Jonathan; Jojic, Vladimir; Koller, Daphne

Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A Chinese restaurant process prior accounts for the unknown number of genomes in the sample. Inference is made by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs across one synthetic dataset and eight metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, and yield a higher assembly score.

Self-assembled biomimetic nanoreactors I: Polymeric template

NASA Astrophysics Data System (ADS)

McTaggart, Matt; Malardier-Jugroot, Cecile; Jugroot, Manish

2015-09-01

The variety of nanoarchitectures made feasible by the self-assembly of alternating copolymers opens new avenues for biomimicry. Indeed, self-assembled structures allow the development of nanoreactors which combine the efficiency of high surface area metal active centres to the effect of confinement due to the very small cavities generated by the self-assembly process. A novel self-assembly of high molecular weight alternating copolymers is characterized in the present study. The self-assembly is shown to organize into nanosheets, providing a 2 nm hydrophobic cavity with a 1D confinement.

High-speed assembly language (80386/80387) programming for laser spectra scan control and data acquisition providing improved resolution water vapor spectroscopy

NASA Technical Reports Server (NTRS)

Allen, Robert J.

1988-01-01

An assembly language program using the Intel 80386 CPU and 80387 math co-processor chips was written to increase the speed of data gathering and processing, and provide control of a scanning CW ring dye laser system. This laser system is used in high resolution (better than 0.001 cm-1) water vapor spectroscopy experiments. Laser beam power is sensed at the input and output of white cells and the output of a Fabry-Perot. The assembly language subroutine is called from Basic, acquires the data and performs various calculations at rates greater than 150 faster than could be performed by the higher level language. The width of output control pulses generated in assembly language are 3 to 4 microsecs as compared to 2 to 3.7 millisecs for those generated in Basic (about 500 to 1000 times faster). Included are a block diagram and brief description of the spectroscopy experiment, a flow diagram of the Basic and assembly language programs, listing of the programs, scope photographs of the computer generated 5-volt pulses used for control and timing analysis, and representative water spectrum curves obtained using these programs.

Deployable centralizers

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

Grubelich, Mark C.; Su, Jiann-Cherng; Knudsen, Steven D.

2017-02-28

A centralizer assembly is disclosed that allows for the assembly to be deployed in-situ. The centralizer assembly includes flexible members that can be extended into the well bore in situ by the initiation of a gas generating device. The centralizer assembly can support a large load carrying capability compared to a traditional bow spring with little or no installation drag. Additionally, larger displacements can be produced to centralize an extremely deviated casing.

Peptide Assembly-Driven Metal-Organic Framework (MOF) Motors for Micro Electric Generator

PubMed Central

Ikezoe, Yasuhiro; Fang, Justin; Wasik, Tomasz L.; Uemura, Takashi; Zheng, Yongtai; Kitagawa, Susumu

2014-01-01

Peptide-MOF motors, whose motions are driven by anisotropic surface gradients created via peptide self-assembly around nanopores of MOFs, can rotate microscopic rotors and magnet fast enough to generate electric power of 0.1 µW. To make the peptide-MOF generator recyclable, a new MOF is applied as a host motor engine, which has a more rigid framework with higher H2O affinity so that peptide release occurs more efficiently via guest exchange without the destruction of MOF. PMID:25418936

Demonstration of a Variable Phase Turbine Power System for Low Temperature Geothermal Resources

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

Hays, Lance G

2014-07-07

A variable phase turbine assembly will be designed and manufactured having a turbine, operable with transcritical, two-phase or vapor flow, and a generator – on the same shaft supported by process lubricated bearings. The assembly will be hermetically sealed and the generator cooled by the refrigerant. A compact plate-fin heat exchanger or tube and shell heat exchanger will be used to transfer heat from the geothermal fluid to the refrigerant. The demonstration turbine will be operated separately with two-phase flow and with vapor flow to demonstrate performance and applicability to the entire range of low temperature geothermal resources. The vapormore » leaving the turbine is condensed in a plate-fin refrigerant condenser. The heat exchanger, variable phase turbine assembly and condenser are all mounted on single skids to enable factory assembly and checkout and minimize installation costs. The system will be demonstrated using low temperature (237F) well flow from an existing large geothermal field. The net power generated, 1 megawatt, will be fed into the existing power system at the demonstration site. The system will demonstrate reliable generation of inexpensive power from low temperature resources. The system will be designed for mass manufacturing and factory assembly and should cost less than $1,200/kWe installed, when manufactured in large quantities. The estimated cost of power for 300F resources is predicted to be less than 5 cents/kWh. This should enable a substantial increase in power generated from low temperature geothermal resources.« less

Alkaline Phosphatase Activity : an overlooked player on the phosphate behavior in macrotidal estuaries

NASA Astrophysics Data System (ADS)

Delmas, Daniel; Labry, Claire; Youenou, Agnes; Quere, Julien; Auguet, Jean Christophe; Montanie, Helene

2014-05-01

The non-conservative behavior of phosphate within the estuarine salinity gradient is essentially assigned to physico-chemical processes, such as desorption at low salinity and to benthic exchanges. Microbial phosphatase activity (APA), generally related to phosphate deficiency, is seldom studied in phosphate rich estuarine waters. In order to address the impact of microbial activity (bacterial abundance, production BSP, APA) on phosphate behavior, we studied these activities on a seasonal basis within the salinity gradient of two macrotidal estuaries presenting different levels of suspended solids. Whatever the season the Charente estuary is characterized by high levels of Suspended Particulate Matter (SPM > 1g.L-1), particularly in the Maximum Turbidity Zone (MTZ) located at the 5-10 psu. In this area characterized by high BSP and APA there is a significant increase of PO4 levels especially during summer. In the Aulne estuary the particle load is significantly lower (1/10) but high BSP and APA are equally recorded. In the highly turbid waters of the Charente estuary, active phytoplankton is virtually absent as pheopigments constitute up to 80% of the total pigments, particularly in the MTZ, therefore APA may essentially have a bacterial origin. In the Aulne estuary attached bacteria are dominant, both in numbers and production, and their distribution along the haline gradient perfectly follows those of APA and phosphate levels. These observations, associated with the very close relationships observed between APA, SPM and BSP, suggest that APA derive mainly from bacterial (attached) origin and operate at the expense of particulate phosphorus and hence contribute to PO4 regeneration, especially in spring and summer. Finally, as APA increased as PO4, whereas the reverse is observed in both fresh and marine waters, an original scheme for APA regulation, related to the large dominance of attached bacteria can be described for the estuarine waters.

Decreased plasma prorenin levels in primary aldosteronism: potential diagnostic implications.

PubMed

Berge, Constance; Courand, Pierre-Yves; Harbaoui, Brahim; Paget, Vinciane; Khettab, Fouad; Bricca, Giampiero; Fauvel, Jean-Pierre; Lantelme, Pierre

2015-01-01

Primary aldosteronism could exert a negative feedback on prorenin secretion, of possibly different magnitude, whether it is related to an aldosterone-producing adenoma (APA) or an idiopathic hyperaldosteronism (IHA). The objectives of this study were to evaluate the level of prorenin in three subgroups: APA, IHA, and essential hypertension; and the performance of the aldosterone-to-prorenin ratio (APR) for the diagnosis of an APA. Seven hundred and forty-six hypertensive patients with a standardized work-up, including a prorenin measurement, were considered. Ninety-six patients without neutral treatment and 38 patients with other forms of secondary hypertension were excluded. APA and IHA were categorized according to computed tomography scan, adrenal venous sampling, pathological analysis and improvement of hypertension after surgery. Thirty-five patients had a diagnosis of APA, 57 of IHA and 504 of essential hypertension. Prorenin was lower in APA and IHA than in essential hypertension (32.9, 40.4 and 50.3  pg/ml, respectively; P < 0.001). APR was higher in patients with APA and IHA than in those with essential hypertension (24.0, 11.8, and 4.0  pmol/l per pg/ml, respectively; P < 0.001). The APR was more discriminant than the aldosterone-to-renin ratio to identify APA compared to IHA (area under the receiver operating curve at 0.750 and 0.639, respectively; P = 0.04). The optimal cut-off values were 22  pmol/l per pg/ml for APR (sensitivity 57.0%, specificity 93.0%) and 440  pmol/l per pg/ml for aldosterone-to-renin ratio (sensitivity 54.3%, specificity 82.5%). Primary aldosteronism and particularly its most caricatural form, that is APA, seems associated with a lower level of prorenin than essential hypertension. The APR could be included in the diagnostic strategy of APA.

The subtyping of primary aldosteronism by adrenal vein sampling: sequential blood sampling causes factitious lateralization.

PubMed

Rossitto, Giacomo; Battistel, Michele; Barbiero, Giulio; Bisogni, Valeria; Maiolino, Giuseppe; Diego, Miotto; Seccia, Teresa M; Rossi, Gian Paolo

2018-02-01

The pulsatile secretion of adrenocortical hormones and a stress reaction occurring when starting adrenal vein sampling (AVS) can affect the selectivity and also the assessment of lateralization when sequential blood sampling is used. We therefore tested the hypothesis that a simulated sequential blood sampling could decrease the diagnostic accuracy of lateralization index for identification of aldosterone-producing adenoma (APA), as compared with bilaterally simultaneous AVS. In 138 consecutive patients who underwent subtyping of primary aldosteronism, we compared the results obtained simultaneously bilaterally when starting AVS (t-15) and 15 min after (t0), with those gained with a simulated sequential right-to-left AVS technique (R ⇒ L) created by combining hormonal values obtained at t-15 and at t0. The concordance between simultaneously obtained values at t-15 and t0, and between simultaneously obtained values and values gained with a sequential R ⇒ L technique, was also assessed. We found a marked interindividual variability of lateralization index values in the patients with bilaterally selective AVS at both time point. However, overall the lateralization index simultaneously determined at t0 provided a more accurate identification of APA than the simulated sequential lateralization indexR ⇒ L (P = 0.001). Moreover, regardless of which side was sampled first, the sequential AVS technique induced a sequence-dependent overestimation of lateralization index. While in APA patients the concordance between simultaneous AVS at t0 and t-15 and between simultaneous t0 and sequential technique was moderate-to-good (K = 0.55 and 0.66, respectively), in non-APA patients, it was poor (K = 0.12 and 0.13, respectively). Sequential AVS generates factitious between-sides gradients, which lower its diagnostic accuracy, likely because of the stress reaction arising upon starting AVS.

Vessel structural support system

DOEpatents

Jenko, James X.; Ott, Howard L.; Wilson, Robert M.; Wepfer, Robert M.

1992-01-01

Vessel structural support system for laterally and vertically supporting a vessel, such as a nuclear steam generator having an exterior bottom surface and a side surface thereon. The system includes a bracket connected to the bottom surface. A support column is pivotally connected to the bracket for vertically supporting the steam generator. The system also includes a base pad assembly connected pivotally to the support column for supporting the support column and the steam generator. The base pad assembly, which is capable of being brought to a level position by turning leveling nuts, is anchored to a floor. The system further includes a male key member attached to the side surface of the steam generator and a female stop member attached to an adjacent wall. The male key member and the female stop member coact to laterally support the steam generator. Moreover, the system includes a snubber assembly connected to the side surface of the steam generator and also attached to the adjacent wall for dampening lateral movement of the steam generator. In addition, the system includes a restraining member of "flat" attached to the side surface of the steam generator and a bumper attached to the adjacent wall. The flat and the bumper coact to further laterally support the steam generator.

Should title lengths really adhere to the American Psychological Association's twelve word limit?

PubMed

Hallock, Robert M; Dillner, Kari M

2016-04-01

The publication manual for the American Psychological Association (APA) suggests that title lengths do not exceed 12 words, yet journals do not prevent longer titles. Here, we examined title lengths in APA journals to see how many exceeded the APA's suggested limit. First, we conducted a systematic analysis of 235 articles in the current issues of 23 APA journals. A total of 52% of titles were more than 12 words long. Second, we examined articles from APA journals that were at least 50 years old to examine whether title lengths have changed over time. Our results suggested that the average title lengths have indeed increased with time. One of 2 courses should be taken. Perhaps science is becoming more complex that longer titles are needed in order to convey the primary message to the reader. If this is the case, then the APA's word limit should be increased. On the other hand, however, maybe editor and reviewers should try to enforce the current word limit to force writers to be succinct. Either way, editors should make their preferences clear so that the trend for longer titles does not continue unchecked. (c) 2016 APA, all rights reserved).

Vascular complications in patients with aldosterone producing adenoma in Japan: comparative study with essential hypertension. The Research Committee of Disorders of Adrenal Hormones in Japan.

PubMed

Takeda, R; Matsubara, T; Miyamori, I; Hatakeyama, H; Morise, T

1995-05-01

The incidence of vascular complications in 224 patients with aldosterone-producing adenoma (APA) which was proven on adrenal surgery, was compared to that in 224 sex- and age-matched patients with essential hypertension (EHT). The incidence of cerebral hemorrhage was significantly higher (p < 0.05) in the patients with APA when compared to the EHT group. On the other hand, the incidence of myocardial infarction and/or congestive heart failure in the APA group was lower, although this difference did not reach statistical significance. Diastolic blood pressure in the APA group was significantly higher (p < 0.001) in the EHT group. However, a significant difference in diastolic blood pressure was not detected between the APA groups with and without vascular complications, whereas in the EHT group diastolic blood pressure was significantly higher (p < 0.001) in cases with vascular complications as compared to those without complications. As a possible factor contributing to the higher incidence of cerebral hemorrhage in the APA group, proteinuria was suggested. It was recommended that patients with primary aldosteronism should undergo operation when localization of the APA is established.

Segmentation of the Himalayas as revealed by arc-parallel gravity anomalies.

PubMed

Hetényi, György; Cattin, Rodolphe; Berthet, Théo; Le Moigne, Nicolas; Chophel, Jamyang; Lechmann, Sarah; Hammer, Paul; Drukpa, Dowchu; Sapkota, Soma Nath; Gautier, Stéphanie; Thinley, Kinzang

2016-09-21

Lateral variations along the Himalayan arc are suggested by an increasing number of studies and carry important information about the orogen's segmentation. Here we compile the hitherto most complete land gravity dataset in the region which enables the currently highest resolution plausible analysis. To study lateral variations in collisional structure we compute arc-parallel gravity anomalies (APaGA) by subtracting the average arc-perpendicular profile from our dataset; we compute likewise for topography (APaTA). We find no direct correlation between APaGA, APaTA and background seismicity, as suggested in oceanic subduction context. In the Himalayas APaTA mainly reflect relief and erosional effects, whereas APaGA reflect the deep structure of the orogen with clear lateral boundaries. Four segments are outlined and have disparate flexural geometry: NE India, Bhutan, Nepal &India until Dehradun, and NW India. The segment boundaries in the India plate are related to inherited structures, and the boundaries of the Shillong block are highlighted by seismic activity. We find that large earthquakes of the past millennium do not propagate across the segment boundaries defined by APaGA, therefore these seem to set limits for potential rupture of megathrust earthquakes.

Fabrication of Gold-Coated Ultra-Thin Anodic Porous Alumina Substrates for Augmented SERS

PubMed Central

Toccafondi, Chiara; Proietti Zaccaria, Remo; Dante, Silvia; Salerno, Marco

2016-01-01

Anodic porous alumina (APA) is a nanostructured material used as a template in several nanotechnological applications. We propose the use of APA in ultra-thin form (<100 nm) for augmented surface-enhanced Raman scattering (SERS). Here, the effect of in-depth thinning of the APA nanostructures for possible maximization of SERS was addressed. Anodization was carried out on ultra-thin films of aluminum on glass and/or silicon, followed by pore-opening. Gold (Au) was overcoated and micro-Raman/SERS measurements were carried out on test target analytes. Finite integration technique simulations of the APA-Au substrate were used both for the experimental design and simulations. It was observed that, under optimized conditions of APA and Au thickness, the SERS enhancement is higher than on standard APA-Au substrates based on thin (~100 nm) APA by up to a factor of ~20 for test molecules of mercaptobenzoic acid. The agreement between model and experimental results confirms the current understanding of SERS as being mainly due to the physical origin of plasmon resonances. The reported results represent one step towards micro-technological, integrated, disposable, high-sensitivity SERS chemical sensors and biosensors based on similar substrates. PMID:28773525

Segmentation of the Himalayas as revealed by arc-parallel gravity anomalies

PubMed Central

Hetényi, György; Cattin, Rodolphe; Berthet, Théo; Le Moigne, Nicolas; Chophel, Jamyang; Lechmann, Sarah; Hammer, Paul; Drukpa, Dowchu; Sapkota, Soma Nath; Gautier, Stéphanie; Thinley, Kinzang

2016-01-01

Lateral variations along the Himalayan arc are suggested by an increasing number of studies and carry important information about the orogen’s segmentation. Here we compile the hitherto most complete land gravity dataset in the region which enables the currently highest resolution plausible analysis. To study lateral variations in collisional structure we compute arc-parallel gravity anomalies (APaGA) by subtracting the average arc-perpendicular profile from our dataset; we compute likewise for topography (APaTA). We find no direct correlation between APaGA, APaTA and background seismicity, as suggested in oceanic subduction context. In the Himalayas APaTA mainly reflect relief and erosional effects, whereas APaGA reflect the deep structure of the orogen with clear lateral boundaries. Four segments are outlined and have disparate flexural geometry: NE India, Bhutan, Nepal & India until Dehradun, and NW India. The segment boundaries in the India plate are related to inherited structures, and the boundaries of the Shillong block are highlighted by seismic activity. We find that large earthquakes of the past millennium do not propagate across the segment boundaries defined by APaGA, therefore these seem to set limits for potential rupture of megathrust earthquakes. PMID:27649782

PAVE: program for assembling and viewing ESTs.

PubMed

Soderlund, Carol; Johnson, Eric; Bomhoff, Matthew; Descour, Anne

2009-08-26

New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. The PAVE (Program for Assembling and Viewing ESTs) assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

75 FR 65483 - Proposed Reissuance of General NPDES Permits (GP) for Alaskan Medium-Size Suction Dredging...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-25

... proposed rule'' for which the agency ``is required by section 553 of the Administrative Procedure Act (APA... permits are permits, not rulemakings, under the APA and thus not subject to APA rulemaking requirements or...

78 FR 20316 - Final Issuance of General NPDES Permits (GP) for Small Suction Dredges in Idaho

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-04

... Procedure Act (APA), or any other law, to publish general notice of proposed rulemaking.'' The RFA exempts... permits are permits, not rulemakings, under the APA and thus not subject to APA rulemaking requirements or...

Investigation of the Asphalt Pavement Analyzer (APA) testing program in Nebraska.

DOT National Transportation Integrated Search

2008-03-01

The asphalt pavement analyzer (APA) has been widely used to evaluate hot-mix asphalt (HMA) rutting potential in mix : design and quality control-quality assurance (QC-QA) applications, because the APA testing and its data analyses are : relatively si...

Development of a Microfluidic Platform to Analyze Evolution of Programmed Bacterial Death

DTIC Science & Technology

2015-12-20

We modulated the final concentrations of 6- APA and IPTG in droplets by varying their concentrations in the injection phase. At 25µg/ml 6- APA , the...in comparison, when the population was induced by 1mM IPTG, the cells grew to a higher density; this is due to the degradation of 6- APA by BlaM (red...line in Figure 4A). Similarly, when the concentration of 6- APA was increased to Surfactant)molecules) Stable)droplets) +) +) Droplet)injec6on

Affine Projection Algorithm with Improved Data-Selective Method Using the Condition Number

NASA Astrophysics Data System (ADS)

Ban, Sung Jun; Lee, Chang Woo; Kim, Sang Woo

Recently, a data-selective method has been proposed to achieve low misalignment in affine projection algorithm (APA) by keeping the condition number of an input data matrix small. We present an improved method, and a complexity reduction algorithm for the APA with the data-selective method. Experimental results show that the proposed algorithm has lower misalignment and a lower condition number for an input data matrix than both the conventional APA and the APA with the previous data-selective method.

Hydrolysis of ibuprofenoyl-CoA and other 2-APA-CoA esters by human acyl-CoA thioesterases-1 and -2 and their possible role in the chiral inversion of profens.

PubMed

Qu, Xiao; Allan, Amanda; Chui, Grace; Hutchings, Thomas J; Jiao, Ping; Johnson, Lawrence; Leung, Wai Y; Li, Portia K; Steel, Georgina R; Thompson, Andrew S; Threadgill, Michael D; Woodman, Timothy J; Lloyd, Matthew D

2013-12-01

Ibuprofen and related 2-arylpropanoic acid (2-APA) drugs are often given as a racemic mixture and the R-enantiomers undergo activation in vivo by metabolic chiral inversion. The chiral inversion pathway consists of conversion of the drug to the coenzyme A ester (by an acyl-CoA synthetase) followed by chiral inversion by α-methylacyl-CoA racemase (AMACR; P504S). The enzymes responsible for hydrolysis of the product S-2-APA-CoA ester to the active S-2-APA drug have not been identified. In this study, conversion of a variety of 2-APA-CoA esters by human acyl-CoA thioesterase-1 and -2 (ACOT-1 and -2) was investigated. Human recombinant ACOT-1 and -2 (ACOT-1 and -2) were both able to efficiently hydrolyse a variety of 2-APA-CoA substrates. Studies with the model substrates R- and S-2-methylmyristoyl-CoA showed that both enzymes were able to efficiently hydrolyse both of the epimeric substrates with (2R)- and (2S)- methyl groups. ACOT-1 is located in the cytosol and is able to hydrolyse 2-APA-CoA esters exported from the mitochondria and peroxisomes for inhibition of cyclo-oxygenase-1 and -2 in the endoplasmic reticulum. It is a prime candidate to be the enzyme responsible for the pharmacological action of chiral inverted drugs. ACOT-2 activity may be important in 2-APA toxicity effects and for the regulation of mitochondrial free coenzyme A levels. These results support the idea that 2-APA drugs undergo chiral inversion via a common pathway. Copyright © 2013 Elsevier Inc. All rights reserved.

Effects of femtosecond laser and other surface treatments on the bond strength of metallic and ceramic orthodontic brackets to zirconia

PubMed Central

García-Sanz, Verónica; Bellot-Arcís, Carlos; Mendoza-Yero, Omel; Doñate-Buendía, Carlos; Montero, Javier; Albaladejo, Alberto

2017-01-01

Femtosecond laser has been proposed as a method for conditioning zirconia surfaces to boost bond strength. However, metallic or ceramic bracket bonding to femtosecond laser-treated zirconia surfaces has not been tested. This study compared the effects of four conditioning techniques, including femtosecond laser irradiation, on shear bond strength (SBS) of metallic and ceramic brackets to zirconia.Three hundred zirconia plates were divided into five groups: 1) control (C); 2) sandblasting (APA); 3) silica coating and silane (SC); 4) femtosecond laser (FS); 5) sandblasting followed by femtosecond laser (APA+SC). A thermal imaging camera measured temperature changes in the zirconia during irradiation. Each group was divided into 2 subgroups (metallic vs ceramic brackets). SBS was evaluated using a universal testing machine. The adhesive remnant index (ARI) was registered and surfaces were observed under SEM. Surface treatment and bracket type significantly affected the bracket-zirconia bond strength. SBS was significantly higher (p<0.001) for ceramic brackets in all groups (APA+FS > APA > FS > SC > control) than metallic brackets (APA+FS > FS > SC > APA > control). For metallic brackets, groups SC (5.99 ± 1.86 MPa), FS (6.72 ± 2.30 MPa) and APA+FS (7.22 ± 2.73 MPa) reported significantly higher bond strengths than other groups (p < 0.05). For ceramic brackets, the highest bond strength values were obtained in groups APA (25.01 ± 4.45 MPa), FS (23.18 ± 6.51 MPa) and APA+FS (29.22 ± 8.20 MPa).Femtosecond laser enhances bond strength of ceramic and metallic brackets to zirconia. Ceramic brackets provide significantly stronger adhesion than metallic brackets regardless of the surface treatment method. PMID:29049418

Apa2H1, the first head domain of Apa2 trimeric autotransporter adhesin, activates mouse bone marrow-derived dendritic cells and immunization with Apa2H1 protects against Actinobacillus pleuropneumoniae infection.

PubMed

Qin, Wanhai; Wang, Lei; Zhai, Ruidong; Ma, Qiuyue; Liu, Jianfang; Bao, Chuntong; Sun, Diangang; Zhang, Hu; Sun, Changjiang; Feng, Xin; Gu, Jingmin; Du, Chongtao; Han, Wenyu; Langford, P R; Lei, Liancheng

2017-01-01

Actinobacillus pleuropneumoniae is the causative pathogen of porcine pleuropneumonia, which results in large economic losses in the pig industry worldwide. There are, however, no effective subunit vaccines are available in the market owing to the various serotypes and the absence of cross-protection against this pathogen. Therefore, the selection of protective components is of great significance for vaccine development. We previously showed that trimeric autotransporter adhesins are important virulence factors of A. pleuropneumoniae. To determine the potential role in vaccine development of the functional head domain (Apa2H1) of Apa2, a trimeric autotransporter adhesin found in A. pleuropneumoniae, we obtained nature-like trimeric Apa2H1 using a prokaryotic expression system and co-culture of Apa2H1 with bone marrow derived dendritic cells (BMDCs) in vitro resulted in maturation of BMDCs, characterised by the up-regulation of CD83, MHC-II, CCR7, ICAM-I and the increased expression of factors related to B lymphoid cells stimulation, such as proliferation-inducing ligand (APRIL), B lymphocyte stimulator (BLyS) and B cell activating factor (BAFF). The in vivo results showed that vaccination with Apa2H1 resulted in the robust production of antigen-specific antibodies, modestly induced mixed Th1 and Th2 immunity, impaired bacterial colonization and dissemination, and improved mouse survival rates. This study is the first to show that Apa2H1 is antigenic and can be used as a component of a subunit vaccine against A. pleuropneumoniae infection, providing valuable reference material for the development of an effective vaccine against A. pleuropneumoniae. Copyright © 2016 Elsevier Ltd. All rights reserved.

Psi Chi/APA Edwin B. Newman Graduate Research Award.

PubMed

2017-12-01

The Edwin B. Newman Graduate Research Award is sponsored jointly by Psi Chi, the national honor society in psychology, and the APA. The award is presented annually to the psychology graduate student who submits the best research paper that was published or presented at a national, regional, or state psychological association conference during the past calendar year. The Edwin B. Newman Graduate Research Award was established in 1979. The award was established to recognize young researchers at the beginning of their professional lives and to commemorate both the 50th anniversary of Psi Chi and the 100th anniversary of psychology as a science (dating from the founding of Wundt's laboratory). It was named for Dr. Edwin B. Newman, the first national president of Psi Chi (1929) and one of its founders. He was a prolific researcher and a long-time chair of the Department of Psychology at Harvard University. Newman was a member of APA's Board of Directors, served as recording secretary of the board from 1962 to 1967, and was parliamentarian for the APA Council of Representatives for many years. He served both Psi Chi and APA in a distinguished manner for half a century. The Edwin B. Newman Graduate Research Award is given jointly by Psi Chi and APA. Members of the 2017 Edwin B. Newman Award Committee were Shawn Carlton, PhD, Psi Chi representative; Christina Frederick-Recascino, PhD; John Norcross, PhD, APA representative; Karenna Malavanti, PhD, Psi Chi representative; Steven Kohn, PhD, Psi Chi representative; Warren Fass, PhD, Psi Chi representative; Chris Lovelace, PhD, Psi Chi representative; and Cathy Epkins, PhD, APA representative. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Alkaline phosphatase activity related to phosphorus stress of microphytoplankton in different trophic conditions

NASA Astrophysics Data System (ADS)

Ivančić, Ingrid; Pfannkuchen, Martin; Godrijan, Jelena; Djakovac, Tamara; Marić Pfannkuchen, Daniela; Korlević, Marino; Gašparović, Blaženka; Najdek, Mirjana

2016-08-01

The northern Adriatic (NA) is a favorable basin for studying the adaptive strategies of plankton to a variety of conditions along the steep gradients of environmental parameters over the year. Earlier studies identified phosphorus (P)-limitation as one of the key stresses within the NA that shape the biological response in terms of biodiversity and metabolic adjustments. A wide range of reports supports the notion that P-limitation is a globally important phenomenon in aquatic ecosystems. In this study P stress of marine microphytoplankton was determined at species level along a trophic gradient in the NA. In P-limitation all species with considerable contributions to the diatom community expressed alkaline phosphatase activity (APA), compared to only a few marginal dinoflagellate species. Nevertheless, APA expressing species did not always dominate the phytoplankton community, suggesting that APA is also an important strategy for species to survive and maintain active metabolism outside of their mass abundances. A symbiotic relationship could be supposed for diatoms that did not express APA themselves and probably benefited from APA expressed by attached bacteria. APA was not expressed by any microphytoplankton species during the autumn when P was not limiting, while most of the species did express APA during the P-limitation. This suggests that APA expression is regulated by orthophosphate availability. The methods employed in this study allowed the microscopic detection of APA for each microphytoplankton cell with simultaneous morphologic/taxonomic analysis. This approach uncovered a set of strategies to compete in P-limited conditions within the marine microphytoplankton community. This study confirms the role of P-limitation as a shaping factor in marine ecosystems.

p-Aminophenylacetic acid-mediated synthesis of monodispersed titanium oxide hybrid microspheres in ethanol solution.

PubMed

Zhang, Hongye; Xie, Yun; Liu, Zhimin; Tao, Ranting; Sun, Zhenyu; Ding, Kunlun; An, Guimin

2009-10-15

Monodispersed TiO2 hybrid microspheres were prepared via the hydrolysis of titanium isopropoxide (TTIP) in ethanol solution containing p-aminophenylacetic acid (APA). The effects of the APA:TTIP molar ratio, water content, reaction time and reaction temperature on the morphology of the resultant spheres were investigated. The products were characterized by scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, thermogravimetric analysis, and X-ray diffraction. It was demonstrated that the diameters of the resultant TiO2 spheres could be tuned in the range of 380-800 nm by changing the APA:TTIP molar ratio (1:3 to 3:1) and water content (1-3 v/v%) in the reaction medium, and that increasing the APA:TTIP molar ratio led to larger TiO2 hybrid spheres while increasing the water content decreased their size. The loading content of APA in the hybrid spheres could reach 20 wt.% as they were prepared with the APA:TTIP ratio of 3:1. The possible formation mechanism of the hybrid spheres was also investigated. It was found that APA slowed down the hydrolysis rate of the titanium precursor so that resulted in the formation of the TiO2 spheres. In addition, the APA present in TiO2 spheres acted as a reducing agent to in situ convert HAuCl4 into metallic Au on the surface of the TiO2 spheres. The catalytic activity of the resultant Au/APA-TiO2 composite was examined using transfer hydrogenation of phenylacetone with 2-propanol, and it was indicated that the catalyst displayed high efficiency for this reaction.

Effects of femtosecond laser and other surface treatments on the bond strength of metallic and ceramic orthodontic brackets to zirconia.

PubMed

García-Sanz, Verónica; Paredes-Gallardo, Vanessa; Bellot-Arcís, Carlos; Mendoza-Yero, Omel; Doñate-Buendía, Carlos; Montero, Javier; Albaladejo, Alberto

2017-01-01

Femtosecond laser has been proposed as a method for conditioning zirconia surfaces to boost bond strength. However, metallic or ceramic bracket bonding to femtosecond laser-treated zirconia surfaces has not been tested. This study compared the effects of four conditioning techniques, including femtosecond laser irradiation, on shear bond strength (SBS) of metallic and ceramic brackets to zirconia.Three hundred zirconia plates were divided into five groups: 1) control (C); 2) sandblasting (APA); 3) silica coating and silane (SC); 4) femtosecond laser (FS); 5) sandblasting followed by femtosecond laser (APA+SC). A thermal imaging camera measured temperature changes in the zirconia during irradiation. Each group was divided into 2 subgroups (metallic vs ceramic brackets). SBS was evaluated using a universal testing machine. The adhesive remnant index (ARI) was registered and surfaces were observed under SEM. Surface treatment and bracket type significantly affected the bracket-zirconia bond strength. SBS was significantly higher (p<0.001) for ceramic brackets in all groups (APA+FS > APA > FS > SC > control) than metallic brackets (APA+FS > FS > SC > APA > control). For metallic brackets, groups SC (5.99 ± 1.86 MPa), FS (6.72 ± 2.30 MPa) and APA+FS (7.22 ± 2.73 MPa) reported significantly higher bond strengths than other groups (p < 0.05). For ceramic brackets, the highest bond strength values were obtained in groups APA (25.01 ± 4.45 MPa), FS (23.18 ± 6.51 MPa) and APA+FS (29.22 ± 8.20 MPa).Femtosecond laser enhances bond strength of ceramic and metallic brackets to zirconia. Ceramic brackets provide significantly stronger adhesion than metallic brackets regardless of the surface treatment method.

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

PubMed Central

2012-01-01

Background Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. Results Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80–120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were designed for the identified markers. The assembly was annotated by Blast2GO and 14,740 (12%) of annotated contigs were associated with functional proteins. Conclusions Before availability of pepper genome sequence, assembling transcriptomes of this economically important crop was required to generate thousands of high-quality molecular markers that could be used in breeding programs. In order to have a better understanding of the assembled sequences and to identify candidate genes underlying QTLs, we annotated the contigs of Sanger-EST and Illumina transcriptome assemblies. These and other information have been curated in a database that we have dedicated for pepper project. PMID:23110314

Dual energy CT kidney stone differentiation in photon counting computed tomography

NASA Astrophysics Data System (ADS)

Gutjahr, R.; Polster, C.; Henning, A.; Kappler, S.; Leng, S.; McCollough, C. H.; Sedlmair, M. U.; Schmidt, B.; Krauss, B.; Flohr, T. G.

2017-03-01

This study evaluates the capabilities of a whole-body photon counting CT system to differentiate between four common kidney stone materials, namely uric acid (UA), calcium oxalate monohydrate (COM), cystine (CYS), and apatite (APA) ex vivo. Two different x-ray spectra (120 kV and 140 kV) were applied and two acquisition modes were investigated. The macro-mode generates two energy threshold based image-volumes and two energy bin based image-volumes. In the chesspattern-mode four energy thresholds are applied. A virtual low energy image, as well as a virtual high energy image are derived from initial threshold-based images, while considering their statistically correlated nature. The energy bin based images of the macro-mode, as well as the virtual low and high energy image of the chesspattern-mode serve as input for our dual energy evaluation. The dual energy ratio of the individually segmented kidney stones were utilized to quantify the discriminability of the different materials. The dual energy ratios of the two acquisition modes showed high correlation for both applied spectra. Wilcoxon-rank sum tests and the evaluation of the area under the receiver operating characteristics curves suggest that the UA kidney stones are best differentiable from all other materials (AUC = 1.0), followed by CYS (AUC ≍ 0.9 compared against COM and APA). COM and APA, however, are hardly distinguishable (AUC between 0.63 and 0.76). The results hold true for the measurements of both spectra and both acquisition modes.

Generativity does not necessarily satisfy all your needs: Associations among cultural demand for generativity, generative concern, generative action, and need satisfaction in the elderly in four cultures.

PubMed

Hofer, Jan; Busch, Holger; Au, Alma; Poláčková Šolcová, Iva; Tavel, Peter; Wong, Teresa Tsien

2016-03-01

The present study examines the association between various facets of generativity, that is, cultural demand for generativity, generative concern, and generative action, with the satisfaction of the needs for relatedness, competence, and autonomy in samples of elderly from Cameroon, China (Hong Kong), the Czech Republic, and Germany. Participants provided information on self-transcendence values (internalized cultural demand), generative concern and action, and need satisfaction. Results suggest, first, that internalized cultural demand affects generative action indirectly through generative concern, second, that generative concern has a positive direct effect on need satisfaction, but that, third, there is also an indirect effect of generative concern on need satisfaction through generative action, which, fourth, is positive for the needs for relatedness and competence but negative for the need for autonomy. These findings were culture-invariant in our study, suggesting generalizability to other cultures. They are discussed with respect to the role of values in generativity and a possible trade-off of generative action for the satisfaction of needs at least in the elderly. (c) 2016 APA, all rights reserved).

75 FR 3731 - Proposed Issuance of a General NPDES Permit for Small Suction Dredging-Permit Number IDG-37-0000

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-22

... Procedure Act (APA), or any other law, to publish general notice of proposed rulemaking.'' The RFA exempts... permits are permits, not rulemakings, under the APA and thus not subject to APA rulemaking requirements or...

77 FR 123 - Final Reissuance of General NPDES Permits (GP) for Facilities Related to Oil and Gas Extraction

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-03

... Administrative Procedure Act (APA), or any other law, to publish general notice of proposed rulemaking.'' The RFA... NPDES general permits are permits, not rulemakings, under the APA and thus not subject to APA rulemaking...

78 FR 34910 - Approval and Promulgation of Implementation Plans; Maryland; Revisions to the State...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-11

... Procedure Act (APA), which authorizes agencies to dispense with public participation and which allows an... otherwise provided for in the APA). DATES: This action is effective June 11, 2013. ADDRESSES: EPA has... Administrative Procedure Act (APA) [[Page 34911

78 FR 17661 - Proposed Reissuance of a General NPDES Permit for Oil and Gas Exploration Facilities in the...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-22

... Administrative Procedure Act (APA), or any other law, to publish general notice of proposed rulemaking.'' The RFA... NPDES general permits are permits, not rulemakings, under the APA and thus not subject to APA rulemaking...

Comprehending APA Style through Manuscript Analysis.

ERIC Educational Resources Information Center

Smith, Gabie E.; Eggleston, Tami J.

2001-01-01

Describes an activity designed to enhance undergraduate student comprehension of the American Psychological Association (APA) manual and style where students examined a poorly written paper for errors in relation to the APA guidelines. Reports the results of a study that tested the effectiveness of the activity. (CMK)

APA References for Psychologists in Schools & Education.

ERIC Educational Resources Information Center

American Psychological Association, Washington, DC.

Since its inauguration, the American Psychological Association (APA) Center for Psychology in Schools and Education (CPSE) has provided an integrated approach to coordinating education, public interest, scientific, and practice issues in education. This publication provides a compilation of APA books, journals, newsletters, videotapes, audiotapes,…

Corporate funding and conflicts of interest: a primer for psychologists.

PubMed

Pachter, Wendy S; Fox, Ronald E; Zimbardo, Philip; Antonuccio, David O

2007-12-01

A presidential task force on external funding was established by the American Psychological Association (APA) in 2003 to review APA policies, procedures, and practices regarding the acceptance of funding and support from private corporations for educational and training programs; continuing education offerings; research projects; publications; advertising; scientific and professional meetings and conferences; and consulting, practice, and advocacy relationships. This article, based on the Executive Summary of the APA Task Force on External Funding Final Report, presents the findings and unanimous recommendations of the task force in the areas of association income, annual convention, research and journals, continuing education, education, practice, and conflicts of interest and ethics. The task force concluded that it is important for both APA and individual psychologists to become familiar with the challenges that corporate funding can pose to their integrity. The nature and extent of those challenges led the task force to recommend that APA develop explicit policies, educational materials, and continuing education programs to preserve the independence of psychological science, practice, and education. (Copyright) 2007 APA.

Endoscopy and antiplatelet agents. European Society of Gastrointestinal Endoscopy (ESGE) Guideline.

PubMed

Boustière, C; Veitch, A; Vanbiervliet, G; Bulois, P; Deprez, P; Laquiere, A; Laugier, R; Lesur, G; Mosler, P; Nalet, B; Napoleon, B; Rembacken, B; Ajzenberg, N; Collet, J P; Baron, T; Dumonceau, J-M

2011-05-01

With the increasing use of antiplatelet agents (APA), their management during the periendoscopic period has become a more common and more difficult problem. The increase in use is due to the availability of new drugs and the widespread use of drug-eluting coronary stents. Acute coronary syndromes can occur when APA therapy is withheld for noncardiovascular interventions. Guidelines about APA management during the periendoscopic period are traditionally based on assessments of the procedure-related risk of bleeding and the risk of thrombosis if APA are stopped. New data allow better assessment of these risks, of the necessary duration of APA discontinuation before endoscopy, of the use of alternative procedures (mostly for endoscopic retrograde cholangiopancreatography [ERCP]), and of endoscopic methods that can be used to prevent bleeding (following colonic polypectomy). This guideline makes graded, evidence-based, recommendations for the management of APA for all currently performed endoscopic procedures. A short summary and two tables are included for quick reference. © Georg Thieme Verlag KG Stuttgart · New York.

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

PubMed

Mariano, Diego C B; Pereira, Felipe L; Aguiar, Edgar L; Oliveira, Letícia C; Benevides, Leandro; Guimarães, Luís C; Folador, Edson L; Sousa, Thiago J; Ghosh, Preetam; Barh, Debmalya; Figueiredo, Henrique C P; Silva, Artur; Ramos, Rommel T J; Azevedo, Vasco A C

2016-12-15

The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .

Identification of the Mycobacterium marinum Apa antigen O-mannosylation sites reveals important glycosylation variability with the M. tuberculosis Apa homologue.

PubMed

Coddeville, Bernadette; Wu, Sz-Wei; Fabre, Emeline; Brassart, Colette; Rombouts, Yoann; Burguière, Adeline; Kremer, Laurent; Khoo, Kay-Hooi; Elass-Rochard, Elisabeth; Guérardel, Yann

2012-10-22

The 45/47 kDa Apa, an immuno-dominant antigen secreted by Mycobacterium tuberculosis is O-mannosylated at multiple sites. Glycosylation of Apa plays a key role in colonization and invasion of the host cells by M. tuberculosis through interactions of Apa with the host immune system C-type lectins. Mycobacterium marinum (M.ma) a fish pathogen, phylogenetically close to M. tuberculosis, induces a granulomatous response with features similar to those described for M. tuberculosis in human. Although M.ma possesses an Apa homologue, its glycosylation status is unknown, and whether this represents a crucial element in the pathophysiology induced by M.ma remains to be addressed. To this aim, we have identified two concanavalin A-reactive 45/47 kDa proteins from M.ma, which have been further purified by a two-step anion exchange chromatography process. Advanced liquid chromatography-nanoESI mass spectrometry-based proteomic analyses of peptides, derived from either tryptic digestion alone or in combination with the Asp-N endoproteinase, established that M.ma Apa possesses up to seven distinct O-mannosylated sites with mainly single mannose substitutions, which can be further extended at the Ser/Thr/Pro rich region near the N-terminus. This opens the way to further studies focussing on the involvement and biological functions of Apa O-mannosylation using the M.ma/zebrafish model. Copyright © 2012 Elsevier B.V. All rights reserved.

APA-style human milk fat analogue from silkworm pupae oil: Enzymatic production and improving storage stability using alkyl caffeates.

PubMed

Liu, Xi; Wang, Xudong; Pang, Na; Zhu, Weijie; Zhao, Xingyu; Wang, Fangqin; Wu, Fuan; Wang, Jun

2015-12-08

Silkworm pupae oil derived from reeling waste is a rich source of α-linolenic acid (ALA), which has multipal applications. ALAs were added in sn-1, 3 positions in a triacylglycerol (TAG) to produce an APA-human milk fat analogues (APA-HMFAs, A: α-linolenic acid, P: palmitic acid). The optimum condition is that tripalmitin to free fatty acids of 1:12 (mole ratio) at 65 °C for 48 h using lipase Lipozyme RM IM. Results show that, the major TAG species that comprised APA-HMFAs were rich in ALA and palmitic acid, which contained 64.52% total unsaturated fatty acids (UFAs) and 97.05% PA at the sn-2 position. The melting point of APA was -27.5 °C which is much lower than tripalmitin (40.5 °C) indicating more plastic character. In addition, the practical application of alkyl caffeates as liposoluble antioxidants in APA was developed. Alkyl caffeate showed a superior IC50 (1.25-1.66 μg/mL) compared to butyl hydroxy anisd (1.67 μg/mL) and L-ascorbic acid-6-palmitate (L-AP) (1.87 μg/mL) in DPPH analysis. The addition of ethyl caffeate to oil achieved a higher UFAs content (73.58%) at high temperatures. Overall, APA was obtained from silkworm pupae oil successfully, and the addition of caffeates extended storage ranges for APA-HMFAs.

Boosting BCG-primed responses with a subunit Apa vaccine during the waning phase improves immunity and imparts protection against Mycobacterium tuberculosis

PubMed Central

Nandakumar, Subhadra; Kannanganat, Sunil; Dobos, Karen M.; Lucas, Megan; Spencer, John S.; Amara, Rama Rao; Plikaytis, Bonnie B.; Posey, James E.; Sable, Suraj B.

2016-01-01

Heterologous prime–boosting has emerged as a powerful vaccination approach against tuberculosis. However, optimal timing to boost BCG-immunity using subunit vaccines remains unclear in clinical trials. Here, we followed the adhesin Apa-specific T-cell responses in BCG-primed mice and investigated its BCG-booster potential. The Apa-specific T-cell response peaked 32–52 weeks after parenteral or mucosal BCG-priming but waned significantly by 78 weeks. A subunit-Apa-boost during the contraction-phase of BCG-response had a greater effect on the magnitude and functional quality of specific cellular and humoral responses compared to a boost at the peak of BCG-response. The cellular response increased following mucosal BCG-prime–Apa-subunit-boost strategy compared to Apa-subunit-prime–BCG-boost approach. However, parenteral BCG-prime–Apa-subunit-boost by a homologous route was the most effective strategy in-terms of enhancing specific T-cell responses during waning in the lung and spleen. Two Apa-boosters markedly improved waning BCG-immunity and significantly reduced Mycobacterium tuberculosis burdens post-challenge. Our results highlight the challenges of optimization of prime–boost regimens in mice where BCG drives persistent immune-activation and suggest that boosting with a heterologous vaccine may be ideal once the specific persisting effector responses are contracted. Our results have important implications for design of prime–boost regimens against tuberculosis in humans. PMID:27173443

APA-style human milk fat analogue from silkworm pupae oil: Enzymatic production and improving storage stability using alkyl caffeates

PubMed Central

Liu, Xi; Wang, Xudong; Pang, Na; Zhu, Weijie; Zhao, Xingyu; Wang, Fangqin; Wu, Fuan; Wang, Jun

2015-01-01

Silkworm pupae oil derived from reeling waste is a rich source of α-linolenic acid (ALA), which has multipal applications. ALAs were added in sn-1, 3 positions in a triacylglycerol (TAG) to produce an APA-human milk fat analogues (APA-HMFAs, A: α-linolenic acid, P: palmitic acid). The optimum condition is that tripalmitin to free fatty acids of 1:12 (mole ratio) at 65 °C for 48 h using lipase Lipozyme RM IM. Results show that, the major TAG species that comprised APA-HMFAs were rich in ALA and palmitic acid, which contained 64.52% total unsaturated fatty acids (UFAs) and 97.05% PA at the sn-2 position. The melting point of APA was −27.5 °C which is much lower than tripalmitin (40.5 °C) indicating more plastic character. In addition, the practical application of alkyl caffeates as liposoluble antioxidants in APA was developed. Alkyl caffeate showed a superior IC50 (1.25–1.66 μg/mL) compared to butyl hydroxy anisd (1.67 μg/mL) and L-ascorbic acid-6-palmitate (L-AP) (1.87 μg/mL) in DPPH analysis. The addition of ethyl caffeate to oil achieved a higher UFAs content (73.58%) at high temperatures. Overall, APA was obtained from silkworm pupae oil successfully, and the addition of caffeates extended storage ranges for APA-HMFAs. PMID:26643045

Water droplets as template for next-generation self-assembled poly-(etheretherketone) with cardo membranes.

PubMed

Gugliuzza, Annarosa; Aceto, Marianna Carmela; Macedonio, Francesca; Drioli, Enrico

2008-08-28

Next generation PEEK-WC membranes have been fabricated by using an innovative self-assembly technique. Patterned architectures have been achieved via a solvent-reduced and water-assisted process, resulting in honeycomb packed geometry. The membranes exhibit monodisperse pores with size and shape comparable to those left by templating water droplets. Influencing factors for the formation of self-assembled poly-(etheretherketone) with Cardo [PEEK-WC] membranes have been evaluated, identifying the critical parameters for nucleation, growth, and propagation of the droplet-mobile arrays through the overall films. Structure-transport relationships have been discussed according to the results achieved from the implementation of membrane distillation processes, yielding indication about the suitability of self-assembled PEEK-WC films to work as interfaces in contactor operations.

High speed internal permanent magnet machine and method of manufacturing the same

DOEpatents

Alexander, James Pellegrino [Ballston Lake, NY; EL-Refaie, Ayman Mohamed Fawzi [Niskayuna, NY; Lokhandwalla, Murtuza [Clifton Park, NY; Shah, Manoj Ramprasad [Latham, NY; VanDam, Jeremy Daniel [West Coxsackie, NY

2011-09-13

An internal permanent magnet (IPM) machine is provided. The IPM machine includes a stator assembly and a stator core. The stator core also includes multiple stator teeth. The stator assembly is further configured with stator windings to generate a magnetic field when excited with alternating currents and extends along a longitudinal axis with an inner surface defining a cavity. The IPM machine also includes a rotor assembly and a rotor core. The rotor core is disposed inside the cavity and configured to rotate about the longitudinal axis. The rotor assembly further includes a shaft. The shaft further includes multiple protrusions alternately arranged relative to multiple bottom structures provided on the shaft. The rotor assembly also includes multiple stacks of laminations disposed on the protrusions and dovetailed circumferentially around the shaft. The rotor assembly further includes multiple permanent magnets for generating a magnetic field, which interacts with the stator magnetic field to produce torque. The permanent magnets are disposed between the stacks. The rotor assembly also includes multiple bottom wedges disposed on the bottom structures of the shaft and configured to hold the multiple stacks and the multiple permanent magnets.

Design and assembly of a catalyst bed gas generator for the catalytic decomposition of high concentration hydrogen peroxide propellants and the catalytic combustion of hydrocarbon/air mixtures

NASA Technical Reports Server (NTRS)

Lohner, Kevin A. (Inventor); Mays, Jeffrey A. (Inventor); Sevener, Kathleen M. (Inventor)

2004-01-01

A method for designing and assembling a high performance catalyst bed gas generator for use in decomposing propellants, particularly hydrogen peroxide propellants, for use in target, space, and on-orbit propulsion systems and low-emission terrestrial power and gas generation. The gas generator utilizes a sectioned catalyst bed system, and incorporates a robust, high temperature mixed metal oxide catalyst. The gas generator requires no special preheat apparatus or special sequencing to meet start-up requirements, enabling a fast overall response time. The high performance catalyst bed gas generator system has consistently demonstrated high decomposition efficiency, extremely low decomposition roughness, and long operating life on multiple test articles.

2010 Annual Report of the American Psychological Association

ERIC Educational Resources Information Center

American Psychologist, 2011

2011-01-01

This report presents the 2010 annual report of the American Psychological Association (APA). It provides the highlights of the association's and individual directorate's activities to APA members. APA continued its efforts to advance psychological practice and ensure the public's access to high-quality psychological services, apply psychological…

The Community College Presidency: An Asian Pacific American Perspective.

ERIC Educational Resources Information Center

Fujimoto, M. Jack

1996-01-01

Analyzes the status of Asian Pacific Americans (APAs) in higher education compared to their representation in chief executive positions, describing a glass ceiling effect and common stereotypes regarding APAs. Reviews characteristics of chief executive officers in California community colleges. Provides strategies for increasing APA representation…

Development of an Aircraft Approach and Departure Atmospheric Profile Generation Algorithm

NASA Technical Reports Server (NTRS)

Buck, Bill K.; Velotas, Steven G.; Rutishauser, David K. (Technical Monitor)

2004-01-01

In support of NASA Virtual Airspace Modeling and Simulation (VAMS) project, an effort was initiated to develop and test techniques for extracting meteorological data from landing and departing aircraft, and for building altitude based profiles for key meteorological parameters from these data. The generated atmospheric profiles will be used as inputs to NASA s Aircraft Vortex Spacing System (AVOLSS) Prediction Algorithm (APA) for benefits and trade analysis. A Wake Vortex Advisory System (WakeVAS) is being developed to apply weather and wake prediction and sensing technologies with procedures to reduce current wake separation criteria when safe and appropriate to increase airport operational efficiency. The purpose of this report is to document the initial theory and design of the Aircraft Approach Departure Atmospheric Profile Generation Algorithm.

A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.

PubMed

Melicher, Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher, Julia H

2014-03-12

The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.

Effective de novo assembly of fish genome using haploid larvae.

PubMed

Iwasaki, Yuki; Nishiki, Issei; Nakamura, Yoji; Yasuike, Motoshige; Kai, Wataru; Nomura, Kazuharu; Yoshida, Kazunori; Nomura, Yousuke; Fujiwara, Atushi; Kobayashi, Takanori; Ototake, Mitsuru

2016-02-01

Recent improvements in next-generation sequencing technology have made it possible to do whole genome sequencing, on even non-model eukaryote species with no available reference genomes. However, de novo assembly of diploid genomes is still a big challenge because of allelic variation. The aim of this study was to determine the feasibility of utilizing the genome of haploid fish larvae for de novo assembly of whole-genome sequences. We compared the efficiency of assembly using the haploid genome of yellowtail (Seriola quinqueradiata) with that using the diploid genome obtained from the dam. De novo assembly from the haploid and the diploid sequence reads (100 million reads per each datasets) generated by the Ion Proton sequencer (200 bp) was done under two different assembly algorithms, namely overlap-layout-consensus (OLC) and de Bruijn graph (DBG). This revealed that the assembly of the haploid genome significantly reduced (approximately 22% for OLC, 9% for DBG) the total number of contigs (with longer average and N50 contig lengths) when compared to the diploid genome assembly. The haploid assembly also improved the quality of the scaffolds by reducing the number of regions with unassigned nucleotides (Ns) (total length of Ns; 45,331,916 bp for haploids and 67,724,360 bp for diploids) in OLC-based assemblies. It appears clear that the haploid genome assembly is better because the allelic variation in the diploid genome disrupts the extension of contigs during the assembly process. Our results indicate that utilizing the genome of haploid larvae leads to a significant improvement in the de novo assembly process, thus providing a novel strategy for the construction of reference genomes from non-model diploid organisms such as fish. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Software for pre-processing Illumina next-generation sequencing short read sequences

PubMed Central

2014-01-01

Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness. Conclusions Trimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects. PMID:24955109

ANL Critical Assembly Covariance Matrix Generation

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

McKnight, Richard D.; Grimm, Karl N.

2014-01-15

This report discusses the generation of a covariance matrix for selected critical assemblies that were carried out by Argonne National Laboratory (ANL) using four critical facilities-all of which are now decommissioned. The four different ANL critical facilities are: ZPR-3 located at ANL-West (now Idaho National Laboratory- INL), ZPR-6 and ZPR-9 located at ANL-East (Illinois) and ZPPr located at ANL-West.

Peptide assembly-driven metal-organic framework (MOF) motors for micro electric generators

DOE PAGES

Ikezoe, Yasuhiro; Fang, Justin; Wasik, Tomasz L.; ...

2014-11-22

Peptide–metal–organic framework (Pep-MOF) motors, whose motions are driven by anisotropic surface tension gradients created via peptide self-assembly around frameworks, can rotate microscopic rotors and magnets fast enough to generate an electric power of 0.1 μW. Finally, a new rigid Pep-MOF motor can be recycled by refilling the peptide fuel into the nanopores of the MOF.

Assembly of cucumber (Cucumis sativus L.) somaclones

NASA Astrophysics Data System (ADS)

Skarzyńska, Agnieszka; Kuśmirek, Wiktor; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Nowak, Robert M.

2017-08-01

The development of next generation sequencing opens the possibility of using sequencing in various plant studies, such as finding structural changes and small polymorphisms between species and within them. Most analyzes rely on genomic sequences and it is crucial to use well-assembled genomes of high quality and completeness. Herein we compare commonly available programs for genomic assembling and newly developed software - dnaasm. Assemblies were tested on cucumber (Cucumis sativus L.) lines obtained by in vitro regeneration (somaclones), showing different phenotypes. Obtained results shows that dnaasm assembler is a good tool for short read assembly, which allows obtaining genomes of high quality and completeness.

Swine transcriptome characterization by combined Iso-Seq and RNA-seq for annotating the emerging long read-based reference genome

USDA-ARS?s Scientific Manuscript database

PacBio long-read sequencing technology is increasingly popular in genome sequence assembly and transcriptome cataloguing. Recently, a new-generation pig reference genome was assembled based on long reads from this technology. To finely annotate this genome assembly, transcriptomes of nine tissues fr...

Interplay between Short- and Long-Term Plasticity in Cell-Assembly Formation

PubMed Central

Hiratani, Naoki; Fukai, Tomoki

2014-01-01

Various hippocampal and neocortical synapses of mammalian brain show both short-term plasticity and long-term plasticity, which are considered to underlie learning and memory by the brain. According to Hebb’s postulate, synaptic plasticity encodes memory traces of past experiences into cell assemblies in cortical circuits. However, it remains unclear how the various forms of long-term and short-term synaptic plasticity cooperatively create and reorganize such cell assemblies. Here, we investigate the mechanism in which the three forms of synaptic plasticity known in cortical circuits, i.e., spike-timing-dependent plasticity (STDP), short-term depression (STD) and homeostatic plasticity, cooperatively generate, retain and reorganize cell assemblies in a recurrent neuronal network model. We show that multiple cell assemblies generated by external stimuli can survive noisy spontaneous network activity for an adequate range of the strength of STD. Furthermore, our model predicts that a symmetric temporal window of STDP, such as observed in dopaminergic modulations on hippocampal neurons, is crucial for the retention and integration of multiple cell assemblies. These results may have implications for the understanding of cortical memory processes. PMID:25007209

American Psychological Association: Annual Report, 2008

ERIC Educational Resources Information Center

American Psychologist, 2009

2009-01-01

This article presents the 2008 annual reports from the various directorates and offices of the American Psychological Association (APA). In 2008, APA continued to work on initiatives, programs, and products that lend value to the member's psychology career, support the future of their discipline, and serve the public. APA's goal is to strengthen…

77 FR 30241 - Representation Procedures and Rulemaking Authority

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-22

... the informal rulemaking procedures in the Administrative Procedure Act (APA), 5 U.S.C. 553, and... stricter requirements in sections 556 and 557 of the APA, this hearing will comply with those informal rulemaking procedures under the APA. See, e.g. United States v. Allegheny-Ludlum Steel Corp., 406 US 742...

77 FR 19079 - Removal of Regulations on Black Lung Benefits

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-30

.... Regulatory Procedures We follow the Administrative Procedure Act (APA) rulemaking procedures specified in 5 U.S.C. 553 when we develop regulations. Generally, the APA requires that an agency provide prior notice and opportunity for public comment before issuing a final rule. The APA provides exceptions to its...

Teaching Scientific Writing: Measuring Student Learning in an Intensive APA Skills Course

ERIC Educational Resources Information Center

Luttrell, Vickie R.; Bufkin, Jana L.; Eastman, Valerie J.; Miller, Robin

2010-01-01

The "Publication Manual of the American Psychological Association" (American Psychological Association [APA], 2010) provides a widely utilized template for preparing research reports in the behavioral sciences. Because learning APA style is integral to disciplinary socialization, our department recently implemented a 1-hr course in scientific…

APA, Meet Google: Graduate Students' Approaches to Learning Citation Style

ERIC Educational Resources Information Center

Van Note Chism, Nancy; Weerakoon, Shrinika

2012-01-01

Inspired by Perkins' Theories of Difficulty concept, this exploratory study examined the learning patterns of graduate students as they grappled with using the style sheet of the American Psychological Association (APA). The researchers employed task performance analysis of three APA formatting tasks, interviews, and observation during a "think…

76 FR 80226 - Technical Amendments

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-23

... final rule, effective upon publication. Generally, the Administrative Procedure Act (APA) requires a.... Additionally, the APA requires that a final rule must have a delayed effective date of 30 days from the date of... delayed effective date requirement under the APA. 5 U.S.C. 553(d)(3). Again the technical change conforms...

APA's Role in Fostering Good Testing Practices.

ERIC Educational Resources Information Center

Camara, Wayne J.

Psychological testing has played a major role in the American Psychological Association (APA) because testing and assessment are important aspects of what psychologists do; tests assist psychologists in diagnosis and treatment. From its earliest years, APA has had one or more committees concerned with testing. The present Committee on…

APA's Guidelines for Test User Qualifications: An Executive Summary.

ERIC Educational Resources Information Center

Turner, Samuel M.; DeMers, Stephen T.; Fox, Heather Roberts; Reed, Geoffrey M.

2001-01-01

Describes the American Psychological Association's (APA's) development of the Task Force on Test User Qualifications, explaining the APA's purpose in developing guidelines for the use of psychological tests. Highlights the historical background, the scope of the guidelines, generic knowledge and skills considered important for good test use, and…

[Exercise-referral to a specialist in adapted physical activity (APA) : a pilot project].

PubMed

Brugnerotto, Adeline; Cardinaux, Regula; Ueltschi, Yan; Bauwens, Marine; Nanchen, David; Cornuz, Jacques; Bize, Raphaël; Auer, Reto

2016-11-02

Family physicians have a key role in the promotion of physical activity, in particular in identifying and counseling persons who have a sedentary lifestyle. Some patients could benefit from intensive individual counseling. Physicians are often not aware of all physical activity promotion activities in the community that they could recommend their patients. In a pilot study, we have tested and adapted the referral of patients from family physicians to specialists in adapted physical activity (APAs). APAs are trained to assess and guide persons towards physical activities adapted to their needs and pathologies and thus towards an increase in physical activity. Pilot data suggest that, while few patients were oriented to the APAs in the pilot project, family physicians appreciate the possibility of collaborating with the APAs.

The effect of exhausting aerobic exercise on the timing of anticipatory postural adjustments.

PubMed

Strang, A J; Choi, H J; Berg, W P

2008-03-01

The aim of the study was to investigate the influence of exhausting aerobic exercise on the timing of anticipatory postural adjustments (APAs). The APAs of 12 participants were recorded at baseline, after a .VO2max running test, and again following a 45-min rest period. APAs were induced using a rapid bilateral arm-raising maneuver, and were analyzed in the rectus abdominis, hamstring group, gluteal group, and lumbar and thoracic paraspinal muscles using electromyography. Postural stability was assessed by monitoring anterior/posterior displacement of the center of pressure using a force plate. We hypothesized that APA onset would be ear lier following exhausting aerobic exercise as compared to the baseline measures, but that this effect would be transient (i.e., APA onset following the rest period would not differ from that at baseline). Exhausting aerobic exercise resulted in a significantly earlier APA in one of the 5 muscles evaluated, the thoracic paraspinal group, and this effect persisted 45-min postexercise. Exhausting aerobic exercise did not affect postural stability during the rapid arm-raising maneuver. The findings lend tentative support for the notion that earlier APAs constitute a functional adaptation by the motor system to maintain postural stability in the presence of fatigue.

Psychology, public policy, and advocacy: Past, present, and future.

PubMed

Garrison, Ellen Greenberg; DeLeon, Patrick H; Smedley, Brian D

2017-11-01

This article offers a historical perspective on the contributions of the field of psychology and the American Psychological Association (APA) to the public policy arena. It traces APA's involvement from a 1956 Council of Representatives resolution on the application of psychology to inform public policy to current advocacy initiatives related to psychological science, practice, and education in the public interest. Attention is directed to APA's early policy structures together with the development of affiliated state, provincial, and territorial psychological associations and the first political action committee for psychology. The criteria for engagement in advocacy and the goals and functions of APA's policy and advocacy initiatives, including the APA Congressional and Executive Branch Science Fellowship Program, are also discussed. The evolution of psychology's public policy role is illustrated by an increasing level of federal advocacy engagement and effectiveness over time, as well as by the emergence of psychology leaders in Congress and the Executive Branch. The authors' concluding reflections on the future of psychology in the public policy arena derive from their many years of experience working on or with Capitol Hill, at APA as elected officials or senior staff, and in various roles in academia, think tanks, service delivery, and the private sector. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

On-Orbit Checkout and Activation of the ISS Oxygen Generation System

NASA Technical Reports Server (NTRS)

Bagdigian, Robert M.; Prokhorov, Kimberlee S.

2007-01-01

NASA has developed and; deployed an Oxygen Generation System (OGS) into the Destiny Module of the International Space Station (ISS). The major. assembly; included in this system is the Oxygen Generator Assembly. (OGA) which was developed under NASA contract by Hamilton Sundstrand Space Systems International (HSSSI), Inc. This paper summarizes the installation of the system into the Destiny Module, its initial checkout and periodic preventative maintenance activities, and its operational activation. Trade studies and analyses that were conducted with the goal of mitigating on-orbit operational risks are also discussed.

Self-assembly of bimodal particles inside emulsion droplets

NASA Astrophysics Data System (ADS)

Cho, Young-Sang; Yi, Gi-Ra; Yang, Seung-Man; Kim, Young-Kuk; Choi, Chul-Jin

2010-08-01

Colloidal dispersion of bimodal particles were self-organized inside water-in-oil emulsion droplets by evaporationdriven self-assembly method. After droplet shrinkage by heating the complex fluid system, small numbers of microspheres were packed into minimal second moment clusters, which are partially coated with silica nanospheres, resulting in the generation of patchy particles. The patchy particles in this study possess potential applications for selfassembly of non-isotropic particles such as dimmers or tetramers for colloidal photonic crystals with diamond lattice structures. The composite micro-clusters of amidine polystyrene microspheres and titania nanoparticles were also generated by evaporation-driven self-assembly to fabricate nonspherical hollow micro-particles made of titania shell.

Highly stable aerosol generator

DOEpatents

DeFord, H.S.; Clark, M.L.

1981-11-03

An improved compressed air nebulizer has been developed such that a uniform aerosol particle size and concentration may be produced over long time periods. This result is achieved by applying a vacuum pressure to the makeup assembly and by use of a vent tube between the atmosphere and the makeup solution. By applying appropriate vacuum pressures to the makeup solution container and by proper positioning of the vent tube, a constant level of aspirating solution may be maintained within the aspirating assembly with aspirating solution continuously replaced from the makeup solution supply. This device may also be adapted to have a plurality of aerosol generators and only one central makeup assembly. 2 figs.

Highly stable aerosol generator

DOEpatents

DeFord, Henry S.; Clark, Mark L.

1981-01-01

An improved compressed air nebulizer has been developed such that a uniform aerosol particle size and concentration may be produced over long time periods. This result is achieved by applying a vacuum pressure to the makeup assembly and by use of a vent tube between the atmosphere and the makeup solution. By applying appropriate vacuum pressures to the makeup solution container and by proper positioning of the vent tube, a constant level of aspirating solution may be maintained within the aspirating assembly with aspirating solution continuously replaced from the makeup solution supply. This device may also be adapted to have a plurality of aerosol generators and only one central makeup assembly.

Fast and accurate de novo genome assembly from long uncorrected reads

PubMed Central

Vaser, Robert; Sović, Ivan; Nagarajan, Niranjan

2017-01-01

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment–based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster. PMID:28100585

Comparative production of 6-aminopenicillanic acid by different E. coli strains and their acridine orange (AO) induced mutants.

PubMed

Arshad, Rubina; Farooq, Shafqat; Ali, Syed Shahid

2007-11-01

The present study was conducted to see the difference in production of 6-APA I) between wild strains of E. coli collected from local environment and their acridine orange (AO) induced mutants and ii) between mutants and E. coli strains (ATCC 11105 and ATCC 9637) of American Type Culture Collection (ATCC) used commercially for enzymatic production of 6-APA. The optimum conditions for bioconversion were standardized and 6-APA was obtained in crystalline form. Relative PGA activity of local and foreign E. coli strains varied significantly with the highest being 12.7 in mutant strain (BDCS-N-M36) and the lowest 4.3 mg 6-APA h(-1) mg(-1) wet cells in foreign strain (ATCC 11105). The enzyme activity exhibited by mutant strain (BDCS-N-M36) was also two folds higher compared to that in wild parent BDCS-N-W50 (6.3 mg 6-APA h(-1) mg(-1) wet cells). The overall production of 6-APA and conversion ratios ranged between 0.25-0.41 g of 6-APA per 0.5 g of penicillin G and 51-83%, respectively. Maximum conversion ratio (83%) was achieved by using crude cells of mutant strain (BDCS-N-M36) which is the highest value ever reported by crude cells on a shake-flask scale whereas reported 6-APA production by immobilized cells is 60-90% in batch and continuous systems. Results are being discussed with reference to importance of local bacterial strains and their significance for industrially important enzymes.

Anticipatory postural adjustments contribute to age-related changes in compensatory steps associated with unilateral perturbations.

PubMed

Hyodo, Masaki; Saito, Mayumi; Ushiba, Junichi; Tomita, Yutaka; Minami, Mihoko; Masakado, Yoshihisa

2012-07-01

Compensatory steps are essential for preventing falls following perturbations. This study aimed to explore age-related changes in compensatory steps to unilateral perturbations, specifically in terms of whether anticipatory postural adjustments (APAs) play a role in stabilizing lateral balance. Five young and five elderly male adults participated. The split-belt treadmill was used to provide bi- and unilateral perturbations, as forward or backward transitions, applied 10 times in random order. Backward steps evoked by unilateral forward perturbations were evaluated. We measured temporal characteristics, mediolateral (ML) center of mass (COM) motion, and ML step length of compensatory steps. Compensatory steps to unexpected perturbations showed delayed onset of foot-off (FO) and expanded lateral swing length in elderly compared to young subjects. Differences in COM motions and step width arose related to APAs. Elderly subjects showing APAs exhibited no significant differences in ML COM, ML COM velocity, or ML swing length compared to young subjects. However, elderly subjects without APAs showed significant changes toward instability in these parameters. The fact that APAs play a notable role, particularly in the elderly, in stability offers a new insight into preventing falls. However, APAs occurred in 29% of the steps of young and 35% of the steps of elderly subjects. If the occurrence of APAs in elderly people in response to compensatory steps was more frequent, fall risk would be reduced. Further studies, particularly into APA frequency, might contribute to improved intervention to prevent falls. Copyright © 2012 Elsevier B.V. All rights reserved.

Charge neutralization apparatus for ion implantation system

DOEpatents

Leung, Ka-Ngo; Kunkel, Wulf B.; Williams, Malcom D.; McKenna, Charles M.

1992-01-01

Methods and apparatus for neutralization of a workpiece such as a semiconductor wafer in a system wherein a beam of positive ions is applied to the workpiece. The apparatus includes an electron source for generating an electron beam and a magnetic assembly for generating a magnetic field for guiding the electron beam to the workpiece. The electron beam path preferably includes a first section between the electron source and the ion beam and a second section which is coincident with the ion beam. The magnetic assembly generates an axial component of magnetic field along the electron beam path. The magnetic assembly also generates a transverse component of the magnetic field in an elbow region between the first and second sections of the electron beam path. The electron source preferably includes a large area lanthanum hexaboride cathode and an extraction grid positioned in close proximity to the cathode. The apparatus provides a high current, low energy electron beam for neutralizing charge buildup on the workpiece.

Method of reducing multipole content in a conductor assembly during manufacture

DOEpatents

Meinke, Rainer [Melbourne, FL

2011-08-09

A method for manufacture of a conductor assembly. The assembly is of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In an example embodiment one or more first coil rows are formed. The assembly has multiple coil rows about an axis with outer coil rows formed about inner coil rows. A determination is made of deviations from specifications associated with the formed one or more first coil rows. One or more deviations correspond to a magnitude of a multipole field component which departs from a field specification. Based on the deviations, one or more wiring patterns are generated for one or more second coil rows to be formed about the one or more first coil rows. The one or more second coil rows are formed in the assembly. The magnitude of each multipole field component that departs from the field specification is offset.

Method of reducing multipole content in a conductor assembly during manufacture

DOEpatents

Meinke, Rainer

2013-08-20

A method for manufacture of a conductor assembly. The assembly is of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In an example embodiment one or more first coil rows are formed. The assembly has multiple coil rows about an axis with outer coil rows formed about inner coil rows. A determination is made of deviations from specifications associated with the formed one or more first coil rows. One or more deviations correspond to a magnitude of a multipole field component which departs from a field specification. Based on the deviations, one or more wiring patterns are generated for one or more second coil rows to be formed about the one or more first coil rows. The one or more second coil rows are formed in the assembly. The magnitude of each multipole field component that departs from the field specification is offset.

Rotary shaft sealing assembly

DOEpatents

Dietle, Lannie L; Schroeder, John E; Kalsi, Manmohan S; Alvarez, Patricio D

2013-08-13

A rotary shaft sealing assembly in which a first fluid is partitioned from a second fluid in a housing assembly having a rotary shaft located at least partially within. In one embodiment a lip seal is lubricated and flushed with a pressure-generating seal ring preferably having an angled diverting feature. The pressure-generating seal ring and a hydrodynamic seal may be used to define a lubricant-filled region with each of the seals having hydrodynamic inlets facing the lubricant-filled region. Another aspect of the sealing assembly is having a seal to contain pressurized lubricant while withstanding high rotary speeds. Another rotary shaft sealing assembly embodiment includes a lubricant supply providing a lubricant at an elevated pressure to a region between a lip seal and a hydrodynamic seal with a flow control regulating the flow of lubricant past the lip seal. The hydrodynamic seal may include an energizer element having a modulus of elasticity greater than the modulus of elasticity of a sealing lip of the hydrodynamic seal.

Rotary shaft sealing assembly

DOEpatents

Dietle, Lannie L.; Schroeder, John E.; Kalsi, Manmohan S.; Alvarez, Patricio D.

2010-09-21

A rotary shaft sealing assembly in which a first fluid is partitioned from a second fluid in a housing assembly having a rotary shaft located at least partially within. In one embodiment a lip seal is lubricated and flushed with a pressure-generating seal ring preferably having an angled diverting feature. The pressure-generating seal ring and a hydrodynamic seal may be used to define a lubricant-filled region with each of the seals having hydrodynamic inlets facing the lubricant-filled region. Another aspect of the sealing assembly is having a seal to contain pressurized lubricant while withstanding high rotary speeds. Another rotary shaft sealing assembly embodiment includes a lubricant supply providing a lubricant at an elevated pressure to a region between a lip seal and a hydrodynamic seal with a flow control regulating the flow of lubricant past the lip seal. The hydrodynamic seal may include an energizer element having a modulus of elasticity greater than the modulus of elasticity of a sealing lip of the hydrodynamic seal.

Rapid Assembly of Customized TALENs into Multiple Delivery Systems

PubMed Central

Zhang, Zhengxing; Zhang, Siliang; Huang, Xin; Orwig, Kyle E.; Sheng, Yi

2013-01-01

Transcriptional activator-like effector nucleases (TALENs) have become a powerful tool for genome editing. Here we present an efficient TALEN assembly approach in which TALENs are assembled by direct Golden Gate ligation into Gateway® Entry vectors from a repeat variable di-residue (RVD) plasmid array. We constructed TALEN pairs targeted to mouse Ddx3 subfamily genes, and demonstrated that our modified TALEN assembly approach efficiently generates accurate TALEN moieties that effectively introduce mutations into target genes. We generated “user friendly” TALEN Entry vectors containing TALEN expression cassettes with fluorescent reporter genes that can be efficiently transferred via Gateway (LR) recombination into different delivery systems. We demonstrated that the TALEN Entry vectors can be easily transferred to an adenoviral delivery system to expand application to cells that are difficult to transfect. Since TALENs work in pairs, we also generated a TALEN Entry vector set that combines a TALEN pair into one PiggyBac transposon-based destination vector. The approach described here can also be modified for construction of TALE transcriptional activators, repressors or other functional domains. PMID:24244669

Unlocking the effects of gender faultlines on team creativity: is activation the key?

PubMed

Pearsall, Matthew J; Ellis, Aleksander P J; Evans, Joel M

2008-01-01

The purpose of this study was to use faultline theory to examine the effects of gender diversity on team creativity. Results from 80 teams working on an idea generation task indicated that the activation of gender faultlines negatively affected the number and overall creativity of ideas. However, gender faultlines that were not activated had no effect. Results also indicated that the relationship between activated gender faultlines and team creativity was partially mediated by the level of conflict within the team. Specifically, emotional conflict partially mediated the effects of activated gender faultlines on the number of ideas generated. Implications are discussed, as well as possible limitations and directions for future research. 2008 APA

77 FR 24397 - Approval and Promulgation of Implementation Plans: Georgia; Approval of Substitution for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-24

... Administrative Procedures Act (APA) which, upon finding ``good cause,'' authorizes agencies to dispense with... 30-day delayed effective date otherwise provided for in the APA). DATES: This action is effective... in the section 553(b)(3)(B) of the APA which, upon finding ``good cause,'' authorizes agencies to...

78 FR 26690 - Hours of Service (HOS) of Drivers; Application for Renewal and Expansion of American Pyrotechnics...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-07

... Association (APA) Exemption From the 14-Hour Rule During Independence Day Celebrations AGENCY: Federal Motor... exemption; request for comments. SUMMARY: The American Pyrotechnics Association (APA) has requested a renewal of its exemption for 48 APA member-companies from FMCSA's regulation that drivers of commercial...

50 CFR 660.60 - Specifications and management measures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... by a single notification in the Federal Register if good cause exists under the APA to waive notice... of the Administrative Procedure Act (APA). Changes to trip limits are effective at the times stated... APA to waive notice and comment. (1) Automatic actions are used in the Pacific whiting fishery to: (i...

77 FR 25717 - Proposed Issuance of a General NPDES Permit for Small Suction Dredging

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-01

... required by section 553 of the Administrative Procedure Act (APA), or any other law, to publish general... entities.'' EPA has concluded that NPDES general permits are permits, not rulemakings, under the APA and thus not subject to APA rulemaking requirements or the RFA. Notwithstanding that general permits are...

77 FR 429 - Clarification and Further Guidance on the Fireworks Approvals Policy

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-05

...) and the American Pyrotechnic Association (APA) Standard 87-1. PHMSA understands that it is a common... approval is requested conforms to the APA Standard 87-1, and the descriptions and technical information... manufacturer must sign and certify that the device for which the approval is requested conforms to the APA...

75 FR 33501 - Definitions for Regulations Affecting All Savings Associations; Money Market Deposit Accounts

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-14

... notice and comment is unnecessary under the Administrative Procedure Act (APA) and is implementing this... for dispensing with the 30-day delay required by the Administrative Procedure Act (APA). OTS... reason, OTS has determined for good cause that public notice and comment is unnecessary under the APA...

76 FR 59085 - Appeals of Post Office Closings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-23

..., 60 Stat. 237, 1946 (APA), `` `adjudication' means agency process for formulation of an order.'' 5 U.S.C. 551(7). Appeals initiated under section 404(d) are not formal adjudications under the APA (5 U.S... office that an appeal has been initiated. \\3\\ ``Informal adjudications are not covered by the APA at all...

77 FR 1857 - Women-Owned Small Business Federal Contract Program

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-12

... accordance with the Administrative Procedures Act (APA) and SBA regulations. 5 U.S.C. 553 and 13 CFR 101.108. The APA provides an exception to this standard rulemaking process where an agency finds good cause to... quickly as possible. IV. Justification for Immediate Effective Date of Interim Final Rule The APA requires...

Smooth Approximation l 0-Norm Constrained Affine Projection Algorithm and Its Applications in Sparse Channel Estimation

PubMed Central

2014-01-01

We propose a smooth approximation l 0-norm constrained affine projection algorithm (SL0-APA) to improve the convergence speed and the steady-state error of affine projection algorithm (APA) for sparse channel estimation. The proposed algorithm ensures improved performance in terms of the convergence speed and the steady-state error via the combination of a smooth approximation l 0-norm (SL0) penalty on the coefficients into the standard APA cost function, which gives rise to a zero attractor that promotes the sparsity of the channel taps in the channel estimation and hence accelerates the convergence speed and reduces the steady-state error when the channel is sparse. The simulation results demonstrate that our proposed SL0-APA is superior to the standard APA and its sparsity-aware algorithms in terms of both the convergence speed and the steady-state behavior in a designated sparse channel. Furthermore, SL0-APA is shown to have smaller steady-state error than the previously proposed sparsity-aware algorithms when the number of nonzero taps in the sparse channel increases. PMID:24790588

Structural Insights into Central Hypertension Regulation by Human Aminopeptidase A*

PubMed Central

Yang, Yang; Liu, Chang; Lin, Yi-Lun; Li, Fang

2013-01-01

Hypertension is regulated through both the central and systemic renin-angiotensin systems. In the central renin-angiotensin system, zinc-dependent aminopeptidase A (APA) up-regulates blood pressure by specifically cleaving the N-terminal aspartate, but not the adjacent arginine, from angiotensin II, a process facilitated by calcium. Here, we determined the crystal structures of human APA and its complexes with different ligands and identified a calcium-binding site in the S1 pocket of APA. Without calcium, the S1 pocket can bind both acidic and basic residues through formation of salt bridges with the charged side chains. In the presence of calcium, the binding of acidic residues is enhanced as they ligate the cation, whereas the binding of basic residues is no longer favorable due to charge repulsion. Of the peptidomimetic inhibitors of APA, amastatin has higher potency than bestatin by fitting better in the S1 pocket and interacting additionally with the S3′ subsite. These results explain the calcium-modulated substrate specificity of APA in central hypertension regulation and can guide the design and development of brain-targeting antihypertensive APA inhibitors. PMID:23888046

Structural insights into central hypertension regulation by human aminopeptidase A.

PubMed

Yang, Yang; Liu, Chang; Lin, Yi-Lun; Li, Fang

2013-08-30

Hypertension is regulated through both the central and systemic renin-angiotensin systems. In the central renin-angiotensin system, zinc-dependent aminopeptidase A (APA) up-regulates blood pressure by specifically cleaving the N-terminal aspartate, but not the adjacent arginine, from angiotensin II, a process facilitated by calcium. Here, we determined the crystal structures of human APA and its complexes with different ligands and identified a calcium-binding site in the S1 pocket of APA. Without calcium, the S1 pocket can bind both acidic and basic residues through formation of salt bridges with the charged side chains. In the presence of calcium, the binding of acidic residues is enhanced as they ligate the cation, whereas the binding of basic residues is no longer favorable due to charge repulsion. Of the peptidomimetic inhibitors of APA, amastatin has higher potency than bestatin by fitting better in the S1 pocket and interacting additionally with the S3' subsite. These results explain the calcium-modulated substrate specificity of APA in central hypertension regulation and can guide the design and development of brain-targeting antihypertensive APA inhibitors.

Method and apparatus for assembling permanent magnet rotors

DOEpatents

Hsu, J.S.; Adams, D.J.

1999-06-22

A permanent magnet assembly for assembly in large permanent magnet motors and generators includes a two-piece carrier that can be slid into a slot in the rotor and then secured in place using a set screw. The invention also provides an auxiliary carrier device with guide rails that line up with the teeth of the rotor, so that a permanent magnet assembly can be pushed first into a slot, and then down the slot to its proper location. An auxiliary tool is provided to move the permanent magnet assembly into position in the slot before it is secured in place. Methods of assembling and disassembling the magnet assemblies in the rotor are also disclosed. 2 figs.

Optical diagnostics integrated with laser spark delivery system

DOEpatents

Yalin, Azer [Fort Collins, CO; Willson, Bryan [Fort Collins, CO; Defoort, Morgan [Fort Collins, CO; Joshi, Sachin [Fort Collins, CO; Reynolds, Adam [Fort Collins, CO

2008-09-02

A spark delivery system for generating a spark using a laser beam is provided, and includes a laser light source and a laser delivery assembly. The laser delivery assembly includes a hollow fiber and a launch assembly comprising launch focusing optics to input the laser beam in the hollow fiber. The laser delivery assembly further includes exit focusing optics that demagnify an exit beam of laser light from the hollow fiber, thereby increasing the intensity of the laser beam and creating a spark. Other embodiments use a fiber laser to generate a spark. Embodiments of the present invention may be used to create a spark in an engine. Yet other embodiments include collecting light from the spark or a flame resulting from the spark and conveying the light for diagnostics. Methods of using the spark delivery systems and diagnostic systems are provided.

Fiber laser coupled optical spark delivery system

DOEpatents

Yalin, Azer [Fort Collins, CO; Willson, Bryan [Fort Collins, CO; Defoort, Morgan [Fort Collins, CO; Joshi, Sachin [Fort Collins, CO; Reynolds, Adam [Fort Collins, CO

2008-03-04

A spark delivery system for generating a spark using a laser beam is provided, and includes a laser light source and a laser delivery assembly. The laser delivery assembly includes a hollow fiber and a launch assembly comprising launch focusing optics to input the laser beam in the hollow fiber. The laser delivery assembly further includes exit focusing optics that demagnify an exit beam of laser light from the hollow fiber, thereby increasing the intensity of the laser beam and creating a spark. Other embodiments use a fiber laser to generate a spark. Embodiments of the present invention may be used to create a spark in an engine. Yet other embodiments include collecting light from the spark or a flame resulting from the spark and conveying the light for diagnostics. Methods of using the spark delivery systems and diagnostic systems are provided.

Assembly of the epithelial Na+ channel evaluated using sucrose gradient sedimentation analysis.

PubMed

Cheng, C; Prince, L S; Snyder, P M; Welsh, M J

1998-08-28

Three subunits, alpha, beta, and gamma, contribute to the formation of the epithelial Na+ channel. To investigate the oligomeric assembly of the channel complex, we used sucrose gradient sedimentation analysis to determine the sedimentation properties of individual subunits and heteromultimers comprised of multiple subunits. When the alpha subunit was expressed alone, it first formed an oligomeric complex with a sedimentation coefficient of 11 S, and then generated a higher order multimer of 25 S. In contrast, individual beta and gamma subunits predominately assembled into 11 S complexes. We obtained similar results with expression in cells and in vitro. When we co-expressed beta with alpha or with alpha plus gamma, the beta subunit assembled into a 25 S complex. Glycosylation of the alpha subunit was not required for assembly into a 25 S complex. We found that the alpha subunit formed intra-chain disulfide bonds. Although such bonds were not required to generate an oligomeric complex, under nonreducing conditions the alpha subunit formed a complex that migrated more homogeneously at 25 S. This suggests that intra-chain disulfide bonds may stabilize the complex. These data suggest that the epithelial Na+ channel subunits form high order oligomeric complexes and that the alpha subunit contains the information that facilitates such formation. Interestingly, the ability of the alpha, but not the beta or gamma, subunit to assemble into a 25 S homomeric complex correlates with the ability of these subunits to generate functional channels when expressed alone.

GSTA1 Expression Is Correlated With Aldosterone Level in KCNJ5-Mutated Adrenal Aldosterone-Producing Adenoma.

PubMed

Li, Xintao; Wang, Baojun; Tang, Lu; Zhang, Yu; Chen, Luyao; Gu, Liangyou; Zhang, Fan; Ouyang, Jinzhi; Zhang, Xu

2018-03-01

KCNJ5 mutation is a major cause of aldosterone-producing adenomas (APAs). The development of APA apart from KCNJ5 mutation is less investigated. To investigate other mechanisms affecting aldosterone secretion apart from KCNJ5. Six pairs of KCNJ5-mutated, high and low aldosterone-secreting APAs, five non-KCNJ5-mutated APAs, and four normal adrenal glands were assayed by Affymetrix GeneChip Human Transcriptome Array 2.0. A total of 113 APA samples were investigated to explore the expression of glutathione-S-transferase A1 (GSTA1). H295R cells were used to verify the function of GSTA1. GSTA1 was the top gene downregulated in high-aldosterone KCNJ5-mutated APAs. GSTA1 was also downregulated in KCNJ5-mutated APAs compared with wild-type KCNJ5 APAs. Accordingly, mutant KCNJ5 decreased GSTA1 messenger RNA and protein expression levels. GSTA1 overexpression suppressed aldosterone secretion whether in wild-type or mutant KCNJ5 H295R cells. Adding ethacrynic acid or silencing of GSTA1 increased aldosterone secretion by increasing reactive oxygen species (ROS), superoxide, H2O2 levels, and Ca2+ influx. The expression of the transcription factors NR4A1, NR4A2, and CAMK1 and intracellular Ca2+ were significantly upregulated by GSTA1 inhibition. The reduced form of NAD phosphate oxidase inhibitor or H2O2 scavenger or blocking calmodulin or calcium channels could significantly reduce aldosterone secretion in GSTA1-inhibited cells. (1) GSTA1 expression is reversely correlated with aldosterone level in KCNJ5-mutated APAs, (2) GSTA1 regulates aldosterone secretion by ROS and Ca2+ signaling, and (3) KCNJ5 mutation downregulates GSTA1 expression, and overexpression of GSTA1 reverses increased aldosterone in KCNJ5-mutated adrenal cells.

Structures of yeast Apa2 reveal catalytic insights into a canonical AP₄A phosphorylase of the histidine triad superfamily.

PubMed

Hou, Wen-Tao; Li, Wen-Zhe; Chen, Yuxing; Jiang, Yong-Liang; Zhou, Cong-Zhao

2013-08-09

The homeostasis of intracellular diadenosine 5',5″'-P(1),P(4)-tetraphosphate (Ap4A) in the yeast Saccharomyces cerevisiae is maintained by two 60% sequence-identical paralogs of Ap4A phosphorylases (Apa1 and Apa2). Enzymatic assays show that, compared to Apa1, Apa2 has a relatively higher phosphorylase activity towards Ap3A (5',5″'-P(1),P(3)-tetraphosphate), Ap4A, and Ap5A (5',5″'-P(1),P(5)-tetraphosphate), and Ap4A is the favorable substrate for both enzymes. To decipher the catalytic insights, we determined the crystal structures of Apa2 in the apo-, AMP-, and Ap4A-complexed forms at 2.30, 2.80, and 2.70Å resolution, respectively. Apa2 is an α/β protein with a core domain of a twisted eight-stranded antiparallel β-sheet flanked by several α-helices, similar to the galactose-1-phosphate uridylyltransferase (GalT) members of the histidine triad (HIT) superfamily. However, a unique auxiliary domain enables an individual Apa2 monomer to possess an intact substrate-binding cleft, which is distinct from previously reported dimeric GalT proteins. This cleft is perfectly complementary to the favorable substrate Ap4A, the AMP and ATP moieties of which are perpendicular to each other, leaving the α-phosphate group exposed at the sharp turn against the catalytic residue His161. Structural comparisons combined with site-directed mutagenesis and activity assays enable us to define the key residues for catalysis. Furthermore, multiple-sequence alignment reveals that Apa2 and homologs represent canonical Ap4A phosphorylases, which could be grouped as a unique branch in the GalT family. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads

PubMed Central

2013-01-01

Background Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. The advent of next generation sequencing has led to the development of numerous computational tools to analyze and assemble the millions to billions of short sequencing reads produced by these technologies. While these tools filled an important gap, current approaches for storing, processing, and analyzing short read datasets generally have remained simple and lack the complexity needed to efficiently model the produced reads and assemble them correctly. Results Previously, we presented an overlap graph coarsening scheme for modeling read overlap relationships on multiple levels. Most current read assembly and analysis approaches use a single graph or set of clusters to represent the relationships among a read dataset. Instead, we use a series of graphs to represent the reads and their overlap relationships across a spectrum of information granularity. At each information level our algorithm is capable of generating clusters of reads from the reduced graph, forming an integrated graph modeling and clustering approach for read analysis and assembly. Previously we applied our algorithm to simulated and real 454 datasets to assess its ability to efficiently model and cluster next generation sequencing data. In this paper we extend our algorithm to large simulated and real Illumina datasets to demonstrate that our algorithm is practical for both sequencing technologies. Conclusions Our overlap graph theoretic algorithm is able to model next generation sequencing reads at various levels of granularity through the process of graph coarsening. Additionally, our model allows for efficient representation of the read overlap relationships, is scalable for large datasets, and is practical for both Illumina and 454 sequencing technologies. PMID:24564333

cis-Apa: a practical linker for the microwave-assisted preparation of cyclic pseudopeptides via RCM cyclative cleavage.

PubMed

Baron, Alice; Verdié, Pascal; Martinez, Jean; Lamaty, Frédéric

2011-02-04

A new linker cis-5-aminopent-3-enoic acid (cis-Apa) was prepared for the synthesis of cyclic pseudopeptides by cyclization-cleavage by using ring-closing methatesis (RCM). We developed a new synthetic pathway for the preparation of the cis-Apa linker that was tested in the cyclization-cleavage process of different RGD peptide sequences. Different macrocyclic peptidomimetics were prepared by using this integrated microwave-assisted method, showing that the readily available cis-Apa amino acid is well adapted as a linker in the cyclization-cleavage process.

Adam M. Reid: APA/APAGS Award for Distinguished Graduate Student in Professional Psychology.

PubMed

2015-11-01

The APA/APAGS Award for Distinguished Graduate Student in Professional Psychology is awarded on an annual basis by the APA Board of Professional Affairs (BPA) and the American Psychological Association of Graduate Students (APAGS) to a graduate student who has demonstrated outstanding practice and application of psychology. One of the 2015 award winners is Adam M. Reid, who received this award "for his community service, in which he has integrated the highest standards of professional psychological clinical practice and science." Adam's award citation, biography, and a selected bibliography are presented here. (c) 2015 APA, all rights reserved).

APA/APAGS Award for Distinguished Graduate Student in Professional Psychology: Octavio Andres Santos.

PubMed

2017-12-01

The APA/APAGS Award for Distinguished Graduate Student in Professional Psychology is awarded annually by the APA Board of Professional Affairs (BPA) and the American Psychological Association of Graduate Students (APAGS) to a graduate student who has demonstrated outstanding practice and application of psychology. The 2017 award winner is Octavio Andres Santos, who has demonstrated through several initiatives "effective engagement with advocacy, professional organizations, and research in the area of health disparities and multicultural/multilingual assessment." Santos's award citation, biography, and a selected bibliography are presented here. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

First Results from the DUNE 35-ton Prototype using Cosmics

NASA Astrophysics Data System (ADS)

Insler, Jonathan; DUNE Collaboration

2016-03-01

The 35-ton prototype for the Deep Underground Neutrino Experiment (DUNE) Far Detector is a single-phase liquid argon time projection chamber (LAr-TPC) integrated detector that will take cosmics data for a two month run beginning in February 2016. The 35-ton prototype will characterize DUNE's Far Detector technology performance and provide a sample of real data for DUNE reconstruction algorithms. The 35-ton prototype has two drift volumes of lengths 2.23 m and 0.23 m on either side of its anode plane assembly (APA) and makes use of wire planes with wrapped wires and a photon detection system (PDS) utilizing photon detection panels read out by silicon photomultipliers (SiPMs). Data from the 35-ton LAr detector are expected to provide rich information on scintillation light and charged particle tracks. We present a preliminary analysis of cosmics data taken with the 35-ton detector with a focus on stopping muons.

A digital future for the history of psychology?

PubMed

Green, Christopher D

2016-08-01

This article discusses the role that digital approaches to the history of psychology are likely to play in the near future. A tentative hierarchy of digital methods is proposed. A few examples are briefly described: a digital repository, a simple visualization using ready-made online database and tools, and more complex visualizations requiring the assembly of the database and, possibly, the analytic tools by the researcher. The relationship of digital history to the old "New Economic History" (Cliometrics) is considered. The question of whether digital history and traditional history need be at odds or, instead, might complement each other is woven throughout. The rapidly expanding territory of digital humanistic research outside of psychology is briefly discussed. Finally, the challenging current employment trends in history and the humanities more broadly are considered, along with the role that digital skills might play in mitigating those factors for prospective academic workers. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

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

Berland, Brian Spencer; Lanning, Bruce Roy; Stowell, Jr., Michael Wayne

This disclosure describes system and methods for creating an autonomous electrochromic assembly, and systems and methods for use of the autonomous electrochromic assembly in combination with a window. Embodiments described herein include an electrochromic assembly that has an electrochromic device, an energy storage device, an energy collection device, and an electrochromic controller device. These devices may be combined into a unitary electrochromic insert assembly. The electrochromic assembly may have the capability of generating power sufficient to operate and control an electrochromic device. This control may occur through the application of a voltage to an electrochromic device to change its opacitymore » state. The electrochromic assembly may be used in combination with a window.« less

Representations of mechanical assembly sequences

NASA Technical Reports Server (NTRS)

Homem De Mello, Luiz S.; Sanderson, Arthur C.

1991-01-01

Five types of representations for assembly sequences are reviewed: the directed graph of feasible assembly sequences, the AND/OR graph of feasible assembly sequences, the set of establishment conditions, and two types of sets of precedence relationships. (precedence relationships between the establishment of one connection between parts and the establishment of another connection, and precedence relationships between the establishment of one connection and states of the assembly process). The mappings of one representation into the others are established. The correctness and completeness of these representations are established. The results presented are needed in the proof of correctness and completeness of algorithms for the generation of mechanical assembly sequences.

Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model

PubMed Central

Padilla, Jennifer E.; Liu, Wenyan; Seeman, Nadrian C.

2012-01-01

We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary size from a small set of tiles according to the tile substitution algorithm that generates them. Enabling coordinated hierarchical assembly in the aTAM makes possible the efficient encoding of the recursive process of tile substitution. PMID:23226722

Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model.

PubMed

Padilla, Jennifer E; Liu, Wenyan; Seeman, Nadrian C

2012-06-01

We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary size from a small set of tiles according to the tile substitution algorithm that generates them. Enabling coordinated hierarchical assembly in the aTAM makes possible the efficient encoding of the recursive process of tile substitution.

Self-assembled nanotubes from single fluorescent amino acid

NASA Astrophysics Data System (ADS)

Babar, Dipak Gorakh; Sarkar, Sabyasachi

2017-04-01

Self-assembly of biomolecules has gained increasing attention as it generates various supramolecular structural assemblies having potential applications principally in biomedical sciences. Here, we show that amino acid like tryptophan or tyrosine readily aggregates as nanotubes via a simple self-assembly process. These were characterized by FTIR, scanning electron microscopy, and by fluorescence microscopy. Nanotubes prepared from tryptophan are having 200 nm inner diameter and those from tyrosine are having the same around 50 nm diameter.

Research on multi - channel interactive virtual assembly system for power equipment under the “VR+” era

NASA Astrophysics Data System (ADS)

Ren, Yilong; Duan, Xitong; Wu, Lei; He, Jin; Xu, Wu

2017-06-01

With the development of the “VR+” era, the traditional virtual assembly system of power equipment has been unable to satisfy our growing needs. In this paper, based on the analysis of the traditional virtual assembly system of electric power equipment and the application of VR technology in the virtual assembly system of electric power equipment in our country, this paper puts forward the scheme of establishing the virtual assembly system of power equipment: At first, we should obtain the information of power equipment, then we should using OpenGL and multi texture technology to build 3D solid graphics library. After the completion of three-dimensional modeling, we can use the dynamic link library DLL package three-dimensional solid graphics generation program to realize the modularization of power equipment model library and power equipment model library generated hidden algorithm. After the establishment of 3D power equipment model database, we set up the virtual assembly system of 3D power equipment to separate the assembly operation of the power equipment from the space. At the same time, aiming at the deficiency of the traditional gesture recognition algorithm, we propose a gesture recognition algorithm based on improved PSO algorithm for BP neural network data glove. Finally, the virtual assembly system of power equipment can really achieve multi-channel interaction function.

Performance and model of a full-scale up-flow anaerobic sludge blanket (UASB) to treat the pharmaceutical wastewater containing 6-APA and amoxicillin.

PubMed

Chen, Zhiqiang; Wang, Hongcheng; Chen, Zhaobo; Ren, Nanqi; Wang, Aijie; Shi, Yue; Li, Xiaoming

2011-01-30

A full-scale test was conducted with an up-flow anaerobic sludge blanket (UASB) pre-treating pharmaceutical wastewater containing 6-aminopenicillanic acid (6-APA) and amoxicillin. The aim of the study is to investigate the performance of UASB in the condition of a high chemical oxygen demand (COD) loading rate from 12.57 to 21.02 kgm(-3)d(-1) and a wide pH from 5.57 to 8.26, in order to provide a reference for treating the similar chemical synthetic pharmaceutical wastewater containing 6-APA and amoxicillin. The results demonstrated that the UASB average percentage reduction in COD, 6-APA and amoxicillin were 52.2%, 26.3% and 21.6%, respectively. In addition, three models, built on the back propagation neural network (BPNN) theory and linear regression techniques were developed for the simulation of the UASB system performance in the biodegradation of pharmaceutical wastewater containing 6-APA and amoxicillin. The average error of COD, 6-APA and amoxicillin were -0.63%, 2.19% and 5.40%, respectively. The results indicated that these models built on the BPNN theory were well-fitted to the detected data, and were able to simulate and predict the removal of COD, 6-APA and amoxicillin by UASB. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

Walking delays anticipatory postural adjustments but not reaction times in a choice reaction task.

PubMed

Haridas, C; Gordon, I T; Misiaszek, J E

2005-06-01

During standing, anticipatory postural adjustments (APAs) and focal movements are delayed while performing a choice reaction task, compared with a simple reaction task. We hypothesized that APAs and focal movements of a choice reaction task would be similarly delayed during walking. Furthermore, reaction times are delayed during walking compared with standing. We further hypothesized that APAs and focal movements would be delayed during walking, compared with standing, for both simple and choice reaction tasks. Subjects either walked or stood on a treadmill while holding on to stable handles. They were asked to push or pull on the handles in response to a visual cue. Muscle activity was recorded from muscles of the leg (APA) and arm (RT). Our results were in agreement with previous work showing APA onset was delayed in the choice reaction task compared with the simple reaction task. In addition, the interval between the onset of APA and focal movement activity increased with choice reaction tasks. The task of walking did not delay the onset of focal movement for either the simple or choice reaction tasks. Walking did delay the onset of the APA, but only during choice reaction tasks. The results suggest the added demand of walking does not significantly modify the control of focal arm movements. However, additional attentional demands while walking may compromise anticipatory postural control.

Metoclopramide unmasks potentially misleading contralateral suppression in patients undergoing adrenal vein sampling for primary aldosteronism.

PubMed

Rossitto, Giacomo; Miotto, Diego; Battistel, Michele; Barbiero, Giulio; Maiolino, Giuseppe; Bisogni, Valeria; Sanga, Viola; Rossi, Gian Paolo

2016-11-01

As metoclopramide stimulates aldosterone secretion, we tested its usefulness in the assessment of lateralization of primary aldosteronism by adrenal vein sampling (AVS). Prospective within-patient study in consecutive patients undergoing AVS for primary aldosteronism subtyping. We compared the diagnostic accuracy of baseline and postmetoclopramide lateralization index and relative (to cortisol) aldosterone secretion indices (RASI) for each adrenal gland with aldosterone-producing adenoma (APA) determined by the four corners criteria as the reference diagnosis. We recruited 93 consecutive patients (mean age: 52 years; women 31%). Metoclopramide increased plasma aldosterone in the inferior vena cava and in both adrenal veins. The postmetoclopramide lateralization index was accurate in identifying APA, but did not increase diagnostic accuracy over baseline lateralization index, because the RASI increased similarly in both sides. Conversely, metoclopramide raised RASI to values more than 0.90 bilaterally in non-APA patients allowing accurate identification of factitious aldosterone suppression. In contrast, RASI was 0.90 or less in 48% contralateral to the tumor in APA patients. Regression analysis showed the APA patients with persistent suppression of RASI contralaterally showed a more florid primary aldosteronism phenotype. Metoclopramide does not enhance lateralization of aldosterone excess in APA, but consistently increased the value of RASI in non-APA cases, thus unmasking potentially misleading suppression of aldosterone. Postmetoclopramide RASI may therefore allow a more precise diagnosis when AVS can be achieved only unilaterally.

Generation and context memory.

PubMed

Mulligan, Neil W; Lozito, Jeffrey P; Rosner, Zachary A

2006-07-01

Generation enhances memory for occurrence but may not enhance other aspects of memory. The present study further delineates the negative generation effect in context memory reported in N. W. Mulligan (2004). First, the negative generation effect occurred for perceptual attributes of the target item (its color and font) but not for extratarget aspects of context (location and background color). Second, nonvisual generation tasks with either semantic or nonsemantic generation rules (antonym and rhyme generation, respectively) produced the same pattern of results. In contrast, a visual (or data-driven) generation task (letter transposition) did not disrupt context memory for color. Third, generating nonwords produced no effect on item memory but persisted in producing a negative effect on context memory for target attributes, implying that (a) the negative generation effect in context memory is not mediated by semantic encoding, and (b) the negative effect on context memory can be dissociated from the positive effect on item memory. The results are interpreted in terms of the processing account of generation. The original, perceptual-conceptual version of this account is too narrow, but a modified processing account, based on a more generic visual versus nonvisual processing distinction, accommodates the results. Copyright 2006 APA, all rights reserved.

Optimization of De Novo Short Read Assembly of Seabuckthorn (Hippophae rhamnoides L.) Transcriptome

PubMed Central

Ghangal, Rajesh; Chaudhary, Saurabh; Jain, Mukesh; Purty, Ram Singh; Chand Sharma, Prakash

2013-01-01

Seabuckthorn ( Hippophae rhamnoides L.) is known for its medicinal, nutritional and environmental importance since ancient times. However, very limited efforts have been made to characterize the genome and transcriptome of this wonder plant. Here, we report the use of next generation massive parallel sequencing technology (Illumina platform) and de novo assembly to gain a comprehensive view of the seabuckthorn transcriptome. We assembled 86,253,874 high quality short reads using six assembly tools. At our hand, assembly of non-redundant short reads following a two-step procedure was found to be the best considering various assembly quality parameters. Initially, ABySS tool was used following an additive k-mer approach. The assembled transcripts were subsequently subjected to TGICL suite. Finally, de novo short read assembly yielded 88,297 transcripts (> 100 bp), representing about 53 Mb of seabuckthorn transcriptome. The average length of transcripts was 610 bp, N50 length 1198 BP and 91% of the short reads uniquely mapped back to seabuckthorn transcriptome. A total of 41,340 (46.8%) transcripts showed significant similarity with sequences present in nr protein databases of NCBI (E-value < 1E-06). We also screened the assembled transcripts for the presence of transcription factors and simple sequence repeats. Our strategy involving the use of short read assembler (ABySS) followed by TGICL will be useful for the researchers working with a non-model organism’s transcriptome in terms of saving time and reducing complexity in data management. The seabuckthorn transcriptome data generated here provide a valuable resource for gene discovery and development of functional molecular markers. PMID:23991119

19. Launch Area, general view of Missile Assembly Building and ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

19. Launch Area, general view of Missile Assembly Building and Generator Building VIEW SOUTHWEST - NIKE Missile Battery PR-79, Launch Area, East Windsor Road south of State Route 101, Foster, Providence County, RI

75 FR 52470 - Approval and Promulgation of Implementation Plans Georgia: State Implementation Plan Revision...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-26

...) of the Administrative Procedure Act (APA) which, upon finding ``good cause,'' authorizes agencies to... is good cause under APA section 553(d)(3) for this correction to become effective on the date of publication of this action. Section 553(d)(3) of the APA allows an effective date less than 30 days after...

The Value of Peer Feedback Opportunities for Students in Writing Intensive Classes

ERIC Educational Resources Information Center

Kennette, Lynne N.; Frank, Nichole M.

2013-01-01

The present study was conducted to examine the usefulness of peer feedback on APA-style research papers in a writing-intensive class. Subsequent to APA training, students were asked to review and provide feedback on a classmate's APA-style research report for both content and formatting. Performance on this research report was then compared to…

78 FR 39057 - Hours of Service of Drivers; Renewal and Expansion of American Pyrotechnics Association Exemption...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-28

... Association (APA) from FMCSA's regulation prohibiting drivers of commercial motor vehicles (CMVs) from driving after the 14th hour after coming on duty. The FMCSA renews the exemption for 45 APA member-companies and... carrier is being denied. Additionally, the APA advised FMCSA of the removal from the original renewal...

The Impact of APA and AERA Guidelines on Effect Size Reporting

ERIC Educational Resources Information Center

Peng, Chao-Ying Joanne; Chen, Li-Ting; Chiang, Hsu-Min; Chiang, Yi-Chen

2013-01-01

Given the long history of effect size (ES) indices (Olejnik and Algina, "Contemporary Educational Psychology," 25, 241-286 2000) and various attempts by APA and AERA to encourage the reporting and interpretation of ES to supplement findings from inferential statistical analyses, it is essential to document the impact of APA and AERA standards on…

75 FR 27643 - Prevention of Significant Deterioration (PSD) and Nonattainment New Source Review (NSR): Aggregation

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-18

... (APA) section 705 until the proceeding for judicial review of this rule is completed or EPA completes... section 705 of the APA, ``an agency * * * may postpone the effective date of [an] action taken by it... and Delay of Effective Date Pursuant to section 705 of the APA, the EPA hereby postpones the...

78 FR 77122 - Proposed Modification of a General NPDES Permit for Small Suction Dredging-Permit Number IDG-37-0000

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-20

... required by section 553 of the Administrative Procedure Act (APA), or any other law, to publish general... entities.'' EPA has concluded that NPDES general permits are permits, not rulemakings, under the APA and thus not subject to APA rulemaking requirements or the RFA. Notwithstanding that general permits are...

77 FR 27626 - Approval and Promulgation of Implementation Plans; Commonwealth of Kentucky; Regional Haze State...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-11

... section 553(b)(3)(B) of the Administrative Procedure Act (APA) which, upon finding ``good cause... related to the regional haze SIP revisions. EPA also finds that there is good cause under APA section 553...(d)(3) of the APA allows an effective date less than 30 days after publication ``as otherwise...

77 FR 213 - United States Savings Bonds, Series EE and I

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-04

... (APA). Because this rule relates to United States securities, which are contracts between Treasury and the owner of the security, this rule falls within the contract exception to the APA, 5 U.S.C. 553(a)(2). As a result, the notice, public comment, and delayed effective date provisions of the APA are...

75 FR 9781 - Determination of Nonattainment and Reclassification of the Atlanta, Georgia, 8-Hour Ozone...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-04

... the Administrative Procedure Act (APA) which, upon finding ``good cause,'' authorizes agencies to... marginal to moderate. EPA also finds that there is good cause under APA section 553(d)(3) for this correction to become effective on the date of publication of this action. Section 553(d)(3) of the APA allows...

76 FR 5272 - Removal of Limitation of Approval of Prevention of Significant Deterioration Provisions...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-31

... Administrative Procedure Act (APA). DATES: This action is effective January 31, 2011. ADDRESSES: EPA has...'' exemption in section 553(b)(3)(B) of the APA. That provision authorizes agencies, upon finding ``good cause... CFR 52.53 that no longer serves any purpose. EPA also finds that there is good cause under APA section...

76 FR 5274 - Removal of Limitation of Approval of Prevention of Significant Deterioration Provisions...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-31

... Administrative Procedure Act (APA). DATES: This action is effective January 31, 2011. ADDRESSES: EPA has...)(3)(B) of the APA. That provision authorizes agencies, upon finding ``good cause,'' to dispense with... any purpose. EPA also finds that there is good cause under APA section 553(d)(3) for this action to...

77 FR 9865 - Clarification on the Division 1.1 Fireworks Approvals Policy

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-21

... APA Standard 87-1 (IBR, see Sec. 171.7), and the device passes the thermal stability test. Additionally, the applicant must certify that the firework device conforms to the APA Standard 87-1 and that... approval. While APA Standard 87-1 contains two instances where Division 1.1 fireworks may be approved under...

76 FR 59769 - Clarification on the Division 1.1 Fireworks Approvals Policy

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-27

... test laboratory if the firework device is manufactured in accordance with APA Standard 87-1 (IBR, see... certify that the firework device conforms to the APA Standard 87-1 and that the descriptions and technical... issuing the EX approval. While APA Standard 87-1 references two instances where Division 1.1 fireworks may...

Ensuring the Availability and Quality of School Psychology Doctoral Internships

ERIC Educational Resources Information Center

Harris, Abigail M.

2015-01-01

Currently, only a small percentage of internships accredited by the American Psychological Association (APA) are filled by school psychology interns and only a few of the available APA internship positions are in schools. Program data submitted online to APA indicate that many interns are in sites that meet the guidelines adopted by the Council of…

76 FR 3015 - Prohibitions in Areas Designated by Order; Closure of National Forest System Lands To Protect...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-19

... Cause Statement The Administrative Procedure Act (APA) exempts certain rulemaking from its public notice...)), such as federal lands managed by the Forest Service. Furthermore, the APA allows agencies to promulgate... from public notice and comment rulemaking under the APA (July 24, 1971; 36 FR 13804). Thus, agencies in...

76 FR 78126 - Disclosure Requirements for Depository Institutions Lacking Federal Deposit Insurance (Regulation I)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-16

... and Comment The Administrative Procedure Act (APA) \\11\\ generally requires public notice and an opportunity to comment before promulgation of substantive regulations.\\12\\ The APA provides exceptions to... APA's notice-and-comment requirements. \\11\\ 5 U.S.C. 551 et seq. \\12\\ 5 U.S.C. 553(b), (c). \\13\\ 5 U.S...

APA Handbook of Giftedness and Talent. APA Handbooks in Psychology. APA Reference Books Collection

ERIC Educational Resources Information Center

Pfeiffer, Steven I., Ed.

2017-01-01

This handbook incorporates the most recent thinking and cutting-edge research from a wide range of fields related to gifted education, including developmental and social psychology, the neurosciences, cognitive science, and education. It consists of six sections: (1) History and global perspectives on the gifted field and talent development; (2)…

Multicultural Training in Doctoral School Psychology Programs: In Search of the Model Program?

ERIC Educational Resources Information Center

Kearns, Tori; Ford, Laurie; Brown, Kimberly

The multicultural training (MCT) of APA-accredited School Psychology programs was studied. The sample included faculty and students from five programs nominated for strong MCT and five comparison programs randomly selected from the list of remaining APA-accredited programs. Program training was evaluated using a survey based on APA guidelines for…

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

PubMed

Hulse-Kemp, Amanda M; Maheshwari, Shamoni; Stoffel, Kevin; Hill, Theresa A; Jaffe, David; Williams, Stephen R; Weisenfeld, Neil; Ramakrishnan, Srividya; Kumar, Vijay; Shah, Preyas; Schatz, Michael C; Church, Deanna M; Van Deynze, Allen

2018-01-01

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper ( Capsicum annuum ) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F 1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available  de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F 1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

The effect of load uncertainty on anticipatory muscle activity in catching.

PubMed

Eckerle, Jason J; Berg, William P; Ward, Rose Marie

2012-08-01

To investigate how the CNS copes with load uncertainty in catching, anticipatory postural adjustments (APAs) in one-handed catching of balls of known and unknown weights were compared. Twenty-nine (n = 29) men (mean age = 21.1 years) participated, all of whom had engaged in a sport activity requiring hand-eye coordination. Participants' muscle activity in the biceps brachii, triceps brachii, wrist flexor group, and bilateral erector spinae at L4-5 was recorded using electromyography (EMG) while they caught visually identical balls of four different weights (0.5, 1.33, 2.17, and 3.0 kg). EMG integrals were computed for the 1 s prior to ball drop (pre-drop period), and the interval between ball drop and catch (drop period). Uncertainty about ball weight had no effect on APA activity during the pre-drop period. During the drop period, however, load uncertainty did influence APA activity in the biceps brachii, triceps brachii, and the wrist flexor muscles (i.e., the effect of ball weight on APA magnitude depended on the presence or absence of load knowledge). In the known ball weight condition, participants exhibit greater APA magnitude with increases in ball weight. In contrast, under the unknown ball weight condition, APA magnitude was relatively consistent across ball weights and at a level similar to the APA magnitude for an intermediate weight (i.e., the second heaviest ball of four) in the known weight condition. In catching balls of unknown weights, the CNS appears to scale APA magnitude to afford the greatest chance of catching the ball, regardless of the weight.

Effect of adapted physical activity sessions in the hospital on health-related quality of life for children with cancer: a cross-over randomized trial.

PubMed

Speyer, Elodie; Herbinet, Aline; Vuillemin, Anne; Briançon, Serge; Chastagner, Pascal

2010-12-01

To assess the efficacy of adapted physical activity (APA) on health-related quality of life (HRQoL) of hospitalized children and adolescents with cancer between 9 and 18 years of age. A two-sequence, four-period cross-over study, Activités Physiques en Oncologie Pédiatrique (APOP), compared hospital stay with APA sessions versus hospital stay without APA sessions on children's HRQoL. Children and parents completed the child and parent forms, respectively, of a HRQoL questionnaire, the Child Health Questionnaire, on the last day of hospitalization. We used mixed linear regression to determine the effect of treatment, of treatment order and whether response to previous treatment influenced HRQoL. Thirty children were included (mean age 13.6 ± 2.9 years; 18 males). Cross-over analysis revealed no effect of period or interaction between APA and period. HRQoL was higher when children practiced than did not practice APA during their hospitalization, as reported by both children and parents, for the dimensions physical functioning (P < 0.0001), role/social-physical (P = 0.001), self-esteem (P < 0.0001), and mental health (P < 0.0001). In addition, APA had a significant effect on the behavior dimension (P = 0.01), as reported by children, and on the bodily pain dimension (P = 0.0004), as reported by parents. The highest significant difference in scores between with and without APA was observed for the self-esteem dimension (P < 0.0001) for both children and parents. APA during hospitalization for children with cancer was associated with better HRQoL for most of the HRQoL psychological and physical dimensions. Whether this effect is specific for children with cancer should be explored.

Purkinje Cell Protein 4 Expression Is Associated With DNA Methylation Status in Aldosterone-Producing Adenoma.

PubMed

Kobuke, Kazuhiro; Oki, Kenji; Gomez-Sanchez, Celso E; Ohno, Haruya; Itcho, Kiyotaka; Yoshii, Yoko; Yoneda, Masayasu; Hattori, Noboru

2018-03-01

Aldosterone production is stimulated by activation of calcium signaling in aldosterone-producing adenomas (APAs), and epigenetic factors such as DNA methylation may be associated with the expression of genes involved in aldosterone regulation. Our aim was to investigate the DNA methylation of genes related to calcium signaling cascades in APAs and the association of mutations in genes linked to APAs with DNA methylation levels. Nonfunctioning adrenocortical adenoma (n = 12) and APA (n = 35) samples were analyzed. The KCNJ5 T158A mutation was introduced into human adrenocortical cell lines (HAC15 cells) using lentiviral delivery. DNA methylation array analysis was conducted using adrenal tumor samples and HAC15 cells. The Purkinje cell protein 4 (PCP4) gene was one of the most hypomethylated in APAs. DNA methylation levels in two sites of PCP4 showed a significant inverse correlation with messenger RNA expression in adrenal tumors. Bioinformatics and multiple regression analysis revealed that CCAAT/enhancer binding protein alpha (CEBPA) may bind to the methylation site of the PCP4 promoter. According to chromatin immunoprecipitation assay, CEBPA was bound to the PCP4 hypomethylated region by chromatin immunoprecipitation assay. There were no significant differences in PCP4 methylation levels among APA genotypes. Moreover, KCNJ5 T158A did not influence PCP4 methylation levels in HAC15 cells. We showed that the PCP4 promoter was one of the most hypomethylated in APAs and that PCP4 transcription may be associated with demethylation as well as with CEBPA in APAs. KCNJ5 mutations known to result in aldosterone overproduction were not related to PCP4 methylation in either clinical or in vitro studies.

The effects of muscle vibration on anticipatory postural adjustments.

PubMed

Slijper, Harm; Latash, Mark L

2004-07-23

The current study investigated the influence of changes in sensory information related to postural stability on anticipatory postural adjustments (APAs) in standing subjects. Subjects performed fast arm movements and a load release task while standing on a stable force platform or on an unstable board. We manipulated sensory information through vibration of the Achilles tendons and additional finger touch (contact forces under 1 N). Changes in the background activity of leg, trunk, and arm muscles and displacements of the center of pressure (COP) were quantified within time intervals typical for APAs. In the arm movement task, leg and trunk muscles showed a significant drop in the APAs with finger touch, while the vibration and standing on the unstable board each led to an increase in the APA magnitude. In the load release task, ventral muscles decreased their APA activity with touch, while dorsal muscles showed increased inhibition during APAs. During vibration, dorsal and ventral muscles showed increased excitation and inhibition during APAs, respectively. An additional analysis of APAs at a joint level, has shown that in both tasks, an index related to the co-activation of agonist-antagonist muscle pairs (C-index) was modulated with touch, vibration, and stability particularly in leg muscles. Small changes in the other index related to reciprocal activation (R-index) were found only in trunk muscles. Light touch and vibration induced opposing changes in the C-index, suggesting their opposite effects on the stabilization of a reference point or vertical. We conclude that the central nervous system deploys patterns of adjustments in which increased co-contraction of distal muscles and reciprocal adjustments in trunk muscles are modified to ensure equilibrium under postural instability.

Using Objective, Real-Time Measures to Investigate the Effect of Actual Physical Activity on Affective States in Everyday Life Differentiating the Contexts of Working and Leisure Time in a Sample with Students

PubMed Central

Kanning, Martina

2013-01-01

Multiple studies suggest that physical activity causes positive affective reactions and reduces depressive mood. However, studies and interventions focused mostly on structured activity programs, but rarely on actual physical activity (aPA) in daily life. Furthermore, they seldom account for the context in which the aPA occur (e.g., work, leisure). Using a prospective, real-time assessment design (ambulatory assessment), we investigated the effects of aPA on affective states (valence, energetic arousal, calmness) in real-time during everyday life while controlling for the context. Eighty-seven undergraduates students (Age: M = 24.6; SD = 3.2, females: 54%) participated in this study. aPA was assessed through accelerometers during 24-h. Palmtop devices prompted subjects approximately every 45 min during a 14-h daytime period to assess their affective states and the context. We analyzed within- and between-person effects with hierarchical modeling (HLM 6.0). Multilevel analyses revealed that both aPA and context influenced subsequent affective states. The interaction of aPA and context did predict energetic arousal only. State levels of affects did not differ between men and women. For both men and women, aPA in everyday life has an effect on individual’s affective states. For valence and calmness, it seems to be independent of the context in which the aPA occur. For energetic arousal, men reported to have lower feelings of energy and women reported to have more feelings of energy during leisure time compared to working episodes. PMID:23346064

Gender Difference in Academic Planning Activity among Medical Students

PubMed Central

Nguyen, Huy Van; Giang, Thao Thach

2013-01-01

Background In Vietnam, as doctor of medicine is socially considered a special career, both men and women who are enrolled in medical universities often study topics of medicine seriously. However, as culturally expected, women often perform better than men. Because of this, teaching leadership and management skill (LMS) to develop academic planning activity (APA) for female medical students would also be expected to be more effective than male counterparts. This research aimed to compare by gender the effect of teaching LMS on increasing APA, using propensity score matching (PSM). Methods In a cross-sectional survey utilizing a self-reported structured questionnaire on a systematic random sample of 421 male and female medical students in Hanoi Medical University, this study adopted first regression techniques to construct a fit model, then PSM to create a matched control group in order to allow for evaluating the effect of LMS education. Results There were several interesting gender differences. First, while for females LMS education had both direct and indirect effects on APA, it had only direct effect on males’ APA. Second, after PSM to adjust for the possible confounders to balance statistically two groups – with and without LMS education, there is statistically a significant difference in APA between male and female students, making a net difference of 11% (p<.01), equivalent to 173 students. The difference in APA between exposed and matched control group in males and females was 9% and 20%, respectively. These estimates of 9.0 and 20.0 percentage point increase can be translated into the practice of APA by 142 males and 315 females, respectively, in the population. These numbers of APA among male and female students can be explained by LMS education. Conclusions Gender appears to be a factor explaining in part academic planning activity. PMID:23418467

A case of bilateral aldosterone-producing adenomas differentiated by segmental adrenal venous sampling for bilateral adrenal sparing surgery

PubMed Central

Morimoto, R; Satani, N; Iwakura, Y; Ono, Y; Kudo, M; Nezu, M; Omata, K; Tezuka, Y; Seiji, K; Ota, H; Kawasaki, Y; Ishidoya, S; Nakamura, Y; Arai, Y; Takase, K; Sasano, H; Ito, S; Satoh, F

2016-01-01

Primary aldosteronism due to unilateral aldosterone-producing adenoma (APA) is a surgically curable form of hypertension. Bilateral APA can also be surgically curable in theory but few successful cases can be found in the literature. It has been reported that even using successful adrenal venous sampling (AVS) via bilateral adrenal central veins, it is extremely difficult to differentiate bilateral APA from bilateral idiopathic hyperaldosteronism (IHA) harbouring computed tomography (CT)-detectable bilateral adrenocortical nodules. We report a case of bilateral APA diagnosed by segmental AVS (S-AVS) and blood sampling via intra-adrenal first-degree tributary veins to localize the sites of intra-adrenal hormone production. A 36-year-old man with marked long-standing hypertension was referred to us with a clinical diagnosis of bilateral APA. He had typical clinical and laboratory profiles of marked hypertension, hypokalaemia, elevated plasma aldosterone concentration (PAC) of 45.1 ng dl−1 and aldosterone renin activity ratio of 90.2 (ng dl−1 per ng ml−1 h−1), which was still high after 50 mg-captopril loading. CT revealed bilateral adrenocortical tumours of 10 and 12 mm in diameter on the right and left sides, respectively. S-AVS confirmed excess aldosterone secretion from a tumour segment vein and suppressed secretion from a non-tumour segment vein bilaterally, leading to the diagnosis of bilateral APA. The patient underwent simultaneous bilateral sparing adrenalectomy. Histopathological analysis of the resected adrenals together with decreased blood pressure and PAC of 5.2 ng dl−1 confirmed the removal of bilateral APA. S-AVS was reliable to differentiate bilateral APA from IHA by direct evaluation of intra-adrenal hormone production. PMID:26538381

Self-Assembled Nano-energetic Gas Generators based on Bi2O3

NASA Astrophysics Data System (ADS)

Hobosyan, Mkhitar; Trevino, Tyler; Martirosyan, Karen

2012-10-01

Nanoenergetic Gas-Generators are formulations that rapidly release a large amount of gaseous products and generate a fast moving thermal wave. They are mainly based on thermite systems, which are pyrotechnic mixtures of metal powders (fuel- Al, Mg, etc.) and metal oxides (oxidizer, Bi2O3, Fe2O3, WO3, MoO3 etc.) that can generate an exothermic oxidation-reduction reaction referred to as a thermite reaction. A thermite reaction releases a large amount of energy and can generate rapidly extremely high temperatures. The intimate contact between the fuel and oxidizer can be enhanced by use of nano instead of micro particles. The contact area between oxidizer and metal particles depends from method of mixture preparation. In this work we utilize the self-assembly processes, which use the electrostatic forces to produce ordered and self-organized binary systems. In this process the intimate contact significantly enhances and gives the ability to build an energetic material in molecular level, which is crucial for thepressure discharge efficiency of nano-thermites. The DTA-TGA, Zeta-size analysis and FTIR technique were performed to characterize the Bi2O3 particles. The self-assembly of Aluminum and Bi2O3 was conducted in sonic bath with appropriate solvents and linkers. The resultant thermite pressure discharge values were tested in modified Parr reactor. In general, the self-assembled thermites give much higher-pressure discharge values than the thermites prepared with conventional roll-mixing technique.

Michael K. Scullin: Psi Chi/APA Edwin B. Newman Graduate Research Award.

PubMed

2011-11-01

Presents Michael K. Scullin as the 2011 winner of the American Psychological Association Psi Chi/APA Edwin B. Newman Graduate Research Award. "For an outstanding research paper that examines the relationship between prospective memory in executing a goal and various lapses of time from 20 minutes up to a 12- hour wake delay and a 12-hour sleep delay. The results suggest that consolidation processes active during sleep increase the probability of goal execution. The paper, titled 'Remembering to Execute a Goal: Sleep On It!' was published in Psychological Science in 2010 and was the basis for Michael K. Scullin's selection as the recipient of the 2011 Psi Chi/APA Edwin B. Newman Graduate Research Award. Mark A. McDaniel, PhD, served as faculty research advisor." (PsycINFO Database Record (c) 2011 APA, all rights reserved). 2011 APA, all rights reserved

Amplexicaule A exerts anti-tumor effects by inducing apoptosis in human breast cancer

PubMed Central

Shu, Guangwen; Wan, Dingrong; He, Feng; Loaec, Morgann; Ding, Yali; Li, Jun; Dovat, Sinisa; Yang, Gaungzhong; Song, Chunhua

2016-01-01

Chemotherapy is the main treatment for patients with breast cancer metastases, but natural alternatives have been receiving attention for their potential as novel anti-tumor reagents. Amplexicaule A (APA) is a flavonoid glucoside isolated from rhizomes of Polygonum amplexicaule D. Don var. sinense Forb (PADF). We found that APA has anti-tumor effects in a breast cancer xenograft mouse model and induces apoptosis in breast cancer cell lines. APA increased levels of cleaved caspase-3,-8,-9 and PARP, which resulted from suppression of MCL-1 and BCL-2 expression in the cells. APA also inactivated the Akt/mTOR pathway in breast cancer cells. Thus, APA exerts a strong anti-tumor effect on breast cancer cells, most likely through induction of apoptosis. Our study is the first to identify this novel anti-tumor compound and provides a new strategy for isolation and separation of single compounds from herbs. PMID:26943775

A family of variable step-size affine projection adaptive filter algorithms using statistics of channel impulse response

NASA Astrophysics Data System (ADS)

Shams Esfand Abadi, Mohammad; AbbasZadeh Arani, Seyed Ali Asghar

2011-12-01

This paper extends the recently introduced variable step-size (VSS) approach to the family of adaptive filter algorithms. This method uses prior knowledge of the channel impulse response statistic. Accordingly, optimal step-size vector is obtained by minimizing the mean-square deviation (MSD). The presented algorithms are the VSS affine projection algorithm (VSS-APA), the VSS selective partial update NLMS (VSS-SPU-NLMS), the VSS-SPU-APA, and the VSS selective regressor APA (VSS-SR-APA). In VSS-SPU adaptive algorithms the filter coefficients are partially updated which reduce the computational complexity. In VSS-SR-APA, the optimal selection of input regressors is performed during the adaptation. The presented algorithms have good convergence speed, low steady state mean square error (MSE), and low computational complexity features. We demonstrate the good performance of the proposed algorithms through several simulations in system identification scenario.

Temporal and spatial variability of dissolved organic and inorganic phosphorus, and metrics of phosphorus bioavailability in an upwelling-dominated coastal system

NASA Astrophysics Data System (ADS)

Ruttenberg, Kathleen C.; Dyhrman, Sonya T.

2005-10-01

High-frequency temporal and spatial shifts in the various dissolved P pools (total, inorganic, and organic) are linked to upwelling/relaxation events and to phytoplankton bloom dynamics in the upwelling-dominated Oregon coastal system. The presence and regulation of alkaline phosphatase activity (APA) is apparent in the bulk phytoplankton population and in studies of cell-specific APA using Enzyme Labeled Fluorescence (ELF®). Spatial and temporal variability are also evident in phytoplankton community composition and in APA. The spatial pattern of dissolved phosphorus and APA variability can be explained by bottom-controlled patterns of upwelling, and flushing times of different regions within the study area. The presence of APA in eukaryotic taxa indicates that dissolved organic phosphorus (DOP) may contribute to phytoplankton P nutrition in this system, highlighting the need for a more complete understanding of P cycling and bioavailability in the coastal ocean.

[Eyeball shape in children with emmetropia and myopia].

PubMed

Dolzhich, G I; Shurygina, I P; Shapovalova, V M

1991-01-01

In order to determine the eyeball shape, the authors have carried out ultrasonic biometry of its three major parameters, the anteroposterior axis (APA), horizontal diameter (HD), and vertical diameter (VD), and estimated the ratios of these values (APA/HD and APA/VD) in children with emmetropia (234 eyes) and those with slight and medium-grave myopia (660 eyes), aged 7 to 14. The findings evidence a compressed ellipsoidal shape of the eyeball, presenting as a vertical oval, in all subjects with emmetropic refraction, whatever their age. In myopia the eyeball shape transforms, and all the eyeball sizes are increased, but the APA size is growing more rapidly than the rest sizes, and the eyeball acquires the ball shape with a trend to an elongated ellipsoidal shape. The mean APA length in 7-14-year-old children with emmetropia was up to 23 +/- 0.15 mm, whereas in those with the ball shape of the eyeball it was distended.

Category cued recall evokes a generate-recognize retrieval process.

PubMed

Hunt, R Reed; Smith, Rebekah E; Toth, Jeffrey P

2016-03-01

The experiments reported here were designed to replicate and extend McCabe, Roediger, and Karpicke's (2011) finding that retrieval in category cued recall involves both controlled and automatic processes. The extension entailed identifying whether distinctive encoding affected 1 or both of these 2 processes. The first experiment successfully replicated McCabe et al., but the second, which added a critical baseline condition, produced data inconsistent with a 2 independent process model of recall. The third experiment provided evidence that retrieval in category cued recall reflects a generate-recognize strategy, with the effect of distinctive processing being localized to recognition. Overall, the data suggest that category cued recall evokes a generate-recognize retrieval strategy and that the subprocesses underlying this strategy can be dissociated as a function of distinctive versus relational encoding processes. (c) 2016 APA, all rights reserved).

Breastfeeding is positively associated with child intelligence even net of parental IQ.

PubMed

Kanazawa, Satoshi

2015-12-01

Some previous reviews conclude that breastfeeding is not significantly associated with increased intelligence in children once mother's IQ is statistically controlled. The conclusion may potentially have both theoretical and methodological problems. The National Child Development Study allows the examination of the effect of breastfeeding on intelligence in two consecutive generations of British children. The analysis of the first generation shows that the effect of breastfeeding on intelligence increases from Age 7 to 16. The analysis of the second generation shows that each month of breastfeeding, net of parental IQ and other potential confounds, is associated with an increase of .16 IQ points. Further analyses suggest that some previous studies may have failed to uncover the effect of breastfeeding on child intelligence because of their reliance on one IQ test. (c) 2015 APA, all rights reserved).

Differential Die-Away Instrument: Report on Fuel Assembly Mock-up Measurements with Neutron Generator

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

Goodsell, Alison Victoria; Swinhoe, Martyn Thomas; Henzl, Vladimir

2014-09-18

Fresh fuel experiments for the differential die-away (DDA) project were performed using a DT neutron generator, a 15x15 PWR fuel assembly, and nine 3He detectors in a water tank inside of a shielded cell at Los Alamos National Laboratory (LANL). Eight different fuel enrichments were created using low enriched (LEU) and depleted uranium (DU) dioxide fuel rods. A list-mode data acquisition system recorded the time-dependent signal and analysis of the DDA signal die-away time was performed. The die-away time depended on the amount of fissile material in the fuel assembly and the position of the detector. These experiments were performedmore » in support of the spent nuclear fuel Next Generation Safeguards Initiative DDA project. Lessons learned from the fresh fuel DDA instrument experiments and simulations will provide useful information to the spent fuel project.« less

Advanced scatter search approach and its application in a sequencing problem of mixed-model assembly lines in a case company

NASA Astrophysics Data System (ADS)

Liu, Qiong; Wang, Wen-xi; Zhu, Ke-ren; Zhang, Chao-yong; Rao, Yun-qing

2014-11-01

Mixed-model assembly line sequencing is significant in reducing the production time and overall cost of production. To improve production efficiency, a mathematical model aiming simultaneously to minimize overtime, idle time and total set-up costs is developed. To obtain high-quality and stable solutions, an advanced scatter search approach is proposed. In the proposed algorithm, a new diversification generation method based on a genetic algorithm is presented to generate a set of potentially diverse and high-quality initial solutions. Many methods, including reference set update, subset generation, solution combination and improvement methods, are designed to maintain the diversification of populations and to obtain high-quality ideal solutions. The proposed model and algorithm are applied and validated in a case company. The results indicate that the proposed advanced scatter search approach is significant for mixed-model assembly line sequencing in this company.

Backward assembly planning with DFA analysis

NASA Technical Reports Server (NTRS)

Lee, Sukhan (Inventor)

1995-01-01

An assembly planning system that operates based on a recursive decomposition of assembly into subassemblies, and analyzes assembly cost in terms of stability, directionality, and manipulability to guide the generation of preferred assembly plans is presented. The planning in this system incorporates the special processes, such as cleaning, testing, labeling, etc. that must occur during the assembly, and handles nonreversible as well as reversible assembly tasks through backward assembly planning. In order to increase the planning efficiency, the system avoids the analysis of decompositions that do not correspond to feasible assembly tasks. This is achieved by grouping and merging those parts that can not be decomposable at the current stage of backward assembly planning due to the requirement of special processes and the constraint of interconnection feasibility. The invention includes methods of evaluating assembly cost in terms of the number of fixtures (or holding devices) and reorientations required for assembly, through the analysis of stability, directionality, and manipulability. All these factors are used in defining cost and heuristic functions for an AO* search for an optimal plan.

Timing in audiovisual speech perception: A mini review and new psychophysical data.

PubMed

Venezia, Jonathan H; Thurman, Steven M; Matchin, William; George, Sahara E; Hickok, Gregory

2016-02-01

Recent influential models of audiovisual speech perception suggest that visual speech aids perception by generating predictions about the identity of upcoming speech sounds. These models place stock in the assumption that visual speech leads auditory speech in time. However, it is unclear whether and to what extent temporally-leading visual speech information contributes to perception. Previous studies exploring audiovisual-speech timing have relied upon psychophysical procedures that require artificial manipulation of cross-modal alignment or stimulus duration. We introduce a classification procedure that tracks perceptually relevant visual speech information in time without requiring such manipulations. Participants were shown videos of a McGurk syllable (auditory /apa/ + visual /aka/ = perceptual /ata/) and asked to perform phoneme identification (/apa/ yes-no). The mouth region of the visual stimulus was overlaid with a dynamic transparency mask that obscured visual speech in some frames but not others randomly across trials. Variability in participants' responses (~35 % identification of /apa/ compared to ~5 % in the absence of the masker) served as the basis for classification analysis. The outcome was a high resolution spatiotemporal map of perceptually relevant visual features. We produced these maps for McGurk stimuli at different audiovisual temporal offsets (natural timing, 50-ms visual lead, and 100-ms visual lead). Briefly, temporally-leading (~130 ms) visual information did influence auditory perception. Moreover, several visual features influenced perception of a single speech sound, with the relative influence of each feature depending on both its temporal relation to the auditory signal and its informational content.

Timing in Audiovisual Speech Perception: A Mini Review and New Psychophysical Data

PubMed Central

Venezia, Jonathan H.; Thurman, Steven M.; Matchin, William; George, Sahara E.; Hickok, Gregory

2015-01-01

Recent influential models of audiovisual speech perception suggest that visual speech aids perception by generating predictions about the identity of upcoming speech sounds. These models place stock in the assumption that visual speech leads auditory speech in time. However, it is unclear whether and to what extent temporally-leading visual speech information contributes to perception. Previous studies exploring audiovisual-speech timing have relied upon psychophysical procedures that require artificial manipulation of cross-modal alignment or stimulus duration. We introduce a classification procedure that tracks perceptually-relevant visual speech information in time without requiring such manipulations. Participants were shown videos of a McGurk syllable (auditory /apa/ + visual /aka/ = perceptual /ata/) and asked to perform phoneme identification (/apa/ yes-no). The mouth region of the visual stimulus was overlaid with a dynamic transparency mask that obscured visual speech in some frames but not others randomly across trials. Variability in participants' responses (∼35% identification of /apa/ compared to ∼5% in the absence of the masker) served as the basis for classification analysis. The outcome was a high resolution spatiotemporal map of perceptually-relevant visual features. We produced these maps for McGurk stimuli at different audiovisual temporal offsets (natural timing, 50-ms visual lead, and 100-ms visual lead). Briefly, temporally-leading (∼130 ms) visual information did influence auditory perception. Moreover, several visual features influenced perception of a single speech sound, with the relative influence of each feature depending on both its temporal relation to the auditory signal and its informational content. PMID:26669309

For the benefit of others: generativity and meaning in life in the elderly in four cultures.

PubMed

Hofer, Jan; Busch, Holger; Au, Alma; Poláčková Šolcová, Iva; Tavel, Peter; Tsien Wong, Teresa

2014-12-01

Generativity has been argued to be an important indicator of successful aging. Indeed, generative concern has been found to be associated with meaning in life. In the present study, this relationship is argued to be partly explained through generative goals. Moreover, the path between generative goals and meaning in life is hypothesized to be conditional on belief in the species (assessed through Machiavellianism as a proxy variable). This moderated mediation model is tested with data from 4 cultural samples: 856 Cameroonian, Czech, German, and Hong Kong Chinese participants aged at least 60 years provided information on their generative concern, generative goals, meaning in life, and Machiavellianism. Controlling for effects of relationship, level of education, everyday competence, and cognitive functioning on meaning in life, analyses confirmed the moderated mediation model in all cultural samples. That is, generative concern is partly associated with meaning in life because it leads to generative goals. In turn, these provide individuals with meaning in life. This association, however, depends on belief in the species in that meaning in life does not increase when Machiavellian attitudes compete with generative goals. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Assembly and diploid architecture of an individual human genome via single-molecule technologies

PubMed Central

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-01-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

PubMed

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-08-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

Comparison of de novo assembly statistics of Cucumis sativus L.

NASA Astrophysics Data System (ADS)

Wojcieszek, Michał; Kuśmirek, Wiktor; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Nowak, Robert M.

2017-08-01

Genome sequencing is the core of genomic research. With the development of NGS and lowering the cost of procedure there is another tight gap - genome assembly. Developing the proper tool for this task is essential as quality of genome has important impact on further research. Here we present comparison of several de Bruijn assemblers tested on C. sativus genomic reads. The assessment shows that newly developed software - dnaasm provides better results in terms of quantity and quality. The number of generated sequences is lower by 5 - 33% with even two fold higher N50. Quality check showed reliable results were generated by dnaasm. This provides us with very strong base for future genomic analysis.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

PubMed Central

2013-01-01

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS. PMID:23320958

Pistol-shaped dosimeter charger

DOEpatents

Maples, R.A.

A pistol-shaped charger assembly clamps a cylindrical radiation dosimeter against one edge thereof. A triggerlike lever on the handgrip of the assembly is manually pivoted to actuate a piezoelectric current generator held in the handgrip and thereby charge the dosimeter.

Pistol-shaped dosimeter charger

DOEpatents

Maples, Robert A.

1985-01-01

A pistol-shaped charger assembly clamps a cylindrical radiation dosimeter against one edge thereof. A triggerlike lever on the handgrip of the assembly is manually pivoted to actuate a piezoelectric current generator held in the handgrip and thereby charge the dosimeter.

Programming function into mechanical forms by directed assembly of silk bulk materials

PubMed Central

Patel, Nereus; Duggan, Thomas; Perotto, Giovanni; Shirman, Elijah; Li, Chunmei; Kaplan, David L.; Omenetto, Fiorenzo G.

2017-01-01

We report simple, water-based fabrication methods based on protein self-assembly to generate 3D silk fibroin bulk materials that can be easily hybridized with water-soluble molecules to obtain multiple solid formats with predesigned functions. Controlling self-assembly leads to robust, machinable formats that exhibit thermoplastic behavior consenting material reshaping at the nanoscale, microscale, and macroscale. We illustrate the versatility of the approach by realizing demonstrator devices where large silk monoliths can be generated, polished, and reshaped into functional mechanical components that can be nanopatterned, embed optical function, heated on demand in response to infrared light, or can visualize mechanical failure through colorimetric chemistries embedded in the assembled (bulk) protein matrix. Finally, we show an enzyme-loaded solid mechanical part, illustrating the ability to incorporate biological function within the bulk material with possible utility for sustained release in robust, programmably shapeable mechanical formats. PMID:28028213

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

Meinke, Rainer

A method for manufacture of a conductor assembly. The assembly is of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In an example embodiment one or more first coil rows are formed. The assembly has multiple coil rows about an axis with outer coil rows formed about inner coil rows. A determination is made of deviations from specifications associated with the formed one or more first coil rows. One or more deviations correspond to a magnitude of a multipole field component which departsmore » from a field specification. Based on the deviations, one or more wiring patterns are generated for one or more second coil rows to be formed about the one or more first coil rows. The one or more second coil rows are formed in the assembly. The magnitude of each multipole field component that departs from the field specification is offset.« less

75 FR 49820 - Delegation of Authority to the Director of Its Division of Enforcement

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-16

... the Administrative Procedure Act (``APA'') (5 U.S.C. 553(b)(3)(A)), that this amendment relates solely..., the provisions of the APA regarding notice of the proposed rulemaking, opportunities for public..., which apply only when notice and comment are required by the APA or other law, 5 U.S.C. 603, are not...

78 FR 37132 - Approval and Promulgation of Implementation Plans; Revised Format for Materials Being...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-20

... the ``good cause'' exemption in section 553(b)(3)(B) of the Administrative Procedure Act (APA) which... recodification and miscellaneous revisions to the Florida SIP. EPA also finds that there is good cause under APA.... Section 553(d)(3) of the APA allows an effective date less than 30 days after publication ``as otherwise...

77 FR 64908 - Extension of Administrative Stay; Approval and Promulgation of Implementation Plans; New Mexico...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-24

... the Administrative Procedure Act (APA). EPA previously stayed this rule for 90 days, from July 16... Pursuant to section 705 of the APA, the EPA hereby extends the existing administrative stay of the... obligations under the terms of the NM FIP that arise during the 135 day period. Under section 705 of the APA...

78 FR 46498 - Delegation of Authority to Director of the Division of Enforcement

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-01

...: The Commission finds, in accordance with the Administrative Procedure Act (``APA'') 5 U.S.C. 553(b)(3... relate to a substantive rule. Accordingly, the provisions of the APA regarding notice of rulemaking..., which apply only when notice and comment are required by the APA or other law, 5 U.S.C. 603, are not...

78 FR 72033 - Approval and Promulgation of Implementation Plans; Florida: General Requirements and Gasoline...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-02

... in section 553(b)(3)(B) of the Administrative Procedure Act (APA) which, upon finding ``good cause.... EPA also finds that there is good cause under APA section 553(d)(3) for this correction to become effective on the date of publication of this action. Section 553(d)(3) of the APA allows an effective date...

76 FR 16852 - Hours of Service (HOS) of Drivers; Assessing the Safety Impact of the Exemption From the 14-Hour...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-25

... previous decision granting certain members of the American Pyrotechnics Association (APA) an exemption from... renewed (49 CFR 381.300(b)). APA's Independence Day Operations and the Exemption from 49 CFR 395.3(a)(2) APA is a trade association that represents the domestic fireworks industry. Its members have been...

77 FR 32407 - Medicare Program; Changes to the Medicare Advantage and the Medicare Prescription Drug Benefit...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-01

... with section 553(b) of the Administrative Procedure Act (APA) (5 U.S.C. 553(b)). However, we can waive... the finding and the reasons therefore in the notice. Section 553(b) of the APA ordinarily requires a... constitute a rulemaking that would be subject to the APA notice and comment or delayed effective date...

77 FR 71687 - Federal Employees' Group Life Insurance Program: Court Orders Prior to July 22, 1998

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-04

... preliminarily approved by the Court. Under Section 553(b) of the Administrative Procedure Act (APA) (5 U.S.C... interest. In addition, the APA exempts interpretative rules from proposed rulemaking procedures. This rule... asserts that good cause exists to implement this rule as an interim rule under the APA, 5 U.S.C. 553(b...

76 FR 39769 - Delegation of Authority to the Director of Its Division of Enforcement

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-07

... finds, in accordance with the Administrative Procedure Act (``APA'') (5 U.S.C. 553(b)(3)(A)), that this... rule. Accordingly, the provisions of the APA regarding notice of the proposed rulemaking, opportunities... Flexibility Act, which apply only when notice and comment are required by the APA or other law, 5 U.S.C. 603...

75 FR 75625 - Approval and Promulgation of Implementation Plans; North Carolina: Greensboro-Winston-Salem-High...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-06

...'' exemption in section 553(b)(3)(B) of the Administrative Procedure Act (APA) which, upon finding ``good cause... addition of paragraph (e) to 40 CFR 52.1781. EPA also finds that there is good cause under APA section 553...(d)(3) of the APA allows an effective date less than 30 days after publication ``as otherwise...

78 FR 68782 - Public Meeting on the Improve Tracking of Workplace Injuries and Illnesses Proposed Rule

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-15

... notice and comments requirements in the Administrative Procedure Act (APA) (5 U.S.C. 553) rather than... health standards. Section 553 of the APA, which governs this proposal, does not require a public hearing... presentation'' (5 U.S.C. 553(c)) (emphasis added). To promulgate a proposed regulation, the APA requires the...

75 FR 3870 - Approval and Promulgation of Implementation Plans; South Carolina; Approval of Section 110(a)(1...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-25

... Administrative Procedure Act (APA) which, upon finding ``good cause,'' authorizes agencies to dispense with... submittal (74 FR 26099). EPA also finds that there is good cause under APA section 553(d)(3) for this... APA allows an effective date less than 30 days after publication ``as otherwise provided by the agency...

78 FR 15882 - Medicare Program; Hospital Inpatient Prospective Payment Systems for Acute Care Hospitals and the...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-13

... effect in accordance with section 553(b) of the Administrative Procedure Act (APA) (5 U.S.C. 553(b... incorporates a statement of the finding and the reasons therefore in the notice. Section 553(b) of the APA..., this correcting document does not constitute a rulemaking that would be subject to the APA notice and...

78 FR 4029 - Treasury Tax and Loan Depositaries; Depositaries and Financial Agents of the Government

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-18

... Administrative Procedure Act (APA) requires a federal agency to provide the public with notice and the.... They make minor changes which are statutorily required by the Dodd-Frank Act. The APA permits an agency... under section 553(b)(3)(B) of the APA.\\3\\ NCUA also finds good cause to dispense with the 30-day delayed...

78 FR 67307 - Approval and Promulgation of Implementation Plans; Tennessee; Infrastructure Requirements for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-12

...'' exemption in section 553(b)(3)(B) of the Administrative Procedure Act (APA) which, upon finding ``good cause.... EPA also finds that there is good cause under APA section 553(d)(3) for this correction to become effective on the date of publication of this action. Section 553(d)(3) of the APA allows an effective date...

Wood Products Consumption for Industrial Markets in the United States, Testing a New Research Method

Treesearch

Craig Adair; David B. McKeever

2013-01-01

In early 2012, APA-The Engineered Wood Association conducted studies of three industries: institutional furniture, motor homes, and travel trailers and campers. The survey procedure was the same as that used by APA for many years. Lists of individual manufacturers were purchased, a telephone interviewing company was hired to administer a questionnaire, and APA...

The APA Task Force on Statistical Inference (TFSI) Report as a Framework for Teaching and Evaluating Students' Understandings of Study Validity.

ERIC Educational Resources Information Center

Thompson, Bruce

Web-based statistical instruction, like all statistical instruction, ought to focus on teaching the essence of the research endeavor: the exercise of reflective judgment. Using the framework of the recent report of the American Psychological Association (APA) Task Force on Statistical Inference (Wilkinson and the APA Task Force on Statistical…

Asian/Pacific American Women in Higher Education Administration: Doubly Bound, Doubly Scarce. Issues in Policy, No. 9.

ERIC Educational Resources Information Center

Montez, Joni Mina

This policy brief examines the issue of Asian/Pacific American (APA) women in higher education administration. It reports that APA women face the "double bind" of discrimination because of their minority status and because they are female, and that compared to other minority women fewer APA women enter the education profession. The paper argues…

Are Adolescents Less Mature than Adults?: Minors' Access to Abortion, the Juvenile Death Penalty, and the Alleged APA "Flip-Flop"

ERIC Educational Resources Information Center

Steinberg, Laurence; Cauffman, Elizabeth; Woolard, Jennifer; Graham, Sandra; Banich, Marie

2009-01-01

The American Psychological Association's (APA's) stance on the psychological maturity of adolescents has been criticized as inconsistent. In its Supreme Court amicus brief in "Roper v. Simmons" (2005), which abolished the juvenile death penalty, APA described adolescents as developmentally immature. In its amicus brief in "Hodgson v. Minnesota"…

2012 Annual report of the American Psychological Association.

PubMed

2013-01-01

Provides the 2012 Annual Report of the American Psychological Association. In 2012, APA celebrated its 120th anniversary. It has grown from its original 31 members to the largest association of psychologists in the United States and a worldwide leader within the discipline. This edition of the report introduces each directorate and office within APA and talks about their goals and objectives. the president of APA, Dr. Norman Anderson, also gives a brief report which updates you on the activities of the association during its 120th anniversary as the professional home for psychologists and an advocate for the discipline. PsycINFO Database Record (c) 2013 APA, all rights reserved.

IL-1RA gene-transfected bone marrow-derived mesenchymal stem cells in APA microcapsules could alleviate rheumatoid arthritis.

PubMed

Hu, Jianhua; Li, Hongjian; Chi, Guanhao; Yang, Zhao; Zhao, Yi; Liu, Wei; Zhang, Chao

2015-01-01

In order to investigate the encapsulation of interleukin 1 receptor antagonist (IL-RA) gene-modified mesenchymal stem cells (MSCs) in alginate-poly-L-lysine (APA) microcapsules for the persistent delivery of interleukin 1 receptor antagonist (IL-RA) to treat Rheumatoid arthritis (RA). We transfect mesenchymal stem cells with IL-RA gene, and quantify the IL-RA proteins released from the encapsulated cells followed by microencapsulation of recombinant mesenchymal stem cells, and thus observe the permeability of APA microcapsules and evaluate clinical effects after induction and treatment of collagen-induced arthritis (CIA). The concentration of IL-RA in the supernatant was determined by IL-RA ELISA kit by run in technical triplicates using samples from three separate mice. Encapsulated IL-RA gene-transfected cells were capable of constitutive delivery of IL-RA proteins for at least 30 days. Moreover, the APA microcapsules could inhibit the permeation of fluorescein isothiocyanate-conjuncted immunoglobulin G. Also, it has been found that the APA microcapsules can significantly attenuate collagen induced arthritis after delivering of APA microcapsules to rats. Our results demonstrated that the nonautologous IL-RA gene-transfected stem cells are of potential utility for RA therapy.

Adolescent-to-Parent Abuse as a Form of "Domestic Violence": A Conceptual Review.

PubMed

Holt, Amanda

2016-12-01

Across the Global North, adolescent-to-parent abuse (APA) is becoming recognized as a significant social problem and is receiving attention from researchers, policymakers, and practitioners who work in the intersecting fields of juvenile justice, child protection, and domestic violence. One of the key questions shaping current debates concerns the extent to which APA maps onto the contours of domestic violence, in terms of research and theory, policy, and practice. In particular, to what extent can our established ways of working with domestic violence be applied when working with APA? This article begins by reviewing definitions and prevalence rates of APA. It then considers how the problem fits into the "family conflicts" and "gender-based violence" paradigms that are most frequently used to conceptualize domestic violence. The article then examines how APA represents a similar but distinct phenomenon to adult-instigated domestic violence and identifies how its departures represent particular challenges in working toward its elimination. The article concludes by reviewing intervention programs that work with APA and exploring some of the ways in which they adopt and reject elements of good practice from the domestic violence practice field. © The Author(s) 2015.

The prevalence of CTNNB1 mutations in primary aldosteronism and consequences for clinical outcomes.

PubMed

Wu, Vin-Cent; Wang, Shuo-Meng; Chueh, Shih-Chieh Jeff; Yang, Shao-Yu; Huang, Kuo-How; Lin, Yen-Hung; Wang, Jian-Jhong; Connolly, Rory; Hu, Ya-Hui; Gomez-Sanchez, Celso E; Peng, Kang-Yung; Wu, Kwan-Dun

2017-01-19

Constitutive activation of the Wnt pathway/β-catenin signaling may be important in aldosterone-producing adenoma (APA). However, significant gaps remain in our understanding of the prevalence and clinical outcomes after adrenalectomy in APA patients harboring CTNNB1 mutations. The molecular expression of CYP11B2 and gonadal receptors in adenomas were also explored. Adenomas from 219 APA patients (95 men; 44.2%; aged 50.5 ± 11.9 years) showed a high rate of somatic mutations (n = 128, 58.4%). The majority of them harbored KCNJ5 mutations (n = 116, 52.9%); 8 patients (3.7%, 6 women) had CTNNB1 mutations. Patients with APAs harboring CTNNB1 mutations were older and had shorter duration of hypertension. After adrenalectomy, CTNNB1 mutation carriers had a higher possibility (87.5%) of residual hypertension than other APA patients. APAs harboring CTNNB1 mutations have heterogeneous staining of β-catenin and variable expression of gonadal receptors and both CYP11B1 and CYP11B2. This suggests that CTNNB1 mutations may be more related to tumorigenesis rather than excessive aldosterone production.

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights.

PubMed

Warnke-Sommer, Julia; Ali, Hesham

2016-05-06

The assembly of Next Generation Sequencing (NGS) reads remains a challenging task. This is especially true for the assembly of metagenomics data that originate from environmental samples potentially containing hundreds to thousands of unique species. The principle objective of current assembly tools is to assemble NGS reads into contiguous stretches of sequence called contigs while maximizing for both accuracy and contig length. The end goal of this process is to produce longer contigs with the major focus being on assembly only. Sequence read assembly is an aggregative process, during which read overlap relationship information is lost as reads are merged into longer sequences or contigs. The assembly graph is information rich and capable of capturing the genomic architecture of an input read data set. We have developed a novel hybrid graph in which nodes represent sequence regions at different levels of granularity. This model, utilized in the assembly and analysis pipeline Focus, presents a concise yet feature rich view of a given input data set, allowing for the extraction of biologically relevant graph structures for graph mining purposes. Focus was used to create hybrid graphs to model metagenomics data sets obtained from the gut microbiomes of five individuals with Crohn's disease and eight healthy individuals. Repetitive and mobile genetic elements are found to be associated with hybrid graph structure. Using graph mining techniques, a comparative study of the Crohn's disease and healthy data sets was conducted with focus on antibiotics resistance genes associated with transposase genes. Results demonstrated significant differences in the phylogenetic distribution of categories of antibiotics resistance genes in the healthy and diseased patients. Focus was also evaluated as a pure assembly tool and produced excellent results when compared against the Meta-velvet, Omega, and UD-IDBA assemblers. Mining the hybrid graph can reveal biological phenomena captured by its structure. We demonstrate the advantages of considering assembly graphs as data-mining support in addition to their role as frameworks for assembly.

Toward a molecular programming language for algorithmic self-assembly

NASA Astrophysics Data System (ADS)

Patitz, Matthew John

Self-assembly is the process whereby relatively simple components autonomously combine to form more complex objects. Nature exhibits self-assembly to form everything from microscopic crystals to living cells to galaxies. With a desire to both form increasingly sophisticated products and to understand the basic components of living systems, scientists have developed and studied artificial self-assembling systems. One such framework is the Tile Assembly Model introduced by Erik Winfree in 1998. In this model, simple two-dimensional square 'tiles' are designed so that they self-assemble into desired shapes. The work in this thesis consists of a series of results which build toward the future goal of designing an abstracted, high-level programming language for designing the molecular components of self-assembling systems which can perform powerful computations and form into intricate structures. The first two sets of results demonstrate self-assembling systems which perform infinite series of computations that characterize computably enumerable and decidable languages, and exhibit tools for algorithmically generating the necessary sets of tiles. In the next chapter, methods for generating tile sets which self-assemble into complicated shapes, namely a class of discrete self-similar fractal structures, are presented. Next, a software package for graphically designing tile sets, simulating their self-assembly, and debugging designed systems is discussed. Finally, a high-level programming language which abstracts much of the complexity and tedium of designing such systems, while preventing many of the common errors, is presented. The summation of this body of work presents a broad coverage of the spectrum of desired outputs from artificial self-assembling systems and a progression in the sophistication of tools used to design them. By creating a broader and deeper set of modular tools for designing self-assembling systems, we hope to increase the complexity which is attainable. These tools provide a solid foundation for future work in both the Tile Assembly Model and explorations into more advanced models.

Effect of a Phonon Bottleneck on Exciton and Spin Generation in Self-Assembled In1 -xGaxAs Quantum Dots

NASA Astrophysics Data System (ADS)

Huang, Y. Q.; Buyanova, I. A.; Yang, X. J.; Murayama, A.; Chen, W. M.

2018-04-01

We provide direct experimental evidence for the effect of a phonon bottleneck on exciton and spin generation in self-assembled In0.5Ga0.5As quantum dots (QDs). With the aid of tunable laser spectroscopy, we resolve and identify efficient exciton generation channels in the QDs mediated by longitudinal-optical (LO) phonons from an otherwise inhomogeneously broadened QD emission background that suffers from the phonon bottleneck effect in exciton generation. Spin-generation efficiency is found to be enhanced under the LO-assisted excitation condition due to suppressed spin relaxation accompanying accelerated exciton generation. These findings underline the importance of fine-tuning QD energy levels that will benefit potential spin-optoelectronic applications of QDs by reducing spin loss due to the phonon bottleneck.

Solid oxide fuel cell generator with removable modular fuel cell stack configurations

DOEpatents

Gillett, J.E.; Dederer, J.T.; Zafred, P.R.; Collie, J.C.

1998-04-21

A high temperature solid oxide fuel cell generator produces electrical power from oxidation of hydrocarbon fuel gases such as natural gas, or conditioned fuel gases, such as carbon monoxide or hydrogen, with oxidant gases, such as air or oxygen. This electrochemical reaction occurs in a plurality of electrically connected solid oxide fuel cells bundled and arrayed in a unitary modular fuel cell stack disposed in a compartment in the generator container. The use of a unitary modular fuel cell stack in a generator is similar in concept to that of a removable battery. The fuel cell stack is provided in a pre-assembled self-supporting configuration where the fuel cells are mounted to a common structural base having surrounding side walls defining a chamber. Associated generator equipment may also be mounted to the fuel cell stack configuration to be integral therewith, such as a fuel and oxidant supply and distribution systems, fuel reformation systems, fuel cell support systems, combustion, exhaust and spent fuel recirculation systems, and the like. The pre-assembled self-supporting fuel cell stack arrangement allows for easier assembly, installation, maintenance, better structural support and longer life of the fuel cells contained in the fuel cell stack. 8 figs.

Solid oxide fuel cell generator with removable modular fuel cell stack configurations

DOEpatents

Gillett, James E.; Dederer, Jeffrey T.; Zafred, Paolo R.; Collie, Jeffrey C.

1998-01-01

A high temperature solid oxide fuel cell generator produces electrical power from oxidation of hydrocarbon fuel gases such as natural gas, or conditioned fuel gases, such as carbon monoxide or hydrogen, with oxidant gases, such as air or oxygen. This electrochemical reaction occurs in a plurality of electrically connected solid oxide fuel cells bundled and arrayed in a unitary modular fuel cell stack disposed in a compartment in the generator container. The use of a unitary modular fuel cell stack in a generator is similar in concept to that of a removable battery. The fuel cell stack is provided in a pre-assembled self-supporting configuration where the fuel cells are mounted to a common structural base having surrounding side walls defining a chamber. Associated generator equipment may also be mounted to the fuel cell stack configuration to be integral therewith, such as a fuel and oxidant supply and distribution systems, fuel reformation systems, fuel cell support systems, combustion, exhaust and spent fuel recirculation systems, and the like. The pre-assembled self-supporting fuel cell stack arrangement allows for easier assembly, installation, maintenance, better structural support and longer life of the fuel cells contained in the fuel cell stack.

APA efforts in promoting human rights and social justice.

PubMed

Leong, Frederick T L; Pickren, Wade E; Vasquez, Melba J T

2017-11-01

This article reviews the American Psychological Association's (APA) efforts in promoting human rights and social justice. Beginning with a historical review of the conceptualizations of human rights and social justice, the social challenges that have faced the United States over time are discussed in relation to the APA's evolving mission and strategic initiatives enacted through its boards, committees, and directorates. From early efforts on the Board for Social and Ethical Responsibility in Psychology and the Board of Ethnic Minority Affairs to the establishment of the Public Interest Directorate, the APA's efforts to address these human rights and social justice challenges through its task force reports, guidelines, and policies are described. Specifically, issues related to diversity and underrepresentation of minority group members and perspective within the APA, as well as women's issues (prochoice, violence against women, sexualization of young girls, human trafficking) were central to these efforts. These minority groups included racial and ethnic minority groups; immigrants and refugees; lesbian, gay, bisexual, transgendered, and queer individuals; and those with disabilities. Later attention shifted to broader social justice challenges within a public health perspective, such as AIDS, obesity, and violence. Also included is a brief discussion of the Hoffman Report. The article ends with a discussion of future directions for the APA's efforts related to human rights and social justice related to health disparities, violent extremism, social inequality, migration, cultural and racial diversity, and an evidence-based approach to programming. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Anti-polymer antibodies are correlated with pain and fatigue severity in patients with fibromyalgia syndrome.

PubMed

Sarzi-Puttini, Piercarlo; Atzeni, Fabiola; Di Franco, Manuela; Lama, Nicola; Batticciotto, Alberto; Iannuccelli, Cristina; Dell'Acqua, Donata; de Portu, Simona; Riccieri, Valeria; Carrabba, Mario; Buskila, Dan; Doria, Andrea; Valesini, Guido

2008-02-01

To investigate the prevalence of antipolymer antibody (APA) in patients with fibromyalgia (FM) and to examine its association with FM severity symptoms. The study population consisted of 79 FM patients and 75 controls: 32 with psoriatic arthritis and 43 with rheumatoid arthritis APA levels were indirectly assayed using a commercial ELISA kit from Corgenix (Westmister, Colorado, USA). Optical density (OD) values were recorded on duplicates of each of the reference and patient samples. Among clinical variables we investigated pain, measured according to visual analog scales (VAS: 0-100), fatigue, stiffness, anxiety, depression, all measured by VAS (0-100), and health status measured by Fibromyalgia Impact Questionnaire (FIQ). Sixteen of the 79 FM patients (20.3%) and 12/78 controls (15.4%) were positive for APAs (P = 0.536). Following ROC analysis, area under curve (AUC) was 0.49 (95% CI: 0.40, 0.58). Focusing on FM patients, we observed a correlation between APA titre and pain (tau: - 0.221; P = 0.020) and fatigue (tau: - 0.205; P = 0.032) at univariate analysis. Binomial regression analysis, controlling for clinical and demographic variables, showed that pain (PPR: 0.923; P = 0.007) and fatigue (PPR: 0.948; P = 0.024) were significantly associated with APA test sensitivity. APA test exhibited a low sensitivity in FM patients and it did not distinguish this group of patients from the controls enrolled in this study. Interestingly, positive APA test prevalence increased with less severe pain or fatigue.

A NEUTRONIC REACTOR

DOEpatents

Luebke, E.A.; Vandenberg, L.B.

1959-09-01

A nuclear reactor for producing thermoelectric power is described. The reactor core comprises a series of thermoelectric assemblies, each assembly including fissionable fuel as an active element to form a hot junction and a thermocouple. The assemblies are disposed parallel to each other to form spaces and means are included for Introducing an electrically conductive coolant between the assemblies to form cold junctions of the thermocouples. An electromotive force is developed across the entire series of the thermoelectric assemblies due to fission heat generated in the fuel causing a current to flow perpendicular to the flow of coolant and is distributed to a load outside of the reactor by means of bus bars electrically connected to the outermost thermoelectric assembly.

A Framework for the Development of Automatic DFA Method to Minimize the Number of Components and Assembly Reorientations

NASA Astrophysics Data System (ADS)

Alfadhlani; Samadhi, T. M. A. Ari; Ma’ruf, Anas; Setiasyah Toha, Isa

2018-03-01

Assembly is a part of manufacturing processes that must be considered at the product design stage. Design for Assembly (DFA) is a method to evaluate product design in order to make it simpler, easier and quicker to assemble, so that assembly cost is reduced. This article discusses a framework for developing a computer-based DFA method. The method is expected to aid product designer to extract data, evaluate assembly process, and provide recommendation for the product design improvement. These three things are desirable to be performed without interactive process or user intervention, so product design evaluation process could be done automatically. Input for the proposed framework is a 3D solid engineering drawing. Product design evaluation is performed by: minimizing the number of components; generating assembly sequence alternatives; selecting the best assembly sequence based on the minimum number of assembly reorientations; and providing suggestion for design improvement.

Evaluation of nine popular de novo assemblers in microbial genome assembly.

PubMed

Forouzan, Esmaeil; Maleki, Masoumeh Sadat Mousavi; Karkhane, Ali Asghar; Yakhchali, Bagher

2017-12-01

Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different read coverage and k-mer parameters on the quality of the assembly were also evaluated on both simulated and actual read datasets. Our results show that the performance of assemblers on real and simulated datasets could be significantly different, mainly because of coverage bias. According to outputs on actual read datasets, for all studied read coverages (of 7×, 25× and 100×), SPAdes and IDBA-UD clearly outperformed other assemblers based on NGA50 and accuracy metrics. Velvet is the most conservative assembler with the lowest NGA50 and error rate. Copyright © 2017. Published by Elsevier B.V.

7. PHOTOCOPY, PLANS, ELEVATIONS, AND SECTION DRAWING FOR MISSILE TEST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. PHOTOCOPY, PLANS, ELEVATIONS, AND SECTION DRAWING FOR MISSILE TEST AND ASSEMBLY BUILDING. - NIKE Missile Base SL-40, Missile Test & Assembly Building, South end of launch area, northeast of Generator Building No. 3, Hecker, Monroe County, IL

A Monte Carlo studies of the entrance foil material in a target assembly for FDG production

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

Merouani, A.; El Khayati, N.; EL Ghayour, A.

2015-07-01

In this work, a Monte Carlo simulation was performed for different entrance foil Materials in the target assembly for [{sup 18}F] FDG production, to investigate the neutron generations in the entrance foil. However, the objective is to study a materials that has the more or less similar mechanical properties as the Havar{sup R} foil with less generation of secondary particles and without affecting, the yield of FDG production. (authors)

Peptide assembly-driven metal-organic framework (MOF) motors for micro electric generators.

PubMed

Ikezoe, Yasuhiro; Fang, Justin; Wasik, Tomasz L; Uemura, Takashi; Zheng, Yongtai; Kitagawa, Susumu; Matsui, Hiroshi

2015-01-14

Peptide-metal-organic framework (Pep-MOF) motors, whose motions are driven by anisotropic surface tension gradients created via peptide self-assembly around frameworks, can rotate microscopic rotors and magnets fast enough to generate an electric power of 0.1 μW. A new rigid Pep-MOF motor can be recycled by refilling the peptide fuel into the nanopores of the MOF. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Practical computational toolkits for dendrimers and dendrons structure design.

PubMed

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

Practical computational toolkits for dendrimers and dendrons structure design

NASA Astrophysics Data System (ADS)

Martinho, Nuno; Silva, Liana C.; Florindo, Helena F.; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

Scaffold Free Bio-orthogonal Assembly of 3-Dimensional Cardiac Tissue via Cell Surface Engineering

NASA Astrophysics Data System (ADS)

Rogozhnikov, Dmitry; O'Brien, Paul J.; Elahipanah, Sina; Yousaf, Muhammad N.

2016-12-01

There has been tremendous interest in constructing in vitro cardiac tissue for a range of fundamental studies of cardiac development and disease and as a commercial system to evaluate therapeutic drug discovery prioritization and toxicity. Although there has been progress towards studying 2-dimensional cardiac function in vitro, there remain challenging obstacles to generate rapid and efficient scaffold-free 3-dimensional multiple cell type co-culture cardiac tissue models. Herein, we develop a programmed rapid self-assembly strategy to induce specific and stable cell-cell contacts among multiple cell types found in heart tissue to generate 3D tissues through cell-surface engineering based on liposome delivery and fusion to display bio-orthogonal functional groups from cell membranes. We generate, for the first time, a scaffold free and stable self assembled 3 cell line co-culture 3D cardiac tissue model by assembling cardiomyocytes, endothelial cells and cardiac fibroblast cells via a rapid inter-cell click ligation process. We compare and analyze the function of the 3D cardiac tissue chips with 2D co-culture monolayers by assessing cardiac specific markers, electromechanical cell coupling, beating rates and evaluating drug toxicity.

Redesigning assembly stations using ergonomic methods as a lean tool.

PubMed

Eswaramoorthi, M; John, Mervyn; Rajagopal, C Arjun; Prasad, P S S; Mohanram, P V

2010-01-01

With the current state of the global economy, demand for various products plummeting. To sustain in the market, companies have to reduce cost and improve quality. Today, companies have started implementing new philosophies like TQM, TPM, six sigma and lean manufacturing techniques to remain competitive in the market. Lean manufacturing is an emerging philosophy which continuously strives to reduce waste. The main objective of analyzing the assembly line with a lean perspective is to identify the areas related to human interface with other systems that could lead to the generation of waste. Improper workplace design leads to unreasonable mental or physical burden and results in waste generation like slow work (delay and inventory), and defects, which is named as muri waste. An attempt has been made in this paper to locate muri waste and create a "Lean assembly line". The proposed method, based on the use of Rapid Upper Limb Assessment (RULA) with CATIA V5 platform, has allowed the measurement of a large set of operator posture parameters and assessment of ergonomic stresses. Based on the results, the process stations in the assembly line were redesigned to prevent the generation of waste.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2016-01-01

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

Meiosis-Specific Stable Binding of Augmin to Acentrosomal Spindle Poles Promotes Biased Microtubule Assembly in Oocytes

PubMed Central

Colombié, Nathalie; Głuszek, A. Agata; Meireles, Ana M.; Ohkura, Hiroyuki

2013-01-01

In the oocytes of many animals including humans, the meiotic spindle assembles without centrosomes. It is still unclear how multiple pathways contribute to spindle microtubule assembly, and whether they are regulated differently in mitosis and meiosis. Augmin is a γ-tubulin recruiting complex which “amplifies” spindle microtubules by generating new microtubules along existing ones in mitosis. Here we show that in Drosophila melanogaster oocytes Augmin is dispensable for chromatin-driven assembly of bulk spindle microtubules, but is required for full microtubule assembly near the poles. The level of Augmin accumulated at spindle poles is well correlated with the degree of chromosome congression. Fluorescence recovery after photobleaching shows that Augmin stably associates with the polar regions of the spindle in oocytes, unlike in mitotic cells where it transiently and uniformly associates with the metaphase spindle. This stable association is enhanced by γ-tubulin and the kinesin-14 Ncd. Therefore, we suggest that meiosis-specific regulation of Augmin compensates for the lack of centrosomes in oocytes by actively biasing sites of microtubule generation within the spindle. PMID:23785300

The combination of direct and paired link graphs can boost repetitive genome assembly

PubMed Central

Shi, Wenyu; Ji, Peifeng

2017-01-01

Abstract Currently, most paired link based scaffolding algorithms intrinsically mask the sequences between two linked contigs and bypass their direct link information embedded in the original de Bruijn assembly graph. Such disadvantage substantially complicates the scaffolding process and leads to the inability of resolving repetitive contig assembly. Here we present a novel algorithm, inGAP-sf, for effectively generating high-quality and continuous scaffolds. inGAP-sf achieves this by using a new strategy based on the combination of direct link and paired link graphs, in which direct link is used to increase graph connectivity and to decrease graph complexity and paired link is employed to supervise the traversing process on the direct link graph. Such advantage greatly facilitates the assembly of short-repeat enriched regions. Moreover, a new comprehensive decision model is developed to eliminate the noise routes accompanying with the introduced direct link. Through extensive evaluations on both simulated and real datasets, we demonstrated that inGAP-sf outperforms most of the genome scaffolding algorithms by generating more accurate and continuous assembly, especially for short repetitive regions. PMID:27924003

Assembly of barcode-like nucleic acid nanostructures.

PubMed

Wang, Pengfei; Tian, Cheng; Li, Xiang; Mao, Chengde

2014-10-15

Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

75 FR 75626 - Approval and Promulgation of Implementation Plans; North Carolina: Hickory-Morganton-Lenoir...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-06

...'' exemption in section 553(b)(3)(B) of the Administrative Procedure Act (APA) which, upon finding ``good cause... approve the addition of paragraph (f) to 40 CFR 52.1781. EPA also finds that there is good cause under APA.... Section 553(d)(3) of the APA allows an effective date less than 30 days after publication ``as otherwise...

77 FR 70687 - Approval and Promulgation of Implementation Plans; Florida; Section 128 and 110(a)(2)(E)(ii) and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-27

... Administrative Procedure Act (APA) which, upon finding ``good cause,'' authorizes agencies to dispense with... NAAQS into the Florida SIP. EPA also finds that there is good cause under APA section 553(d)(3) for this correction to become effective on the date of publication of this action. Section 553(d)(3) of the APA allows...

77 FR 4908 - Medicare Program; Hospital Inpatient Prospective Payment Systems for Acute Care Hospitals and the...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-01

... with section 553(b) of the Administrative Procedure Act (APA) (5 U.S.C. 553(b)). However, we can waive... the finding and the reasons therefore in the notice. Section 553(b) of the APA ordinarily requires a... document does not constitute a rulemaking that would be subject to the APA notice and comment or delayed...

The Language of Scholarship: How to Rapidly Locate and Avoid Common APA Errors.

PubMed

Freysteinson, Wyona M; Krepper, Rebecca; Mellott, Susan

2015-10-01

This article is relevant for nurses and nursing students who are writing scholarly documents for work, school, or publication and who have a basic understanding of American Psychological Association (APA) style. Common APA errors on the reference list and in citations within the text are reviewed. Methods to quickly find and reduce those errors are shared. Copyright 2015, SLACK Incorporated.

77 FR 65495 - Medicare Program; Hospital Inpatient Prospective Payment Systems for Acute Care Hospitals and the...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-29

... effect in accordance with section 553(b) of the Administrative Procedure Act (APA) (5 U.S.C. 553(b... incorporates a statement of the finding and the reasons therefore in the notice. Section 553(d) of the APA... document does not constitute a rule that would be subject to the APA notice and comment or delayed...

Informed Consent and Clinical Research Involving Children and Adolescents: Implications of the Revised APA Ethics Code and HIPAA

ERIC Educational Resources Information Center

Fisher, Celia B.

2004-01-01

In 2003, 2 new sets of rules and regulations affecting the conduct of clinical research involving children and adolescents went into effect: the revised American Psychological Association's (APA) Ethical Principles of Psychologists and Code of Conduct (APA, 2002; effective June 1, 2003) and the Privacy Rule (45 CFR Part 160 and A and E of Part…

Self-assembly strategies for the synthesis of functional nanostructured materials

NASA Astrophysics Data System (ADS)

Perego, M.; Seguini, G.

2016-06-01

Self-assembly is the autonomous organization of components into patterns or structures without human intervention. This is the approach followed by nature to generate living cells and represents one of the practical strategies to fabricate ensembles of nanostructures. In static self-assembly the formation of ordered structures could require energy but once formed the structures are stable. The introduction of additional regular features in the environment could be used to template the self-assembly guiding the organization of the components and determining the final structure they form. In this regard self-assembly of block copolymers represents a potent platform for fundamental studies at the nanoscale and for application-driven investigation as a tool to fabricate functional nanostructured materials. Block copolymers can hierarchically assemble into chemically distinct domains with size and periodicity on the order of 10nm or below, offering a potentially inexpensive route to generate large-area nanostructured materials. The final structure characteristics of these materials are dictated by the properties of the elementary block copolymers, like chain length, volume fraction or degree of block incompatibility. Modern synthetic chemistry offers the possibility to design these macromolecules with very specific length scales and geometries, directly embodying in the block copolymers the code that drives their self- assembling process. The understanding of the kinetics and thermodynamics of the block copolymer self-assembly process in the bulk phase as well as in thin films represents a fundamental prerequisite toward the exploitation of these materials. Incorporating block copolymer into device fabrication procedures or directly into devices, as active elements, will lead to the development of a new generation of devices fabricated using the fundamental law of nature to our advantage in order to minimize cost and power consumption in the fabrication process. Moreover the capability to precisely organize these nano-objects on appropriate substrates is the key point to support the technological development of new device concepts with predictable characteristics based on these nano-materials. In the next coming years this area of research, at the intersection between fundamental science and technology, is expected to disclose additional insights in the physics of the self-assembly process and to delineate unforeseen applications for these exciting materials.

Interim status report on lead-cooled fast reactor (LFR) research and development.

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

Tzanos, C. P.; Sienicki, J. J.; Moisseytsev, A.

2008-03-31

This report discusses the status of Lead-Cooled Fast Reactor (LFR) research and development carried out during the first half of FY 2008 under the U.S. Department of Energy Generation IV Nuclear Energy Systems Initiative. Lead-Cooled Fast Reactor research and development has recently been transferred from Generation IV to the Reactor Campaign of the Global Nuclear Energy Partnership (GNEP). Another status report shall be issued at the end of FY 2008 covering all of the LFR activities carried out in FY 2008 for both Generation IV and GNEP. The focus of research and development in FY 2008 is an initial investigationmore » of a concept for a LFR Advanced Recycling Reactor (ARR) Technology Pilot Plant (TPP)/demonstration test reactor (demo) incorporating features and operating conditions of the European Lead-cooled SYstem (ELSY) {approx} 600 MWe lead (Pb)-cooled LFR preconceptual design for the transmutation of waste and central station power generation, and which would enable irradiation testing of advanced fuels and structural materials. Initial scoping core concept development analyses have been carried out for a 100 MWt core composed of sixteen open-lattice 20 by 20 fuel assemblies largely similar to those of the ELSY preconceptual fuel assembly design incorporating fuel pins with mixed oxide (MOX) fuel, central control rods in each fuel assembly, and cooled with Pb coolant. For a cycle length of three years, the core is calculated to have a conversion ratio of 0.79, an average discharge burnup of 108 MWd/kg of heavy metal, and a burnup reactivity swing of about 13 dollars. With a control rod in each fuel assembly, the reactivity worth of an individual rod would need to be significantly greater than one dollar which is undesirable for postulated rod withdrawal reactivity insertion events. A peak neutron fast flux of 2.0 x 10{sup 15} (n/cm{sup 2}-s) is calculated. For comparison, the 400 MWt Fast Flux Test Facility (FFTF) achieved a peak neutron fast flux of 7.2 x 10{sup 15} (n/cm{sup 2}-s) and the initially 563 MWt PHENIX reactor attained 2.0 x 10{sup 15} (n/cm{sup 2}-s) before one of three intermediate cooling loops was shut down due to concerns about potential steam generator tube failures. The calculations do not assume a test assembly location for advanced fuels and materials irradiation in place of a fuel assembly (e.g., at the center of the core); the calculations have not examined whether it would be feasible to replace the central assembly by a test assembly location. However, having only fifteen driver assemblies implies a significant effect due to perturbations introduced by the test assembly. The peak neutron fast flux is low compared with the fast fluxes previously achieved in FFTF and PHENIX. Furthermore, the peak neutron fluence is only about half of the limiting value (4 x 10{sup 23} n/cm{sup 2}) typically used for ferritic steels. The results thus suggest that a larger power level (e.g., 400 MWt) and a larger core would be better for a TPP based upon the ELSY fuel assembly design and which can also perform irradiation testing of advanced fuels and materials. In particular, a core having a higher power level and larger dimensions would achieve a suitable average discharge burnup, peak fast flux, peak fluence, and would support the inclusion of one or more test assembly locations. Participation in the Generation IV International Forum Provisional System Steering Committee for the LFR is being maintained throughout FY 2008. Results from the analysis of samples previously exposed to flowing lead-bismuth eutectic (LBE) in the DELTA loop are summarized and a model for the oxidation/corrosion kinetics of steels in heavy liquid metal coolants was applied to systematically compare the calculated long-term (i.e., following several years of growth) oxide layer thicknesses of several steels.« less

A System for Automatically Generating Scheduling Heuristics

NASA Technical Reports Server (NTRS)

Morris, Robert

1996-01-01

The goal of this research is to improve the performance of automated schedulers by designing and implementing an algorithm by automatically generating heuristics by selecting a schedule. The particular application selected by applying this method solves the problem of scheduling telescope observations, and is called the Associate Principal Astronomer. The input to the APA scheduler is a set of observation requests submitted by one or more astronomers. Each observation request specifies an observation program as well as scheduling constraints and preferences associated with the program. The scheduler employs greedy heuristic search to synthesize a schedule that satisfies all hard constraints of the domain and achieves a good score with respect to soft constraints expressed as an objective function established by an astronomer-user.

Elaborative retrieval: Do semantic mediators improve memory?

PubMed

Lehman, Melissa; Karpicke, Jeffrey D

2016-10-01

The elaborative retrieval account of retrieval-based learning proposes that retrieval enhances retention because the retrieval process produces the generation of semantic mediators that link cues to target information. We tested 2 assumptions that form the basis of this account: that semantic mediators are more likely to be generated during retrieval than during restudy and that the generation of mediators facilitates later recall of targets. Although these assumptions are often discussed in the context of retrieval processes, we noted that there was little prior empirical evidence to support either assumption. We conducted a series of experiments to measure the generation of mediators during retrieval and restudy and to examine the effect of the generation of mediators on later target recall. Across 7 experiments, we found that the generation of mediators was not more likely during retrieval (and may be more likely during restudy), and that the activation of mediators was unrelated to subsequent free recall of targets and was negatively related to cued recall of targets. The results pose challenges for both assumptions of the elaborative retrieval account. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Intergenerational family solidarity: value differences between immigrant groups and generations.

PubMed

Merz, Eva-Maria; Ozeke-Kocabas, Ezgi; Oort, Frans J; Schuengel, Carlo

2009-06-01

Although immigrants may be more dependent on their immediate family for support, they may also experience a wider generation-gap in values regarding intergenerational solidarity, because of processes of acculturation. Based on large scale survey data (N = 2,028), differences between first and second generation immigrants in values regarding intergenerational solidarity were examined among family members in the Netherlands with an immigration background from Turkey, Morocco, Suriname, and The Dutch Antilles. Using a multilevel analytic approach, effects of family and individual characteristics on values regarding intergenerational solidarity were tested, considering the perspectives of two generations. It was found that immigrants with Moroccan and Turkish backgrounds scored higher on values with respect to intergenerational family solidarity than immigrants stemming from Suriname and The Antilles. First generation immigrants placed higher values on family solidarity compared to second generation immigrants. Additionally, religious denomination was a significant predictor of higher values with respect to intergenerational family solidarity. Immigration and acculturation may create great strains in migrant families. Policies to support the fabric of intergenerational solidarity should consider ethnic and religious background and immigration history. Copyright 2009 APA, all rights reserved.

Method and apparatus for assembling permanent magnet rotors

DOEpatents

Hsu, John S.; Adams, Donald J.

1999-01-01

A permanent magnet assembly (22) for assembly in large permanent magnet (PM) motors and generators includes a two-piece carrier (23, 24) that can be slid into a slot (13) in the rotor (10) and then secured in place using a set screw (37). The invention also provides an auxiliary carrier device (50) with guide rails (51) that line up with the teeth (12) of the rotor, so that a permanent magnet assembly (22) can be pushed first into a slot (13), and then down the slot (13) to its proper location. An auxiliary tool (50) is provided to move the permanent magnet assembly (22) into position in the slot (13) before it is secured in place. Methods of assembling and disassembling the magnet assemblies (22) in the rotor (10) are also disclosed.

Waveguide electro-optic modulators based on intrinsically polar self-assembled superlattices (SASs)

NASA Astrophysics Data System (ADS)

Liu, Zhifu; Ho, Seng Tiong; Chang, Seongsik; Zhao, Yiguang; Marks, Tobin J.; Kang, Hu; van der Boom, Milko E.; Zhu, Peiwang

2002-12-01

In this paper we describe methods of fabricating and characterizing organic electro-optic modulators based on intrinsically polar self-assembled superlattices. These structures are intrinsically acentric, and exhibit large second harmonic generation and electro-optic responses without the requirement of poling by an external electric field. A novel wet chemical protection-deprotection approach for the growth of self-assembled superlattices have been developed, and the refractive indices of self-assembled organic electro-optic superlattices may be tuned during the self-assembly process. Prototype electro-optic modulators based on chromophoric self-assembled superlattices have been designed and fabricated. The effective electro-optic coefficient of the self-assembled superlattice film in a phase modulator is estimated as about 20 pm/V at a wavelength of 1064 nm.

Rugged fiber optic probe for raman measurement

DOEpatents

O'Rourke, Patrick E.; Toole, Jr., William R.; Nave, Stanley E.

1998-01-01

An optical probe for conducting light scattering analysis is disclosed. The probe comprises a hollow housing and a probe tip. A fiber assembly made up of a transmitting fiber and a receiving bundle is inserted in the tip. A filter assembly is inserted in the housing and connected to the fiber assembly. A signal line from the light source and to the spectrometer also is connected to the filter assembly and communicates with the fiber assembly. By using a spring-loaded assembly to hold the fiber connectors together with the in-line filters, complex and sensitive alignment procedures are avoided. The close proximity of the filter assembly to the probe tip eliminates or minimizes self-scattering generated by the optical fiber. Also, because the probe can contact the sample directly, sensitive optics can be eliminated.

Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer.

PubMed

Ramos, Rommel Thiago Jucá; Carneiro, Adriana Ribeiro; Soares, Siomar de Castro; dos Santos, Anderson Rodrigues; Almeida, Sintia; Guimarães, Luis; Figueira, Flávia; Barbosa, Eudes; Tauch, Andreas; Azevedo, Vasco; Silva, Artur

2013-03-01

New sequencing platforms have enabled rapid decoding of complete prokaryotic genomes at relatively low cost. The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. One particular problem is the lack of genomes that enable reference-based assembly, such as the one used in the present study, Corynebacterium pseudotuberculosis biovar equi, which causes high economic losses in the US equine industry. The quality treatment strategy incorporated into the assembly pipeline enabled a 16-fold greater use of the sequencing data obtained compared with traditional quality filter approaches. Data preprocessing prior to the de novo assembly enabled the use of known methodologies in the next-generation sequencing data assembly. Moreover, manual curation was proved to be essential for ensuring a quality assembly, which was validated by comparative genomics with other species of the genus Corynebacterium. The present study presents a modus operandi that enables a greater and better use of data obtained from semiconductor sequencing for obtaining the complete genome from a prokaryotic microorganism, C. pseudotuberculosis, which is not a traditional biological model such as Escherichia coli. © 2012 The Authors. Published by Society for Applied Microbiology and Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

APA/APAGS Award for Distinguished Graduate Student in Professional Psychology: Luz Maria Garcini.

PubMed

2016-11-01

The APA/APAGS Award for Distinguished Graduate Student in Professional Psychology is awarded on an annual basis by the APA Board of Professional Affairs (BPA) and the American Psychological Association of Graduate Students (APAGS) to a graduate student who has demonstrated outstanding practice and application of psychology. The 2016 award winners is Luz Maria Garcini, whose commitment to the health and mental health of those recently immigrated has led to research and service that "have greatly benefited the lives of undocumented individuals in the border area of southern California." Garcini's award citation, biography, and a selected bibliography are presented here. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

An occult aldosterone-producing adenoma initially presenting as hyperosmolar hyperglycaemic state.

PubMed

Kuo, Feng-Chih; Hung, Yi-Jen; Hsieh, Chang-Hsun; Hsiao, Fone-Ching

2012-09-01

Aldosterone-producing adenoma (APA), one of the most common causes of primary hyperaldosteronism, is clinically characterized by hypertension, increased sodium retention, increased potassium excretion and altered glucose metabolism. APA can also manifest in the form of hyperosmolar hyperglycaemic state (HHS), which is a life-threatening acute diabetic complication. Infection and inadequate fluid replacement are the common precipitating and predisposing factors for the occurrence of HHS. Here, we report a case of occult APA with the initial presentation of HHS, in which an unusually rapid correction of diabetes was observed after correct diagnosis and surgical resection of the APA. To our knowledge, this is the first case with such manifestations and outcome.

7. UNIT 4, VIEW TO SOUTHEAST, SHOWING GATE MOTOR ASSEMBLY ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. UNIT 4, VIEW TO SOUTHEAST, SHOWING GATE MOTOR ASSEMBLY (CENTER), TURBINE (LEFT FOREGROUND), AND GENERATOR (BACKGROUND) - Washington Water Power Company Monroe Street Plant, Units 4 & 5, South Bank Spokane River, below Monroe Street Bridge, Spokane, Spokane County, WA

6. UNIT 5, VIEW TO SOUTHWEST, SHOWING GATE MOTOR ASSEMBLY ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

6. UNIT 5, VIEW TO SOUTHWEST, SHOWING GATE MOTOR ASSEMBLY (CENTER), TURBINE (RIGHT FOREGROUND), AND GENERATOR (BACKGROUND) - Washington Water Power Company Monroe Street Plant, Units 4 & 5, South Bank Spokane River, below Monroe Street Bridge, Spokane, Spokane County, WA