bluuebunny/crossref_metadata_2025_split huggingface dataset:
Focus on the patentability of computer programs
Authors: Perbal Bernard 
Published: January 2014

AbstractThe Nuts and Bolts section of our Journal (mirrored on the ICCNS society web site), is meant to provide a very practical way to share useful information, that goes beyond the scope of cell signaling and basic CCN protein biology. Considering the number of requests we have had for information related to protection of Intellectual Property (IP), I am pleased to initiate what will be a series of articles that will focus on various IP topics. The inaugural topic is the protection of computer programs. Some colleagues may wonder how and why the patentability of computer programs is a topic of interest for scientists working on CCN proteins… As a matter of fact, to assist us in analyzing the potential involvement of CCN3 in human genetic diseases, we considered developing a computer program designed to analyze large amounts of data. Sharing the concepts and the computer program raised concerns regarding IP and protection of the software that we would handle. We believe that many colleagues have encountered similar problems. This article provides a short focus on computer program patentability. It is aimed to provide basic legal information, and to help our readers in understanding the process. It is not intended to replace IP counselors or technology transfer departments. Future articles will address other practical aspects of IP protection.
Reducing stigma in reproductive health
Authors: Cook Rebecca J. , Dickens Bernard M. 
Published: January 2014

AbstractStigmatization marks individuals for disgrace, shame, and even disgust—spoiling or tarnishing their social identities. It can be imposed accidentally by thoughtlessness or insensitivity; incidentally to another purpose; or deliberately to deter or punish conduct considered harmful to actors themselves, others, society, or moral values. Stigma has permeated attitudes toward recipients of sexual and reproductive health services, and at times to service providers. Resort to contraceptive products, to voluntary sterilization and abortion, and now to medically assisted reproductive care to overcome infertility has attracted stigma. Unmarried motherhood has a long history of shame, projected onto the “illegitimate” (bastard) child. The stigma of contracting sexually transmitted infections has been reinvigorated with HIV infection. Gynecologists and their professional associations, ethically committed to uphold human dignity and equality, especially for vulnerable women for whom they care, should be active to guard against, counteract, and relieve stigmatization of their patients and of related service providers.
A longitudinal study of several potential mediators of the relationship between child maltreatment and posttraumatic stress disorder symptoms
Authors: Shenk Chad E. , Putnam Frank W. , Rausch Joseph R. , Peugh James L. , Noll Jennie G. 
Published: January 2014

AbstractChild maltreatment is a reliable predictor of posttraumatic stress disorder (PTSD) symptoms. However, not all maltreated children develop PTSD symptoms, suggesting that additional mediating variables explain how certain maltreated children develop PTSD symptoms and others do not. The current study tested three potential mediators of the relationship between child maltreatment and subsequent PTSD symptoms: (a) respiratory sinus arrhythmia reactivity, (b) cortisol reactivity, and (c) experiential avoidance, or the unwillingness to experience painful private events, such as thoughts and memories. Maltreated (n= 51) and nonmaltreated groups (n= 59) completed a stressor paradigm, a measure of experiential avoidance, and a semistructured interview of PTSD symptoms. One year later, participants were readministered the PTSD symptoms interview. Results of a multiple mediator model showed the set of potential mediators mediated the relationship between child maltreatment and subsequent PTSD symptoms. However, experiential avoidance was the only significant, specific indirect effect, demonstrating that maltreated children avoiding painful private events after the abuse were more likely to develop a range of PTSD symptoms 1 year later. These results highlight the importance of experiential avoidance in the development of PTSD symptoms for maltreated children, and implications for secondary prevention and clinical intervention models are discussed.
Erratum: Microbial individuality in the natural environment
Authors: Ackermann M 
Published: January 2014

Abstract
Correction to: The ISME Journal (2013) 7, 465–467; doi:10.1038/ismej.2012.131 Since the publication of this article, the author has identified an error contained within the following sentence (located on page 1): However, there is a third possibility that transcends the traditional concept of natureand nurture as determinants of the phenotype: that phenotypic diversity is produced independently of genetic for example, see environmental variation.
Contrasting trends in light pollution across Europe based on satellite observed night time lights
Authors: Bennie Jonathan , Davies Thomas W. , Duffy James P. , Inger Richard , Gaston Kevin J. 
Published: January 2014

AbstractSince the 1970s nighttime satellite images of the Earth from space have provided a striking illustration of the extent of artificial light. Meanwhile, growing awareness of adverse impacts of artificial light at night on scientific astronomy, human health, ecological processes and aesthetic enjoyment of the night sky has led to recognition of light pollution as a significant global environmental issue. Links between economic activity, population growth and artificial light are well documented in rapidly developing regions. Applying a novel method to analysis of satellite images of European nighttime lights over 15 years, we show that while the continental trend is towards increasing brightness, some economically developed regions show more complex patterns with large areas decreasing in observed brightness over this period. This highlights that opportunities exist to constrain and even reduce the environmental impact of artificial light pollution while delivering cost and energy-saving benefits.
Niemann–Pick disease type C2 protein induces triglyceride accumulation in silkworm and mammalian cell lines
Authors: Adachi Tatsuo , Ishii Kenichi , Matsumoto Yasuhiko , Hayashi Yohei , Hamamoto Hiroshi , Sekimizu Kazuhisa 
Published: January 2014

Silkworm haemolymph induced both the cessation of growth and an increase in triglyceride (triacylglycerol) storage in BmN4 cells. We purified the growth inhibitory factor from the silkworm haemolymph and identified this protein as the Bombyx mori PP (promoting protein), an orthologue of NPC2 (Niemann–Pick disease type C2) protein. Recombinant silkworm NPC2 inhibited cellular proliferation and increased triglyceride accumulation in BmN4 cells. Injection of either the recombinant protein or antiserum of NPC2 into living silkworms increased or decreased respectively triglyceride levels in the fat body. A mutation that depletes the cholesterol-binding capacity did not abolish the activity of NPC2. We further revealed that NPC2 induced the phosphorylation of AMPK (AMP-activated protein kinase) and that an AMPK inhibitor suppressed NPC2-dependent triglyceride accumulation. These findings suggest that NPC2 induces triglyceride accumulation via the activation of AMPK independently of its cholesterol-binding capacity in the silkworm.
Comparison of home advantage in men's and women's football leagues in Europe
Authors: Pollard Richard , Gómez Miguel A. 
Published: January 2014

AbstractMost research into home advantage is based on men's sports. This article analyses home advantage in the women's domestic football leagues of Europe and makes a comparison with the corresponding men's football leagues. A total of 47,042 games were included. From 2004 to 2010, home advantage existed in the domestic women's soccer leagues of all 26 European countries analysed, ranging from 51.0% to 58.8% and averaging 54.2%. In every country, this was less than the corresponding men's home advantage which averaged 60.0%. Crowd effects, both on players and referees, and different gender perceptions of territorial protection are plausible reasons for the differences found. Using a regression model that controlled for the competitive balance of each league, as well as for crowd size, the Gender Gap Index, which quantifies the status of women in each country, was a significant predictor of the difference between men's and women's home advantage. As the status of women becomes closer to that of men within a country, the difference in home advantage is less between the men's and women's football leagues.
A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2
Authors: Gill Sukhvinder , Krupovic Mart , Desnoues Nicole , Béguin Pierre , Sezonov Guennadi , Forterre Patrick 
Published: January 2014

Abstract
We report the characterization of a DNA primase/polymerase protein (PolpTN2) encoded by the pTN2 plasmid from Thermococcus nautilus. Sequence analysis revealed that this protein corresponds to a fusion between an N-terminal domain homologous to the small catalytic subunit PriS of heterodimeric archaeal and eukaryotic primases (AEP) and a C-terminal domain related to their large regulatory subunit PriL. This unique domain configuration is not found in other virus- and plasmid-encoded primases in which PriS-like domains are typically fused to different types of helicases. PolpTN2 exhibited primase, polymerase and nucleotidyl transferase activities and specifically incorporates dNTPs, to the exclusion of rNTPs. PolpTN2 could efficiently prime DNA synthesis by the T. nautilus PolB DNA polymerase, suggesting that it is used in vivo as a primase for pTN2 plasmid replication. The N-terminal PriS-like domain of PolpTN2 exhibited all activities of the full-length enzyme but was much less efficient in priming cellular DNA polymerases. Surprisingly, the N-terminal domain possesses reverse transcriptase activity. We speculate that this activity could reflect an ancestral function of AEP proteins in the transition from the RNA to the DNA world.
Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast
Authors: Hirschmann Wolf D. , Westendorf Heidrun , Mayer Andreas , Cannarozzi Gina , Cramer Patrick , Jansen Ralf-Peter 
Published: January 2014

Abstract
The budding yeast multi-K homology domain RNA-binding protein Scp160p binds to &gt;1000 messenger RNAs (mRNAs) and polyribosomes, and its mammalian homolog vigilin binds transfer RNAs (tRNAs) and translation elongation factor EF1alpha. Despite its implication in translation, studies on Scp160p's molecular function are lacking to date. We applied translational profiling approaches and demonstrate that the association of a specific subset of mRNAs with ribosomes or heavy polysomes depends on Scp160p. Interaction of Scp160p with these mRNAs requires the conserved K homology domains 13 and 14. Transfer RNA pairing index analysis of Scp160p target mRNAs indicates a high degree of consecutive use of iso-decoding codons. As shown for one target mRNA encoding the glycoprotein Pry3p, Scp160p depletion results in translational downregulation but increased association with polysomes, suggesting that it is required for efficient translation elongation. Depletion of Scp160p also decreased the relative abundance of ribosome-associated tRNAs whose codons show low potential for autocorrelation on mRNAs. Conversely, tRNAs with highly autocorrelated codons in mRNAs are less impaired. Our data indicate that Scp160p might increase the efficiency of tRNA recharge, or prevent diffusion of discharged tRNAs, both of which were also proposed to be the likely basis for the translational fitness effect of tRNA pairing.
The amino terminal extension of mammalian mitochondrial RNA polymerase ensures promoter specific transcription initiation
Authors: Posse Viktor , Hoberg Emily , Dierckx Anke , Shahzad Saba , Koolmeister Camilla , Larsson Nils-Göran , Wilhelmsson L. Marcus , Hällberg B. Martin , Gustafsson Claes M. 
Published: January 2014

Abstract
Mammalian mitochondrial transcription is executed by a single subunit mitochondrial RNA polymerase (Polrmt) and its two accessory factors, mitochondrial transcription factors A and B2 (Tfam and Tfb2m). Polrmt is structurally related to single-subunit phage RNA polymerases, but it also contains a unique N-terminal extension (NTE) of unknown function. We here demonstrate that the NTE functions together with Tfam to ensure promoter-specific transcription. When the NTE is deleted, Polrmt can initiate transcription in the absence of Tfam, both from promoters and non-specific DNA sequences. Additionally, when in presence of Tfam and a mitochondrial promoter, the NTE-deleted mutant has an even higher transcription activity than wild-type polymerase, indicating that the NTE functions as an inhibitory domain. Our studies lead to a model according to which Tfam specifically recruits wild-type Polrmt to promoter sequences, relieving the inhibitory effect of the NTE, as a first step in transcription initiation. In the second step, Tfb2m is recruited into the complex and transcription is initiated.
Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae
Authors: McIsaac R. Scott , Gibney Patrick A. , Chandran Sunil S. , Benjamin Kirsten R. , Botstein David 
Published: January 2014

Abstract
A conditional gene expression system that is fast-acting, is tunable and achieves single-gene specificity was recently developed for yeast. A gene placed directly downstream of a modified GAL1 promoter containing six Zif268 binding sequences (with single nucleotide spacing) was shown to be selectively inducible in the presence of β-estradiol, so long as cells express the artificial transcription factor, Z3EV (a fusion of the Zif268 DNA binding domain, the ligand binding domain of the human estrogen receptor and viral protein 16). We show the strength of Z3EV-responsive promoters can be modified using straightforward design principles. By moving Zif268 binding sites toward the transcription start site, expression output can be nearly doubled. Despite the reported requirement of estrogen receptor dimerization for hormone-dependent activation, a single binding site suffices for target gene activation. Target gene expression levels correlate with promoter binding site copy number and we engineer a set of inducible promoter chassis with different input–output characteristics. Finally, the coupling between inducer identity and gene activation is flexible: the ligand specificity of Z3EV can be re-programmed to respond to a non-hormone small molecule with only five amino acid substitutions in the human estrogen receptor domain, which may prove useful for industrial applications.
Expression, purification, crystallization and preliminary X-ray analysis of full-length human RIG-I
Authors: Kwok Jane , Hui Kenrie P. Y. , Lescar Julien , Kotaka Masayo 
Published: January 2014

The human innate immune system can detect invasion by microbial pathogens through pattern-recognition receptors that recognize structurally conserved pathogen-associated molecular patterns. Retinoic acid-inducible gene I (RIG-I)-like helicases (RLHs) are one of the two major families of pattern-recognition receptors that can detect viral RNA. RIG-I, belonging to the RLH family, is capable of recognizing intracellular viral RNA from RNA viruses, including influenza virus and Ebola virus. Here, full-length human RIG-I (hRIG-I) was cloned in Escherichia coli and expressed in a recombinant form with a His-SUMO tag. The protein was purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.85 Å resolution; the crystal belonged to space group F23, with unit-cell parameters a = b = c = 216.43 Å, α = β = γ = 90°.
Crystallization and preliminary X-ray analysis of the C-type lectin domain of the spicule matrix protein SM50 fromStrongylocentrotus purpuratus
Authors: Juneja Puneet , Rao Ashit , Cölfen Helmut , Diederichs Kay , Welte Wolfram 
Published: January 2014

Sea urchin spicules have a calcitic mesocrystalline architecture that is closely associated with a matrix of proteins and amorphous minerals. The mechanism underlying spicule formation involves complex processes encompassing spatio-temporally regulated organic–inorganic interactions. C-type lectin domains are present in several spicule matrix proteins inStrongylocentrotus purpuratus, implying their role in spiculogenesis. In this study, the C-type lectin domain of SM50 was overexpressed, purified and crystallized using a vapour-diffusion method. The crystal diffracted to a resolution of 2.85 Å and belonged to space groupP212121, with unit-cell parametersa= 100.6,b= 115.4,c= 130.6 Å, α = β = γ = 90°. Assuming 50% solvent content, six chains are expected to be present in the asymmetric unit.
Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods
Authors: Santoferrara Luciana F. , Grattepanche Jean‐David , Katz Laura A. , McManus George B. 
Published: January 2014

SummaryAssessing microbial diversity requires analysis of all three domains of life, including eukaryotic microbes. We examined the diversity of two ecologically important clades of microbial eukaryotes, ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), by comparing pyrosequencing to Sanger‐sequenced clone libraries and microscopy. Using samples from a large temperate estuary (Long Island Sound, USA), we gained three major insights. First, richness estimates varied by up to one order of magnitude either using different criteria for pyrosequence processing or among pyrosequencing, cloning and microscopy, while taxon identification was almost always coherent. Error‐correcting algorithms for pyrosequences (‘denoising’) reduced discrepancies in richness but also removed known morphospecies from the data. Second, although most of the pyrosequenced operational taxonomic units (OTUs) were distributed within known orders and families, we found evidence of a previously uncharacterized or unknown clade even in these ciliate lineages that have a rich history of morphological description. Third, pyrosequencing allowed the detection of OTUs that were either dominant or extremely rare in different samples. Our findings confirm the potential of pyrosequencing for quantifying microbial diversity, but also highlight the importance of careful evaluation of pyrosequence processing for using this method to address ecological questions.
Pathway of nitrous oxide consumption in isolated Pseudomonas stutzeri strains under anoxic and oxic conditions
Authors: Desloover Joachim , Roobroeck Dries , Heylen Kim , Puig Sebastià , Boeckx Pascal , Verstraete Willy , Boon Nico 
Published: January 2014

SummaryThe microbial consumption of nitrous oxide (N2O) has gained great interest since it was revealed that this process could mitigate the greenhouse effect of N2O. The consumption of N2O results from its reduction to dinitrogen gas (N2) as part of the denitrification process. However, there is ongoing debate regarding an alternative pathway, namely reduction of N2O to NH4+, or assimilatory N2O consumption. To date, this pathway is poorly investigated and lacks unambiguous evidence. Enrichment of denitrifying activated sludge using a mineral nitrogen‐free medium rendered a mixed culture capable of anoxic and oxic N2O consumption. Dilution plating, isolation and deoxyribonucleic acid fingerprinting identified a collection of Pseudomonas stutzeri strains as dominant N2O consumers in both anaerobic and aerobic enrichments. A detailed isotope tracing experiment with a Pseudomonas stutzeri isolate showed that consumption of N2O via assimilatory reduction to NH4+ was absent. Conversely, respiratory N2O reduction was directly coupled to N2 fixation.
The energy‐conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane‐bound complexes, Hdr‐Flox and Rnf
Authors: Meyer Birte , Kuehl Jennifer V. , Price Morgan N. , Ray Jayashree , Deutschbauer Adam M. , Arkin Adam P. , Stahl David A. 
Published: January 2014

SummaryThe adaptation capability of Desulfovibrio to natural fluctuations in electron acceptor availability was evaluated by studying Desulfovibrio alaskensis strain G20 under varying respiratory, fermentative and methanogenic coculture conditions in chemostats. Transition from lactate to pyruvate in coculture resulted in a dramatic shift in the population structure and closer interspecies cell‐to‐cell interactions. Lower methane production rates in coculture than predicted from pyruvate input was attributed to redirection of electron flow to fumarate reduction. Without a methanogenic partner, accumulation of H2 and formate resulted in greater succinate production. Comparative transcript and gene fitness analysis in concert with physiological data of G20 wildtype and mutants demonstrated that pyruvate fermentation involves respiration of cytoplasmically formed fumarate using cytoplasmic and membrane‐bound energy‐conserving complexes, Rnf, Hdr‐Flox‐1 and Hmc. At the low H2/formate levels maintained in coculture, Rnf likely functions as proton‐pumping ferredoxin (Fd) : type‐I cytochrome c oxidoreductase, which transitions to a proton‐pumping Fdred : nicotinamide adenine dinucleotide (NAD+) oxidoreductase at high H2/formate levels during fermentation in monoculture. Hdr‐Flox‐1 is postulated to recycle Fdred via a flavin‐based electron bifurcation involving NADH, Fdox and the thiol/disulphide‐containing DsrC. In a menaquinone (MQ)‐based electron confurcation reaction, the high‐molecular‐weight cytochrome‐c3 complex, Hmc, is proposed to then couple DsrCred and periplasmic H2/formate oxidation using the MQ pool to fuel a membrane‐bound fumarate reductase.
The gill chamber epibiosis of deep‐sea shrimp Rimicaris exoculata: an in‐depth metagenomic investigation and discovery of Zetaproteobacteria
Authors: Jan Cyrielle , Petersen Jillian M. , Werner Johannes , Teeling Hanno , Huang Sixing , Glöckner Frank Oliver , Golyshina Olga V. , Dubilier Nicole , Golyshin Peter N. , Jebbar Mohamed , Cambon‐Bonavita Marie‐Anne 
Published: January 2014

SummaryThe gill chamber of deep‐sea hydrothermal vent shrimp Rimicaris exoculata hosts a dense community of epibiotic bacteria dominated by filamentous Epsilonproteobacteria and Gammaproteobacteria. Using metagenomics on shrimp from the Rainbow hydrothermal vent field, we showed that both epibiont groups have the potential to grow autotrophically and oxidize reduced sulfur compounds or hydrogen with oxygen or nitrate. For carbon fixation, the Epsilonproteobacteria use the reductive tricarboxylic acid cycle, whereas the Gammaproteobacteria use the Calvin–Benson–Bassham cycle. Only the epsilonproteobacterial epibionts had the genes necessary for producing ammonium. This ability likely minimizes direct competition between epibionts and also broadens the spectrum of environmental conditions that the shrimp may successfully inhabit. We identified genes likely to be involved in shrimp–epibiont interactions, as well as genes for nutritional and detoxification processes that might benefit the host. Shrimp epibionts at Rainbow are often coated with iron oxyhydroxides, whose origin is intensely debated. We identified 16S rRNA sequences and functional genes affiliated with iron‐oxidizing Zetaproteobacteria, which indicates that biological iron oxidation might play a role in forming these deposits. Fluorescence in situ hybridizations confirmed the presence of active Zetaproteobacteria in the R. exoculata gill chamber, thus providing the first evidence for a Zetaproteobacteria–invertebrate association.