bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contests and Simulations: Tron: Legacy’s Connections with Technologies
Authors: Wood Aylish 
Published: August 2014

Abstract
the trailer campaign for Tron: Legacy (2010) reintroduces the story-world of Kevin Flynn and the Grid first encountered in Tron (1982), while also showing off the latest incarnation of light cycles, disc battles, and recognizers. Though the film received mixed reviews for its story, the special effects--or F/X--sequences of Tron: Legacy were widely applauded on its release in late 2010. The F/X are central to the ways in which the film imagines the interiority of a computer game, with much of it depicting technological entities (Alter; Bradshaw; Ebert). Stories of technology also reside, however, in the connections between the story-world of Tron: Legacy and a range of contextual materials. In paying attention to these connections, Tron: Legacy offers an opportunity to expand ways of exploring technology in contemporary popular cinema.
Protein Synthesis Initiation in Bacteria
Authors: Grunberg‐Manago Marianne , Studer Sean M , Joseph Simpson 
Published: August 2014

Abstract

Ribosomes are responsible for translating the information in
messenger ribonucleic acids (mRNAs)
to synthesise proteins that the cell needs to carry out its function. Protein synthesis begins with the 30S ribosomal subunit recruiting a mRNA with the help of an initiator transfer RNA and three initiation factors. Successful recruitment of the mRNA results in the formation of the 30S pre‐initiation complex, which is followed by the joining of the 50S ribosomal subunit to form the 70S ribosome. Recent studies indicate the order in which the initiation factors bind and promote the steps in initiation complex formation. The formation of the pre‐initiation/initiation complex is often the rate‐limiting step during the process of translation, as it is influenced by a number of translational regulatory mechanisms. As a result, the process of initiation can play a significant role in gene expression.

Key Concepts:

Translation initiation is a key step for regulating gene expression.

Initiation factors 1, 2 and 3 are essential proteins that promote the binding of the initiator tRNA to the 30S subunit P site and the joining of the 50S subunit.

Initiation factors 1, 2 and 3 are critical for the positioning the mRNA in the correct reading frame for translation.

Efficient requirement of mRNA by the 30S subunit depends on the Shine–Dalgarno sequence in the mRNA forming base pairs with the anti‐Shine–Dalgarno sequence located at the 3′‐end of 16S rRNA.

Kinetic studies have shown the order in which initiation factors bind to the 30S subunit.

Cryo‐EM and crystallographic work have revealed the three‐dimensional location of initiation factors on the 30S subunit and the 70S ribosome.
Proteoglycans
Authors: Schwartz Nancy B 
Published: August 2014

AbstractProteoglycans are complex extracellular macromolecules consisting of a multidomain core protein to which is attached one or more glycosaminoglycan (GAG) chains. They are structurally very diverse, due to variations in length and sequence of the core proteins as well as the abundance, distribution and composition of the GAG chains. Core protein components are often arranged in modules, which have structural and functional significance, and the same module may be found in more than one core protein type. A single core protein type may have different GAG substituents and differing roles in different tissues. Proteoglycans have diverse, but often vital functions in a variety of tissue contexts. Genetic studies of proteoglycan core proteins and their modifying enzymes have elucidated numerous heritable diseases and syndromes emanating both from aberrant biosynthetic and degradative processes.Key Concepts:Glycosaminoglycans (GAG) are linked to proteoglycan core proteins via a limited number ofO‐ orN‐glycosyl bonds.Synthesis of GAG chains proceeds by the sequential action of glycosyltransferases that catalyse transfer of a glycosyl unit from a nucleotide sugar donor to a protein or the non‐reducing end of a sugar acceptor.Proteoglycans are abundant components of the extracellular matrix and may be associated with the cell surface.Although there are only six major classes of proteoglycan types, there is great diversity in structure, size and composition.Important functions have been attributed to both the protein backbone and GAG substituents.Proteoglycans modulate numerous molecular interactions, for example, cell–cell signalling.Heritable proteoglycan disorders exhibit a wide range of phenotypes with examples from all clinical specialties.
Regulation by Covalent Modification
Authors: Martin Bruce L 
Published: August 2014

Abstract

Covalent modifications are enzyme‐catalysed alterations of synthesised proteins and include the addition or removal of chemical groups. Modifications can target a single type of amino acid or multiple amino acids and will change the chemical properties of the site. Consequences on the structure and functions of the protein modified are manifested providing a sensitive method for cellular regulation. The modification of the protein can be reversible or irreversible; in most instances, there are different enzymes responsible for the forward and reverse reactions. Reversible modifications typically associated with the regulation of signalling and metabolic processes and select critical targets can be modified by multiple types of modifications at multiple types of amino acids with multiple number of modifications. Irreversible modifications are more energetically costly requiring the synthesis of new protein before the functional modification can be accomplished if needed.

Key Concepts:

Select enzymes catalyse the transfer of a chemical group from a donor to a target protein.

The target protein is modified on a specific amino acid consistent with the chemistry of the modifying group.

Modifications can influence the properties of the target protein with changes in structure, charge and function.

Enzyme‐catalysed modifications can be reversible or irreversible; reversible modifications typically require different enzymes for the reverse reaction.

Reversible modifications typically associated with regulatory processes or in regulatory steps of metabolic and signalling pathways.

Select critical processes and proteins are targets of multiple types and sites of reversible modifications.

Irreversible modifications require the synthesis of protein.

Irreversible modifications typically associated with physiological cascade processes such as blood coagulation.
Dictyostelium discoideum: Cell Culture and Molecular Tools
Authors: Maniak Markus , Nellen Wolfgang 
Published: August 2014

AbstractDictyostelium discoideumprovides an easy‐to‐grow model system to study virtually all functions typical for higher eukaryotic cells. A variety of specific conditions can induce individual cells to aggregate and initiate a differentiation process resulting in a multicellular structure of low complexity. A plethora of molecular tools is available. These tools include gene disruptions, gene replacements, expression of heterologous proteins, cell type tagging and others, which allow easy genetic manipulation.Dictyostelium discoideumhas proven to be suitable for basic research in chemotaxis, cell differentiation, infection biology, signal transduction, cytoskeletal organisation, nuclear architecture, nutrient uptake and metabolism and many other topics.TheDictyosteliumStock Centre provides a large collection of genetically modified strains, mutants and transformation vectors. Genomic sequences,complementary deoxyribonucleic acidsequences, expression profiles throughout development, genomes of related species and other data are accessible on DictyBase, theDictyosteliumwebsite.Key Concepts:D. discoideumis a suitable model organism to study fundamental biological functions like cell motility, chemotaxis, signal transduction and metabolic pathways.The developmental cycle inD. discoideumis easy to induce and results in only a few different cell types, thus providing a simple system to study cell differentiation.Conditions for growth and maintenance of strains are simple.Gene regulation can be studied on various levels as mechanisms like RNAi, miRNA and chromatin remodelling are similar to those in higher eukaryotes.The intermediate position ofD. discoideumin the phylogenetic tree provides insights into the plant as well as the animal kingdom.Molecular tools like gene disruption, gene replacement, restriction enzyme‐mediated integration (REMI), expression of tagged genes, RNAi and antisense knockdown are available forD. discoideum.BecauseD. discoideumis haploid, genetic alterations are easy to perform.
Insurance and Human Genetics: Insurance Market Perspective
Authors: Hoy Michael 
Published: August 2014

AbstractSuppose individuals have information from genetic tests concerning their mortality or morbidity risk and insurers are not allowed access to it. Higher risks will view insurance as a ‘better deal’ than will lower risks when the price is the same for all and so higher risk consumers will be inclined to purchase more insurance than those with lower risk. The result will be upward pressure on the average market price for insurance. Insurers will react by either raising price or tailoring insurance policies to separate the two types of consumers. In this article, the implications on consumer well‐being in such an economic environment are described and compared to the outcome where insurers are allowed to use the results of genetic tests to price insurance accordingly.Key Concepts:If insurance companies do not have access to genetic test results of their potential customers, then this creates a situation of asymmetric information and a problem of adverse selection.Since ‘bad risks’ will desire more insurance than ‘good risks’ if the price is the same for all, then insurers would end up selling more insurance to the bad risks and so the overall price of insurance may rise as a result.Adverse selection may also result in screening strategies whereby insurers offer higher coverage at a higher unit price in order to attract high risk types with lower risk types enduing up with less insurance coverage.Allowing insurers access to genetic test results leads to greater efficiency of the insurance market but may also create a potential genetic underclass; that is, people who face very high prices for insurance or no insurance at all.Economic models of insurance markets allow one to understand the tradeoffs between effective (efficient) operation of insurance markets and equity concerns.
Down Syndrome: Antenatal Screening Mathematics, Ethics and Its Implementation in theUK
Authors: Reynolds Tim M 
Published: August 2014

AbstractAntenatal screening for Down syndrome involves the application of noninvasive measurements (blood tests or ultrasound scanning) taken early in pregnancy to determine whether a foetus is likely to be affected by Down syndrome, to allow identification of a small proportion of pregnancies (usually up to 5%) in which to carry out an invasive diagnostic test (chorionic villus sampling or amniocentesis). Restriction of the invasive test is advisable because there is a risk of iatrogenic foetal loss as a result of the diagnostic test. New possibilities include analysis of free serum deoxyribonucleic acid to avoid invasive foetal sampling.Although screening is possible, there remains some controversy over whether it should be done. The Eugenics history of the mid‐twentieth century should give pause for thought over the ethical under‐pinning of this ‘routine’ antenatal test.Key Concepts:It is possible to screen for foetal aneuploidies in early pregnancy by using a statistical model of normality, and a statistical model of affected pregnancies, from which a risk can be calculated. In future, it may be possible to directly analyse foetal DNA in maternal plasma to carry out the same function.New screening methods using free DNA in serum may soon be introduced.Screening programmes for genetics disease pose questions about medical ethics which are very difficult to answer.
DNA
Replication Origins
Authors: Rodríguez‐Martínez Marta , Méchali Marcel 
Published: August 2014

Abstract

In all living organisms, genome replication is essential for their development and maintenance. In the genome of simple organisms, such as bacteria and small eukaryotic
deoxyribonucleic acid (DNA)
viruses, DNA replication starts from a well‐characterised single origin. In complex eukaryotes, such as metazoans, DNA replication starts from dozens of thousands of origins spread along the different chromosomes. This high number of origins, together with the technical problems encountered in finding reliable methods for their large‐scale mapping, made difficult their characterisation. However, owing to the new genome‐wide approaches developed in the past few years, we have now a better understanding of how replication origins are established in higher eukaryotes. These studies have shown an intrinsic correlation between replication origins and other genome features, such as gene transcription and epigenetic regulation, and revealed an amazing flexibility in their usage.

Key Concepts:

Replication origins are defined by specific DNA sequences in bacteria, viruses and
Saccharomyces cerevisiae
, but not in
Schizosaccharomyces pombe
and metazoans.

DNA replication origins are activated in a defined temporal order, called timing of DNA replication.

DNA replication origins are flexible: only a subset of them is activated at each cell cycle.

DNA replication takes place at specific subnuclear structures, called replication foci.

The number and position of replication origins to be activated may vary according to the developmental or growing conditions.
Histidine Triad (
HIT
) Superfamily
Authors: Brenner Charles 
Published: August 2014

Abstract

Histidine triad (HIT) enzymes are an ancient superfamily of nucleotide hydrolases and transferases that catalyse mechanistically similar but biologically distinct reactions on nucleotide‐containing substrates in pathways important for cellular growth, apoptosis,
deoxyribonucleic acid
,
ribonucleic acid
, vitamin and carbohydrate metabolism. Four branches of HIT enzymes function as nucleotide hydrolases. These enzymes include homologues and paralogues of histidine triad nucleotide‐binding protein, fragile histidine triad protein, APRATAXIN and scavenger decapping protein, which act in various cellular compartments. One diverse branch of the HIT superfamily contains nucleotide transferases and phosphorylases related to galactose‐1‐phosphate uridylyltransferase, AppppA phosphorylase, adenylylsulfate: phosphate adenylyltransferase, adenosine diphosphate‐glucose phosphorylase and VTC2, the guanosine diphosphate‐
l
‐galactose phosphorylase. This review provides tools to discern the identities and the probable functions of HIT enzymes from their sequences.

Key Concepts:

Histidine triad enzymes act on substrates containing a nucleoside monophosphate linked to distinct leaving groups.

HINT, FHIT, APRATAXIN and DCPS are HIT hydrolases.

GALT and VTC2 are HIT transferases.

Particular HIT enzymes are targeted to different cellular compartments to carry out their functions.

HIT enzymes remove nucleotide adducts from proteins and DNA and transform low‐molecular‐weight metabolites in cells.
Cécile Vogt (1875–1962)
Authors: Satzinger Helga 
Published: August 2014

AbstractCécile Vogt, née Mugnier, was a French neurologist who worked all her life in Germany in collaboration with her German husband, Oskar Vogt. A pioneering woman in medicine and especially in brain research, she contributed substantially to the elucidation of the cellular structure of the brain and its functional interpretation. With her husband, she established the world's largest interdisciplinary brain research institute in the 1930s, which became the forerunner of the Institute for Brain Research of the German Max Planck Society. Cécile and Oskar Vogt had to leave the institute in 1937 under Nazi pressure, but they continued to work in Germany at a private institute in the Black Forest. Their daughters Marthe and Marguerite became pioneering scientists in neuropharmacology and genetics.
Performing high‐powered studies efficiently with sequential analyses
Authors: Lakens Daniël 
Published: August 2014

AbstractRunning studies with high statistical power, while effect size estimates in psychology are often inaccurate, leads to a practical challenge when designing an experiment. This challenge can be addressed by performing sequential analyses while the data collection is still in progress. At an interim analysis, data collection can be stopped whenever the results are convincing enough to conclude that an effect is present, more data can be collected, or the study can be terminated whenever it is extremely unlikely that the predicted effect will be observed if data collection would be continued. Such interim analyses can be performed while controlling the Type 1 error rate. Sequential analyses can greatly improve the efficiency with which data are collected. Additional flexibility is provided by adaptive designs where sample sizes are increased on the basis of the observed effect size. The need for pre‐registration, ways to prevent experimenter bias, and a comparison between Bayesian approaches and null‐hypothesis significance testing (NHST) are discussed. Sequential analyses, which are widely used in large‐scale medical trials, provide an efficient way to perform high‐powered informative experiments. I hope this introduction will provide a practical primer that allows researchers to incorporate sequential analyses in their research. Copyright © 2014 John Wiley & Sons, Ltd.
Lipase‐mediated lipid removal from propolis extract and its antiradical and antimicrobial activity
Authors: Park Hyein , Bae Song Hwan , Park Yooheon , Choi Hyeon‐Son , Suh Hyung Joo 
Published: August 2014

AbstractBACKGROUNDPropolis contains many antioxidants such as polyphenols and flavonoids. However, propolis‐derived lipid components interrupt an efficient isolation of antioxidants from propolis extract. We examined the effectiveness of various lipase treatments for the removal of lipids from propolis extract and evaluated the biological features of the extract.RESULTSLipase OF and Novozyme 435 treatments did not reduce fatty acid level in propolis extract. However, Lipozyme TL IM‐treated propolis extract showed a significant decrease in fatty acid level, suggesting the removal of lipids. Lipozyme RM IM also significantly decreased the fatty acid level of the extract, but was accompanied by the reduction of polyphenols and flavonoids, which are antioxidants. In Lipozyme TL IM treatment, an increase in active flavonoids, such as Artepillin C and kaempferide, was observed, with a slight increase of ferric reducing/antioxidant power (FRAP) radical‐scavenging activity. In addition, antimicrobial activity towards skin health‐related bacteria such as Staphylococcus epidermidis and Propionibacterium acnes was enhanced by Lipozyme TL IM treatment.CONCLUSIONLipozyme TL IM treatment effectively removes lipids from propolis extract and enhances antibacterial activity. Therefore, we suggest that Lipozyme TL IM is a useful lipase for lipid removal of propolis extract. © 2014 Society of Chemical Industry
Transition cropping system impacts on organic wheat yield and quality
Authors: Borrelli Kristy , Koenig Richard , Burke Ian , Gallagher Robert S. , Pittmann Dennis , Snyder Amanda , Fuerst E. Patrick 
Published: August 2014

AbstractOrganic wheat and small grains are produced on relatively few acres in the inland Pacific Northwest. The objective of this study was to examine how the nitrogen (N) dynamics of cropping systems (CSs) produced during the transition phase impacted organic wheat yield and protein levels in the first 2 years of certified organic production. Certified organic spring wheat (SW) was produced in 2006 and winter wheat (WW) in 2007 following nine, 3-year transitional cereal, small grain and legume-intensive CSs. SW and WW following perennial alfalfa + oat/pea forage or 3 years of legume green manure tended to be more productive than wheat that followed systems that contained a small grain crop for at least 1 year during the transition. In addition to increasing soil N, well-established stands of forage and green manure provided adequate cover to reduce weed establishment prior to organic production. Effective weed control strategies were as important as increasing soil inorganic N levels for improving organic wheat production. Choice of crop type, cultivar and rotation is important in organic wheat systems and in this study, WW had better stand establishment, competition with weeds and higher overall yield than SW and would be a better-suited class of wheat for organic production in situations where spring weeds are the dominant problem. Regardless of CS or crop type, supplemental soil fertility (primarily N) during the organic production phase will be necessary to maintain high soil N levels and wheat yields in these dryland systems.
Viruses accumulate in aging infection centers of a fungal forest pathogen
Authors: Vainio Eeva J , Müller Michael M , Korhonen Kari , Piri Tuula , Hantula Jarkko 
Published: August 2014

Abstract
Fungal viruses (mycoviruses) with RNA genomes are believed to lack extracellular infective particles. These viruses are transmitted laterally among fungal strains through mycelial anastomoses or vertically via their infected spores, but little is known regarding their prevalence and patterns of dispersal under natural conditions. Here, we examined, in detail, the spatial and temporal changes in a mycovirus community and its host fungus Heterobasidion parviporum, the most devastating fungal pathogen of conifers in the Boreal forest region. During the 7-year sampling period, viruses accumulated in clonal host individuals as a result of indigenous viruses spreading within and between clones as well as novel strains arriving via airborne spores. Viral community changes produced pockets of heterogeneity within large H. parviporum clones. The appearance of novel viral infections in aging clones indicated that transient cell-to-cell contacts between Heterobasidion strains are likely to occur more frequently than what was inferred from genotypic analyses. Intraspecific variation was low among the three partitivirus species at the study site, whereas the unassigned viral species HetRV6 was highly polymorphic. The accumulation of point mutations during persistent infections resulted in viral diversification, that is, the presence of nearly identical viral sequence variants within single clones. Our results also suggest that co-infections by distantly related viral species are more stable than those between conspecific strains, and mutual exclusion may play a role in determining mycoviral communities.
Improvement of the oil quality of the main oil crops.
Authors: Baldini M. , Ferfuia C. , Vischi M. 
Published: August 2014

Abstract
The growing demand for vegetable oils will increase even more in the near future because of their fundamental role in human and animal nutrition, increasing interest in their non-food applications as biofuel, lubricants, biopolymers, paints, etc. and the rising price of fossil fuels. The development of alternative vegetable oil feedstocks with modified functionality and at the same time maintaining the nutritional quality has therefore become a priority. In particular, modification of the fatty acid composition of vegetable oils specifically suitable for nutrition and/or industrial and other non-food applications has been one of the major challenges of the last few years. This review provides a focus on the improvement in oil quality of the main oil crops cultivated in temperate zones, specifically soybean, rapeseed and sunflower, achieved by conventional breeding based on natural or induced genetic variability and by biotechnological approaches, especially adopting transgenic technology for the identification, isolation and transfer of genes and silencing of genes coding for key enzymes involved in the synthesis of fatty acids.