bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control loop design of sequential switching shunt regulator considering the influence of double section functioning
Authors: Li Fang , You Xiaojie , Li Yan 
Published: December 2013

Sequential switching shunt regulator (S3R) has been widely used in satellites for its simple structure and high reliability. Double section functioning, which has two sections operating simultaneously, is the other operating mode of S3R beside the normal mode. It is inevitable and can lead to larger bus voltage ripple, less controllability and higher switching losses. A detailed analysis based on the double section functioning process description is given on the boundary load current, the main bus voltage ripple and the switching frequency. Considering the influence of double section functioning, a new method of control loop design of S3R is proposed based on the small single mathematical model. A 4.5 kW S3R prototype is built to verify the control loop design, and the load region of double section functioning can be limited as designed.
Developing integrated piezoelectric direct current sensor with actuating and sensing elements
Authors: Wang Dong F. , Suzuki Yasuhiro , Kobayashi Takeshi , Itoh Toshihiro , Maeda Ryutaro 
Published: December 2013

A cantilever‐based, oscillating type MEMS direct current sensor (abbreviated as DC sensor), integrated with both actuating and sensing piezoelectric plates, as well as a micromagnet is proposed to satisfy the increasing needs of DC power supply for monitoring electrical consumption by either a single‐wire or two‐wire appliance cord. A prototype MEMS DC sensor, with a measured resonant frequency of 23 Hz, was microfabricated and characterised. In the case of a two‐wire electrical appliance cord, it was found that the change in the peak‐to‐valley value (abbreviated as P‐V value) of the output voltage was approximately proportional to the applied DC, and increased from 10.4 to 43.2 mV when the DC increased from 0 to 2 A under an excitation voltage of 5 Vpp. The shift of the resonant frequency because of the applied DC is believed to account for the change in the P‐V value (or the maximum value) of the output voltage. In summary, the proposed MEMS DC sensor integrated with both actuating and sensing piezoelectric plates was observed to measure the output voltage constantly and linearly over the applied DC directly in a two‐wire appliance without using a cord separator.
Assessing agricultural risks of climate change in the 21st century in a global gridded crop model intercomparison
Authors: Rosenzweig Cynthia , Elliott Joshua , Deryng Delphine , Ruane Alex C. , Müller Christoph , Arneth Almut , Boote Kenneth J. , Folberth Christian , Glotter Michael , Khabarov Nikolay , Neumann Kathleen , Piontek Franziska , Pugh Thomas A. M. , Schmid Erwin , Stehfest Elke , Yang Hong , Jones James W. 
Published: December 2013

SignificanceAgriculture is arguably the sector most affected by climate change, but assessments differ and are thus difficult to compare. We provide a globally consistent, protocol-based, multimodel climate change assessment for major crops with explicit characterization of uncertainty. Results with multimodel agreement indicate strong negative effects from climate change, especially at higher levels of warming and at low latitudes where developing countries are concentrated. Simulations that consider explicit nitrogen stress result in much more severe impacts from climate change, with implications for adaptation planning.
Production and stabilization of the trimeric influenza hemagglutinin stem domain for potentially broadly protective influenza vaccines
Authors: Lu Yuan , Welsh John P. , Swartz James R. 
Published: December 2013

Significance
The discovery of neutralizing antibodies that block influenza infection by binding to the hemagglutinin (HA) stem domain raised the hope for broadly protective vaccines. These could avoid the need for annual vaccinations and reduce pandemic threats, and the stem subdomain of the trimeric HA ectodomain would be an ideal antigen. However, its production has proven extremely difficult. Here, we describe a simple procedure resulting in high yields of HA stem trimer recognized identically by a panel of neutralizing antibodies as compared with recognition of the full-length HA ectodomain. Cell-free protein synthesis is followed by a simple refolding procedure to produce a rationally mutated stem in which newly exposed protein surfaces are modified and trimerization is induced and covalently stabilized.
Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver
Authors: Mauvoisin Daniel , Wang Jingkui , Jouffe Céline , Martin Eva , Atger Florian , Waridel Patrice , Quadroni Manfredo , Gachon Frédéric , Naef Felix 
Published: December 2013

SignificanceCircadian clocks orchestrate daily rhythms in behavior and physiology using temporal regulation of gene expression to control core clock genes and rhythmic output programs. Although transcription regulation was shown to drive extensive diurnal mRNA rhythms, less is known about the proteins. Here, we provide a proteome-wide study of rhythmic protein accumulation in mouse liver, showing that proteins preferentially accumulate in the morning and during the night. About one-half of these rhythmic proteins could not be explained by rhythmic mRNAs, suggesting that translational or posttranslational regulation plays an important role. Moreover, such rhythms involved many secreted proteins and were clock-independent. Hence, these findings indicate that feeding behavior might determine the rhythmic functions of circulating proteins in the blood.
Imaging the wave functions of adsorbed molecules
Authors: Lüftner Daniel , Ules Thomas , Reinisch Eva Maria , Koller Georg , Soubatch Serguei , Tautz F. Stefan , Ramsey Michael G. , Puschnig Peter 
Published: December 2013

Significance
In quantum mechanics, the electrons in a molecule are described by a mathematical object termed the wave function or molecular orbital. This function determines the chemical and physical properties of matter and consequently there has been much interest in measuring orbitals, despite the fact that strictly speaking they are not quantum-mechanical observables. We show how the amplitude and phase of orbitals can be measured in good agreement with wave functions from ab initio calculations. Not only do such measurements allow wave functions of complex molecules and nanostructures to be determined, they also open up a window into critical discussions of theoretical orbital concepts.
ProbeSelect: selecting differentially expressed probes in transcriptional profile data
Authors: Hosur Raghavendra , Szak Suzanne , Thai Alice , Allaire Norm , Bienkowska Jadwiga 
Published: December 2013

Abstract
Summary: Transcriptional profiling still remains one of the most popular techniques for identifying relevant biomarkers in patient samples. However, heterogeneity in the population leads to poor statistical evidence for selection of most relevant biomarkers to pursue. In particular, human transcriptional differences can be subtle, making it difficult to tease out real differentially expressed biomarkers from the variability inherent in the population. To address this issue, we propose a simple statistical technique that identifies differentially expressed probes in heterogeneous populations as compared with controls.
Availability and implementation: The algorithm has been implemented in Java and available at www.sourceforge.net/projects/probeselect.
Contact: jbienkowska@gmail.com or jadwiga@csail.mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
DIVE: a data intensive visualization engine
Authors: Bromley Dennis , Rysavy Steven J. , Su Robert , Toofanny Rudesh D. , Schmidlin Tom , Daggett Valerie 
Published: December 2013

Abstract
Summary: Modern scientific investigation is generating increasingly larger datasets, yet analyzing these data with current tools is challenging. DIVE is a software framework intended to facilitate big data analysis and reduce the time to scientific insight. Here, we present features of the framework and demonstrate DIVE’s application to the Dynameomics project, looking specifically at two proteins.
Availability and implementation: Binaries and documentation are available at http://www.dynameomics.org/DIVE/DIVESetup.exe.
Contact: daggett@uw.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ORCA: a COBRA toolbox extension for model-driven discovery and analysis
Authors: Mao Longfei , Verwoerd Wynand S. 
Published: December 2013

Abstract
Summary: Over past decades, constraint-based modelling has emerged as an important approach to obtain referential information about mechanisms behind biological phenotypes and identify physiological and perturbed metabolic states at genome-scale. However, application of this novel approach to systems biology in biotechnology is still hindered by the functionalities of the existing modelling software. To augment the usability of the constraint-based approach for various use scenarios, we present ORCA, a Matlab package, which extends the scope of established Constraint-Based Reconstruction and Analysis metabolic modelling and includes three unique functionalities: (i) a framework method integrating three analyses of multi-objective optimization, robustness analysis and fractional benefit analysis, (ii) metabolic pathways identification with futile loop elimination and (iii) a dynamic flux balance analysis framework incorporating kinetic constraints.
Availability and implementation: ORCA is freely available to academic users and is downloadable from https://sourceforge.net/projects/exorca/; a mini-tutorial is supplied in the package for training purposes as well as a software manual.
Contact: Longfei.mao@lincolnuni.ac.nz
Supplementary information: Supplementary data are available at Bioinformatics online.
NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes
Authors: Ofer Dan , Linial Michal 
Published: December 2013

Abstract
Motivation: The evolution of multicellular organisms is associated with increasing variability of molecules governing behavioral and physiological states. This is often achieved by neuropeptides (NPs) that are produced in neurons from a longer protein, named neuropeptide precursor (NPP). The maturation of NPs occurs through a sequence of proteolytic cleavages. The difficulty in identifying NPPs is a consequence of their diversity and the lack of applicable sequence similarity among the short functionally related NPs.
Results: Herein, we describe Neuropeptide Precursor Identifier (NeuroPID), a machine learning scheme that predicts metazoan NPPs. NeuroPID was trained on hundreds of identified NPPs from the UniProtKB database. Some 600 features were extracted from the primary sequences and processed using support vector machines (SVM) and ensemble decision tree classifiers. These features combined biophysical, chemical and informational–statistical properties of NPs and NPPs. Other features were guided by the defining characteristics of the dibasic cleavage sites motif. NeuroPID reached 89–94% accuracy and 90–93% precision in cross-validation blind tests against known NPPs (with an emphasis on Chordata and Arthropoda). NeuroPID also identified NPP-like proteins from extensively studied model organisms as well as from poorly annotated proteomes. We then focused on the most significant sets of features that contribute to the success of the classifiers. We propose that NPPs are attractive targets for investigating and modulating behavior, metabolism and homeostasis and that a rich repertoire of NPs remains to be identified.
Availability: NeuroPID source code is freely available at http://www.protonet.cs.huji.ac.il/neuropid
Contact: michall@cc.huji.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Pathogenic Th2-type follicular helper T cells contribute to the development of lupus inFas-deficient mice
Authors: Futatsugi-Yumikura Shizue , Matsushita Kazufumi , Fukuoka Ayumi , Takahashi Suzuka , Yamamoto Nayu , Yonehara Shin , Nakanishi Kenji , Yoshimoto Tomohiro 
Published: December 2013

AbstractFas mutant mice are well recognized as autoimmune mouse models, which develop symptoms similar to human systemic lupus erythematosus. Although disease severity in Fas mutant mice is greatly affected by the genetic background, the mechanisms affecting pathological heterogeneity among different strains of Fas mutant mice are poorly understood. In this study, we examined the phenotypic differences between Fas-deficient (Fas−/−) mice on the BALB/c and C57BL/6 backgrounds to gain insight into the etiological and pathological heterogeneity of monogenic autoimmune diseases. Fas−/− mice on the BALB/c background (BALB/c-Fas−/−) developed more severe autoimmune disease with high serum auto-antibodies and renal disease compared with those on the C57BL/6 background (C57BL/6-Fas−/−). Splenic B cells were highly activated, and germinal center formation was enhanced in BALB/c-Fas−/− but not in C57BL/6-Fas−/− mice. Follicular helper T (Tfh) cells were equally abundant in the spleens from both strains of Fas−/− mice. However, Tfh cells from BALB/c-Fas−/− mice produced much higher amounts of B-cell-activating cytokines, including IL-4 and IL-10, a phenotype reminiscent of Th2-type Tfh cells described in human studies. Our results revealed a qualitative difference in Tfh cells between the two strains of Fas−/− mice. We propose that the pathogenic Th2-type Tfh cells in BALB/c-Fas−/− mice contribute to the excessive activation of B cells, resulting in high serum immunoglobulin levels and the severe lupus phenotype, which may account for the differential outcomes of human monogenic autoimmune diseases.
Human 4E-T represses translation of bound mRNAs and enhances microRNA-mediated silencing
Authors: Kamenska Anastasiia , Lu Wei-Ting , Kubacka Dorota , Broomhead Helen , Minshall Nicola , Bushell Martin , Standart Nancy 
Published: December 2013

AbstractA key player in translation initiation is eIF4E, the mRNA 5′ cap-binding protein. 4E-Transporter (4E-T) is a recently characterized eIF4E-binding protein, which regulates specific mRNAs in several developmental model systems. Here, we first investigated the role of its enrichment in P-bodies and eIF4E-binding in translational regulation in mammalian cells. Identification of the conserved C-terminal sequences that target 4E-T to P-bodies was enabled by comparison of vertebrate proteins with homologues in Drosophila (Cup and CG32016) and Caenorhabditis elegans by sequence and cellular distribution. In tether function assays, 4E-T represses bound mRNA translation, in a manner independent of these localization sequences, or of endogenous P-bodies. Quantitative polymerase chain reaction and northern blot analysis verified that bound mRNA remained intact and polyadenylated. Ectopic 4E-T reduces translation globally in a manner dependent on eIF4E binding its consensus Y30X4Lϕ site. In contrast, tethered 4E-T continued to repress translation when eIF4E-binding was prevented by mutagenesis of YX4Lϕ, and modestly enhanced the decay of bound mRNA, compared with wild-type 4E-T, mediated by increased binding of CNOT1/7 deadenylase subunits. As depleting 4E-T from HeLa cells increased steady-state translation, in part due to relief of microRNA-mediated silencing, this work demonstrates the conserved yet unconventional mechanism of 4E-T silencing of particular subsets of mRNAs.
The influence of viral RNA secondary structure on interactions with innate host cell defences
Authors: Witteveldt Jeroen , Blundell Richard , Maarleveld Joris J. , McFadden Nora , Evans David J. , Simmonds Peter 
Published: December 2013

AbstractRNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-β mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-α, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses.
Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication
Authors: Aklilu Behailu B. , Soderquist Ryan S. , Culligan Kevin M. 
Published: December 2013

AbstractReplication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division.
Functional domains of the 50S subunit mature late in the assembly process
Authors: Jomaa Ahmad , Jain Nikhil , Davis Joseph H. , Williamson James R. , Britton Robert A. , Ortega Joaquin 
Published: December 2013

AbstractDespite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. We found that RbgA-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins L16, L27, L28, L33a, L35 and L36. Using a novel pulse labeling/quantitative mass spectrometry technique, we show that this particle is physiologically relevant and is capable of maturing into a complete 50S particle. Cryo-electron microscopy and chemical probing revealed that the central protuberance, the GTPase associating region and tRNA-binding sites in this intermediate are unstructured. These findings demonstrate that key functional sites of the 50S subunit remain unstructured until late stages of maturation, preventing the incomplete subunit from prematurely engaging in translation. Finally, structural and biochemical analysis of a ribosome particle depleted of L16 indicate that L16 binding is necessary for the stimulation of RbgA GTPase activity and, in turn, release of this co-factor, and for conversion of the intermediate to a complete 50S subunit.
Molecular evolution of protein-RNA mimicry as a mechanism for translational control
Authors: Katz Assaf , Solden Lindsey , Zou S. Betty , Wiley Navarre William , Ibba Michael 
Published: December 2013

Abstract
Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by the lysyl-tRNA synthetase paralog PoxA. To investigate how recognition of EF-P by PoxA evolved from tRNA recognition by aminoacyl-tRNA synthetases, we compared the roles of EF-P/PoxA polar contacts with analogous interactions in a closely related tRNA/synthetase complex. PoxA was found to recognize EF-P solely via identity elements in the acceptor loop, the domain of the protein that interacts with the ribosome peptidyl transferase center and mimics the 3'-acceptor stem of tRNA. Although the EF-P acceptor loop residues required for PoxA recognition are highly conserved, their conservation was found to be independent of the phylogenetic distribution of PoxA. This suggests EF-P first evolved tRNA mimicry to optimize interactions with the ribosome, with PoxA-catalyzed aminoacylation evolving later as a secondary mechanism to further improve ribosome binding and translation control.
Transcriptional regulation by BglJ–RcsB, a pleiotropic heteromeric activator in Escherichia coli
Authors: Salscheider Silja Lucia , Jahn Andreas , Schnetz Karin 
Published: December 2013

AbstractThe bacterial Rcs phosphorelay signals perturbations of the bacterial cell envelope to its response regulator RcsB, which regulates transcription of multiple loci related to motility, biofilm formation and various stress responses. RcsB is unique, as its set of target loci is modulated by interaction with auxiliary regulators including BglJ. The BglJ–RcsB heteromer is known to activate the HNS repressed leuO and bgl loci independent of RcsB phosphorylation. Here, we show that BglJ–RcsB activates the promoters of 10 additional loci (chiA, molR, sfsB, yecT, yqhG, ygiZ, yidL, ykiA, ynbA and ynjI). Furthermore, we mapped the BglJ–RcsB binding site at seven loci and propose a consensus sequence motif. The data suggest that activation by BglJ–RcsB is DNA phasing dependent at some loci, a feature reminiscent of canonical transcriptional activators, while at other loci BglJ–RcsB activation may be indirect by inhibition of HNS-mediated repression. In addition, we show that BglJ–RcsB activates transcription of bgl synergistically with CRP where it shifts the transcription start by 20 bp from a position typical for class I CRP-dependent promoters to a position typical for class II CRP-dependent promoters. Thus, BglJ–RcsB is a pleiotropic transcriptional activator that coordinates regulation with global regulators including CRP, LeuO and HNS.