bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence that Natural Selection on Codon Usage inDrosophila pseudoobscuraVaries Across Codons
Authors: Kliman Richard M 
Published: February 2014

AbstractLike other species of Drosophila, Drosophila pseudoobscura has a distinct bias toward the usage of C- and G-ending codons. Previous studies have indicated that this bias is due, at least in part, to natural selection. Codon bias clearly differs among amino acids (and other codon classes) in Drosophila, which may reflect differences in the intensity of selection on codon usage. Ongoing natural selection on synonymous codon usage should be reflected in the shapes of the site frequency spectra of derived states at polymorphic positions. Specifically, regardless of other demographic effects on the spectrum, it should be shifted toward higher values for changes from less-preferred to more-preferred codons, and toward lower values for the converse. If the intensity of natural selection is increased, shifts in the site frequency spectra should be more pronounced. A total of 33,729 synonymous polymorphic sites on Chromosome 2 in D. pseudoobscura were analyzed. Shifts in the site frequency spectra are consistent with differential intensity of natural selection on codon usage, with stronger shifts associated with higher codon bias. The shifts, in general, are greater for polymorphic synonymous sites than for polymorphic intron sites, also consistent with natural selection. However, unlike observations in D. melanogaster, codon bias is not reduced in areas of low recombination in D. pseudoobscura; the site frequency spectrum signal for selection on codon usage remains strong in these regions. However, diversity is reduced, as expected. It is possible that estimates of low recombination reflect a recent change in recombination rate.
Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium
Authors: Rincent Renaud , Moreau Laurence , Monod HervÉ , Kuhn Estelle , Melchinger Albrecht E , Malvar Rosa A , Moreno-Gonzalez Jesus , Nicolas StÉphane , Madur Delphine , Combes ValÉrie , Dumas Fabrice , Altmann Thomas , Brunel Dominique , Ouzunova Milena , Flament Pascal , Dubreuil Pierre , Charcosset Alain , Mary-Huard Tristan 
Published: February 2014

Abstract
Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We analytically studied power in association studies by computing noncentrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high linkage disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimating the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers that are not located on the same chromosome than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and were more powerful than classical models.
Nuclear RNAi Contributes to the Silencing of Off-Target Genes and Repetitive Sequences in Caenorhabditis elegans
Authors: Zhou Xufei , Xu Fei , Mao Hui , Ji Jiaojiao , Yin Meng , Feng Xuezhu , Guang Shouhong 
Published: February 2014

Abstract
Small RNAs recognize, bind, and regulate other complementary cellular RNAs. The introduction of small RNAs to eukaryotic cells frequently results in unintended silencing of related, but not identical, RNAs: a process termed off-target gene silencing. Off-target gene silencing is one of the major concerns during the application of small RNA-based technologies for gene discovery and the treatment of human disease. Off-target gene silencing is commonly thought to be due to inherent biochemical limitations of the RNAi machinery. Here we show that following the introduction of exogenous sources of double-stranded RNA, the nuclear RNAi pathway, but not its cytoplasmic counterparts, is the primary source of off-target silencing in Caenorhabditis elegans. In addition, we show that during the normal course of growth and development the nuclear RNAi pathway regulates repetitive gene families. Therefore, we speculate that RNAi off-target effects might not be “mistakes” but rather an intentional and genetically programmed aspect of small RNA-mediated gene silencing, which might allow small RNAs to silence rapidly evolving parasitic nucleic acids. Finally, reducing off-target effects by manipulating the nuclear RNAi pathway in vivo might improve the efficacy of small RNA-based technologies.
NsdD Is a Key Repressor of Asexual Development inAspergillus nidulans
Authors: Lee Mi-Kyung , Kwon Nak-Jung , Choi Jae Min , Lee Im-Soon , Jung Seunho , Yu Jae-Hyuk 
Published: February 2014

AbstractAsexual development (conidiation) of the filamentous fungus Aspergillus nidulans occurs via balanced activities of multiple positive and negative regulators. For instance, FluG (+) and SfgA (−) govern upstream regulation of the developmental switch, and BrlA (+) and VosA (−) control the progression and completion of conidiation. To identify negative regulators of conidiation downstream of FluG-SfgA, we carried out multicopy genetic screens using sfgA deletion strains. After visually screening &gt;100,000 colonies, we isolated 61 transformants exhibiting reduced conidiation. Responsible genes were identified as AN3152 (nsdD), AN7507, AN2009, AN1652, AN5833, and AN9141. Importantly, nsdD, a key activator of sexual reproduction, was present in 10 independent transformants. Furthermore, deletion, overexpression, and double-mutant analyses of individual genes have led to the conclusion that, of the six genes, only nsdD functions in the FluG-activated conidiation pathway. The deletion of nsdD bypassed the need for fluG and flbA∼flbE, but not brlA or abaA, in conidiation, and partially restored production of the mycotoxin sterigmatocystin (ST) in the ΔfluG, ΔflbA, and ΔflbB mutants, suggesting that NsdD is positioned between FLBs and BrlA in A. nidulans. Nullifying nsdD caused formation of conidiophores in liquid submerged cultures, where wild-type strains do not develop. Moreover, the removal of both nsdD and vosA resulted in even more abundant development of conidiophores in liquid submerged cultures and high-level accumulation of brlA messenger (m)RNA even at 16 hr of vegetative growth. Collectively, NsdD is a key negative regulator of conidiation and likely exerts its repressive role via downregulating brlA.
Exploiting the Extraordinary Genetic Polymorphism ofCionafor Developmental Genetics with Whole Genome Sequencing
Authors: Abdul-Wajid Sarah , Veeman Michael T , Chiba Shota , Turner Thomas L , Smith William C 
Published: February 2014

AbstractStudies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca2+ channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.
A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data
Authors: Tamuri Asif U , Goldman Nick , dos Reis Mario 
Published: February 2014

AbstractWe develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in protein-coding genes from phylogenetic data. This improves on a previous maximum-likelihood method. Various penalty functions are used to penalize extreme estimates of the fitnesses, thus correcting overfitting by the previous method. Using a combination of computer simulation and real data analysis, we evaluate the effect of the various penalties on the estimation of the fitnesses and the distribution of S. We show the new method regularizes the estimates of the fitnesses for small, relatively uninformative data sets, but it can still recover the large proportion of deleterious mutations when present in simulated data. Computer simulations indicate that as the number of taxa in the phylogeny or the level of sequence divergence increases, the distribution of S can be more accurately estimated. Furthermore, the strength of the penalty can be varied to study how informative a particular data set is about the distribution of S. We analyze three protein-coding genes (the chloroplast rubisco protein, mammal mitochondrial proteins, and an influenza virus polymerase) and show the new method recovers a large proportion of deleterious mutations in these data, even under strong penalties, confirming the distribution of S is bimodal in these real data. We recommend the use of the new MPL approach for the estimation of the distribution of S in species phylogenies of protein-coding genes.
Neuronal Migration Is Regulated by Endogenous RNAi and Chromatin-Binding Factor ZFP-1/AF10 in Caenorhabditis elegans
Authors: Kennedy Lisa M , Grishok Alla 
Published: February 2014

Abstract
Endogenous short RNAs and the conserved plant homeodomain (PHD) zinc-finger protein ZFP-1/AF10 regulate overlapping sets of genes in Caenorhabditis elegans, which suggests that they control common biological pathways. We have shown recently that the RNAi factor RDE-4 and ZFP-1 negatively modulate transcription of the insulin/PI3 signaling-dependent kinase PDK-1 to promote C. elegans fitness. Moreover, we have demonstrated that the insulin/IGF-1-PI3K-signaling pathway regulates the activity of the DAF-16/FOXO transcription factor in the hypodermis to nonautonomously promote the anterior migrations of the hermaphrodite-specific neurons (HSNs) during embryogenesis of C. elegans. In this study, we implicate the PHD-containing isoform of ZFP-1 and endogenous RNAi in the regulation of HSN migration. ZFP-1 affects HSN migration in part through its negative effect on pdk-1 transcription and modulation of downstream DAF-16 activity. We also identify a novel role for ZFP-1 and RNAi pathway components, including RDE-4, in the regulation of HSN migration in parallel with DAF-16. Therefore, the coordinated activities of DAF-16, ZFP-1, and endogenous RNAi contribute to gene regulation during development to ensure proper neuronal positioning.
In-School Neurofeedback Training for ADHD: Sustained Improvements From a Randomized Control Trial
Authors: Steiner Naomi J. , Frenette Elizabeth C. , Rene Kirsten M. , Brennan Robert T. , Perrin Ellen C. 
Published: February 2014

OBJECTIVE:To evaluate sustained improvements 6 months after a 40-session, in-school computer attention training intervention using neurofeedback or cognitive training (CT) administered to 7- to 11-year-olds with attention-deficit/hyperactivity disorder (ADHD).METHODS:One hundred four children were randomly assigned to receive neurofeedback, CT, or a control condition and were evaluated 6 months postintervention. A 3-point growth model assessed change over time across the conditions on the Conners 3–Parent Assessment Report (Conners 3-P), the Behavior Rating Inventory of Executive Function Parent Form (BRIEF), and a systematic double-blinded classroom observation (Behavioral Observation of Students in Schools). Analysis of variance assessed community-initiated changes in stimulant medication.RESULTS:Parent response rates were 90% at the 6-month follow-up. Six months postintervention, neurofeedback participants maintained significant gains on Conners 3-P (Inattention effect size [ES] = 0.34, Executive Functioning ES = 0.25, Hyperactivity/Impulsivity ES = 0.23) and BRIEF subscales including the Global Executive Composite (ES = 0.31), which remained significantly greater than gains found among children in CT and control conditions. Children in the CT condition showed delayed improvement over immediate postintervention ratings only on Conners 3-P Executive Functioning (ES = 0.18) and 2 BRIEF subscales. At the 6-month follow-up, neurofeedback participants maintained the same stimulant medication dosage, whereas participants in both CT and control conditions showed statistically and clinically significant increases (9 mg [P = .002] and 13 mg [P &lt; .001], respectively).CONCLUSIONS:Neurofeedback participants made more prompt and greater improvements in ADHD symptoms, which were sustained at the 6-month follow-up, than did CT participants or those in the control group. This finding suggests that neurofeedback is a promising attention training treatment for children with ADHD.
Quality Control of Silicone Hydrogel Contact Lenses by Impedance Spectroscopy
Authors: Torres M. , Santhanam K.S.V. 
Published: February 2014

ABSTRACTWe wish to propose an impedance spectroscopic method for the quality control of contact lenses by measuring the pore resistance. Silicone hydrogels are excellent materials for use as contact lenses and their on eye performance is dependent on salt intrusion characteristics which are related to the pore resistance and water uptake. When the contact lenses are placed on the eye, they are expected to permeate ions and molecules to maintain ocular health. The hydrogel pores control the permeability and can be viewed as a quality control parameter. Two models are considered here: in one, the contact lenses are considered as strong rigid films with no permeability. In another, the hydrogels are having ionic permeability. We designed a silicone hydrogel contact lens attachment holder that is amenable for electrochemical impedance measurements. The electrochemical impedance measurements were carried out in an inert medium of 0.1 M Na2SO4. The impedance measurement experimental parameters used were a) AC potential 10 mV rms b) frequency range 0.1-210 kHz and c) open circuit potential of 0.207 V. The impedance variation with frequency was constructed for a number of hydrogels. The ideally acceptable silicone hydrogel contact lenses showed an impedance change with frequency in a sigmoidal fashion with a characteristic phase angle (acceptable in the range of 70-75o). The hydrogel pore resistances for the acceptable contact lenses are in the range of 4.5-11 kΩ. When the impedance showed a linear decrease or no well defined phase angle, the contact lens is considered acting as an insulator-a test for rejection. A test of the model was done with several acceptable contact lenses in the market. This study revealed interesting aspects of the influence of pulsating electric field on the silicone hydrogels.
Towards Understanding a Distinct Hydrogen Peroxide Electrocatalytic Enhancement Using Surfactant-Based Coatings on Silver
Authors: Goodison A. , Gonzalez-Macia L. , Killard A. J. , Morrin A. 
Published: February 2014

ABSTRACTThe detection of hydrogen peroxide has been shown to be very important in recent years due to its role in many industrial applications, as well as in biological reactions. Previously, a commercial silver flake-based ink (PF-410, Acheson®), when screen-printed as films to substrate and subsequently coated with surfactant and salt (sodium dodecylbenezene sulphonate (SDBS) and KCl), have been shown to significantly enhance the electrochemical reduction of hydrogen peroxide – up to 80-fold over non-modified films. In this study, an attempt to understand the effect of the silver material within the ink on the catalytic behaviour of the films, as well as the distinct change in behaviour upon modification with surfactant/salt are examined. Factors including Ag morphology, presence of dispersant and Ag material supplier are all investigated to assess their effects on the electrocatalytic breakdown of hydrogen peroxide. To do this, a range of inks were formulated from various Ag materials, e.g., flakes and nanoparticles of various sizes. These inks were then cast as coatings onto conventional glassy carbon (GC) electrodes, and their electrocatalytic behaviours, both as modified and non-modified films were studied.
Electrical Characterization of Thick InGaN Films for Photovoltaic Applications
Authors: Nakano Yoshitaka , Sang Liwen , Sumiya Masatomo 
Published: February 2014

ABSTRACTWe have electrically characterized a 300 nm-thick unintentionally-doped In0.09Ga0.91N film grown by metal-organic chemical vapor deposition on a GaN template, employing capacitance-voltage (C-V), thermal admittance spectroscopy (TAS), and steady-state photocapacitance spectroscopy (SSPC) techniques on Schottky barrier diodes. TAS measurements revealed a degenerating-like shallow-donor defect with a thermal activation energy of ∼7 meV, which most likely acts as a source of residual carriers with their concentration of ∼1017 cm-3 determined from C-V measurements. Additionally, SSPC measurements revealed two characteristic deep-level defects located at ∼2.07 and ∼3.05 eV below the conduction band, which were densely enhanced near the underlayer. These electronic defects are probably introduced by alloying InN with GaN.
Toxicity Study Needs for Quantum Dots and Nanoparticles in PV Fabrication
Authors: Sadeghimakki Bahareh , Sivoththaman Siva 
Published: February 2014

ABSTRACTQuantum dots (QDs) and nanoparticles (NPs) with tunable optoelectronic properties are actively researched for photovoltaic (PV) fabrication and will enter mainstream manufacturing in the future. The toxicology, health and safety of these new materials are not fully explored yet. In this work, the toxicological potencies of nanomaterials in PV fabrication, study needs, and metrology requirements are presented. Practical processes involving QDs and NPs developed for PV fabrication are presented. Experimental evidence on the presence of airborne nanomaterials in the condensates collected from process environment underlines the need for in-depth toxicity studies before these technologies scale up to the PV manufacturing stage. Required technical capabilities for the metrology tools to accurately detect, identify, and quantify QDs and NPs in PV manufacturing requirements are also presented based on the potential range of nanomaterials to be used in PV technology. These studies are key to develop safe techniques and processing environments, and to establish safety guidelines for PV fabrication with nanomaterials.
Magnetic Field Assisted Electrospinning of Nanofibers Using Solutions with PVDF and Fe3O4Nanoparticles
Authors: Gonzalez Juan A. , Furlan Rogerio , Lopez Raymond , Martinez Luis M. , Fachini Esteban 
Published: February 2014

ABSTRACTThis study aims at investigating the formation of nanofibers containing poly (vinylidene fluoride) (PVDF) and Fe3O4 nanoparticles using magnetic field assisted electrospinning. For this purpose, two Helmholtz coils were mounted on the electrospinning apparatus in order to create a uniform magnetic field. Different separations, angles and magnetic fields are being analyzed. Polymeric solutions containing PVDF, DMF and acetone with a concentration of 18 wt% were adopted (DMF to Acetone ratio of 3 to 1). Iron Oxide Nanopowder (Fe3O4, particle diameter of 20 nm to 30 nm) to PVDF ratios are 1:5, 1:10 and 1:15. The application of the electromagnetic field during fiber deposition results in better orientation of the polymer flow towards the grounded electrode and leads to smoother fibers with diameters in the range of hundreds of nanometers. Blisters, probably related to Fe3O4 agglomerates, were distributed on the surface of all samples of this study. A magnetic field response of the nanofibers with higher magnetic fields was clear observed. By adding more Fe3O4 to the polymeric solution the ferromagnetic response on thin films and nanofibers was improved. The analysis of circular capacitors revealed a full dielectric response.
Effect of Stoichiometry of TiN Electrode on the Switching Behavior of TiN/HfOx/TiN Structures for Resistive RAM
Authors: Morgan Katrina A. , Huang Ruomeng , Pearce Stuart , Zhong Le , Jiang Liudi , de Groot C. H. 
Published: February 2014

ABSTRACTTwo types of TiN/HfOx/TiN devices have been fabricated where the top 200nm TiN electrode has been deposited by two different sputtering methods; reactive, using a titanium target in a nitrogen environment, and non-reactive, using a titanium nitride target. Characterization of the materials shows that the reactive TiN is single-phase stoichiometric TiN with a sheet resistance of 7Ω/square. The non-reactive TiN has a sheet resistance of 300Ω/square and was found to contain significant amounts of oxygen. The resistive switching behavior differs for both devices. The reactive stoichiometric TiN device results in bipolar switching with a Roff/Ron ratio of 50. The non-reactive TiN results in unipolar switching with a Roff/Ron ratio of more than 103, however this device shows poor reproducibility. These results show that an oxygen rich layer between the top electrode and insulator affects the Roff value. It supports the theory of oxygen vacancies leading to the formation of conductive filaments.
A Quality Assurance Program for Human Immunodeficiency Virus Seropositivity Screening of Dried-Blood Spot Specimens
Authors: Hannon W. Harry , Lewis D. Sue , Jones Wanda K. , Powell Mary K. 
Published: February 2014

AbstractEpidemiologic projects have been implemented for using dried-blood spot (DBS) specimens routinely collected on filter paper from neonates as a seroepidemiologic resource to monitor seroprevalence of human immunodeficiency virus (HIV) among child-bearing women. To ensure the quality of the data base produced from the national and other epidemiologic surveys, a quality assurance program was developed to interact with all the neonatal screening laboratories. The focus of the Centers for Disease Control's quality assurance program for HIV seropositivity testing of neonatal blood specimens is to maintain a national program to produce, certify, and provide external quality control materials as DBSs on filter paper, to monitor the filter paper matrix, to operate an external performance surveillance program, and to provide other special and consultative services. The dried-blood control and surveillance materials are certified by rigorous testing for accuracy, stability, and homogeneity. Preliminary results from the first performance evaluation of screening laboratories indicated excellent performance.