bluuebunny/crossref_metadata_2025 huggingface dataset:
A new framework for resolving conflicts over transboundary rivers using bankruptcy methods
Authors: Madani K. , Zarezadeh M. , Morid S.
Published: August 2014

Abstract. A novel bankruptcy approach is proposed for resolving transboundary river conflicts in which the total water demand or claim of the riparian parties is more than the available water. Bankruptcy solution methods can allocate the available water to the conflicting parties with respect to their claims. Four commonly used bankruptcy methods in the economic literature are used here to develop new river bankruptcy solution methods for allocating water to the riparian parties of river systems. Given the non-uniform spatial and temporal distribution of water across river basins, the proposed solution methods are formulated as non-linear network flow optimization models to allocate water with respect to time sensitivity of water deliveries at different locations in a river network during the planning horizon. Once allocation optimization solutions are developed, their acceptability and stability must be evaluated. Thus, a new bankruptcy allocation stability index (BASI) is developed for evaluating the acceptability of river bankruptcy solutions. To show how the proposed river bankruptcy framework can be helpful in practice, the suggested methods are applied to a real-world transboundary river system with eight riparians under various hydrologic regimes. Stability analysis based on the proposed stability evaluation method suggests that the acceptability of allocation rules is sensitive to hydrologic conditions and demand values. This finding has an important policy implication suggesting that fixed allocation rules and treaties may not be reliable for securing cooperation over transboundary water resources as they are vulnerable to changing socioeconomic and climatic conditions as well as hydrologic non-stationarity.
Niger's Delta vulnerability to river floods due to sea level rise
Authors: Musa Z. N. , Popescu I. , Mynett A.
Published: August 2014

Abstract. An evaluation of vulnerability to sea level rise is undertaken for the Niger delta based on 17 physical, social and human influence indicators of exposure, susceptibility and resilience. The assessment used GIS techniques to evaluate and analyse the indicators and the index of coastal vulnerability to floods, if sea level rise conditions are occurring. Each indicator value is based on data extracted from various sources including remote sensing, measured historical data series and literature search. Further indicators are ranked on a scale from 1 to 5 representing "very low" to "very high" vulnerability, based on their values. These ranks are used to determine a similar rank for the defined coastal vulnerability index (CVSLRI). Results indicate that 42.2% of the Niger delta is highly vulnerable to sea level rise; such areas been characterized by low slopes, low topography, high mean wave heights, and unconfined aquifers. Moreover the analysis of social and human influences on the environment indicate high vulnerability to sea level rise due to its ranking for type of aquifer, aquifer hydraulic conductivity, population growth, sediment supply and groundwater consumption. Such results may help decision makers during planning, to take proper adaptive measures for reducing Niger Delta's vulnerability, as well as increasing the resilience to potential future floods.
Heat loss from the Atlantic water layer in the northern Kara Sea: causes and consequences
Authors: Dmitrenko I. A. , Kirillov S. A. , Serra N. , Koldunov N. V. , Ivanov V. V. , Schauer U. , Polyakov I. V. , Barber D. , Janout M. , Lien V. S. , Makhotin M. , Aksenov Y.
Published: August 2014

Abstract. A distinct, subsurface density front along the eastern St. Anna Trough in the northern Kara Sea is inferred from hydrographic observations in 1996 and 2008–2010. Direct velocity measurements show a persistent northward subsurface current (~ 18 cm s−1) along the St. Anna Trough eastern flank. This sheared flow, carrying the outflow from the Barents and Kara seas to the Arctic Ocean, is also evident from shipboard observations as well as from geostrophic velocities and numerical model simulations. Although we cannot substantiate our conclusions by direct observation-based estimates of mixing rates in the area, we hypothesize that the enhanced vertical mixing along the St. Anna Trough eastern flank favors the upward heat loss from the intermediate warm Atlantic water layer. Modeling results support this hypothesis. The upward heat flux inferred from hydrographic data and model simulations is of O(30–100) W m−2. The region of lowered sea ice thickness and concentration seen both in sea ice remote sensing observations and model simulations marks the Atlantic water pathway in the St. Anna Trough and adjacent Nansen Basin continental margin. In fact, the sea ice shows a delayed freeze-up onset during fall and a reduction in the sea ice thickness during winter. This is consistent with our results on the enhanced Atlantic water heat loss along the Atlantic water pathway in the St. Anna Trough.
Contests and Simulations: Tron: Legacy’s Connections with Technologies
Authors: Wood Aylish
Published: August 2014

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

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

Proteoglycans 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

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

Dictyostelium 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

Suppose 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

Antenatal 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

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

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

Cécile 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

Running 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.
Lithofacies and depositional characteristics of gas shales in the western area of the Lower Yangtze, China
Authors: Du Xue‐Bin , Zhang Ming‐Qiang , Lu Yong‐Chao , Ping Cheng , Lu Yang‐Bo
Published: August 2014

The Lower Yangtze is considered as a potentially productive shale gas area in China, but only limited research has thus far been carried out there. On the basis of a detailed investigation of fourteen outcrops, eight lithofacies in the Hetang Formation (510–541 Ma), the Gaojiabian Formation (430–443.4 Ma), the Gufeng Formation (270–281 Ma) and the Dalong Formation (252–263 Ma) have been identified: silicalite, siliceous non‐calcareous mudstone, siliceous shale, carbonaceous shale, calcareous mudstone, silty–shaly interlaminated mudstone, siltstone and limestone. Three types of fossils were also found in the four formations: sponge spicules, radiolarians and graptolites. Moreover, four key outcrops of the fourteen were suitable for more additional detailed analyses and interpretation of their depositional environments and plausible sequence of the stratigraphic system tracts. As a result, the four potential shale gas formations were all divided into third‐order sea‐level sequences. Every third‐order sequence was further divided into four system tracts, corresponding to an early transgressive system tract (ETST), a late transgressive system tract (LTST), an early highstand system tract (EHST) and a late highstand system tract (LHST). On the basis of the interpretation of the lithofacies and depositional environments in the western area of the Lower Yangtze, sediments can be related to hydrothermal and biological processes, terrigenous clastic input and calcium compensation. These processes were interpreted to occur in a sequential order that we divide into three stages. The ETST period was the first stage, in which hydrothermal upwelling from the open ocean produced a siliceous lithological combination. During the second stage corresponding to the LTST + EHST, our results suggest that some biological communities in the stable deep water provided plenty of organic‐rich matter. The LHST period was the third stage, in which terrigenous clastic material was deposited close to the land, and some carbonate sediments began appearing near the platform. 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

BACKGROUND

Propolis 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.

RESULTS

Lipase 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.

CONCLUSION

Lipozyme 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
On the Equivalence of Trolleys and Transplants: The Lack of Intrinsic Difference between ‘Collateral Damage’ and Intended Harm
Authors: NYE HOWARD
Published: August 2014

In this article I attempt to show conclusively that the apparent intrinsic difference between causing collateral damage and directly attacking innocents is an illusion. I show how eleven morally irrelevant alterations can transform an apparently permissible case of harming as a side-effect into an apparently impermissible case of harming as a means. The alterations are as obviously irrelevant as the victims’ skin colour, and consistently treating them as relevant would have unacceptable implications for choices between more and less harmful ways of securing greater goods. This shows not only how the principles philosophers have proposed for distinguishing between these cases cannot withstand scrutiny, but how we can be sure that there are no relevant differences yet to be discovered. I conclude by considering reasons to think that there are deontological constraints against harming, but that they apply just as forcefully against collateral harms as they do against intended harms.
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

Organic 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

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.
Treatment of proteins with dietary polyphenols lowers the formation of AGEs and AGE-induced toxicity
Authors: Zhang Xinchen , Hu Shuting , Chen Feng , Wang Mingfu
Published: August 2014

Advanced glycation endproducts (AGEs) are a group of harmful compounds produced either endogenously or during thermal food processing.
Ultrasensitive detection of cancer cells and glycan expression profiling based on a multivalent recognition and alkaline phosphatase-responsive electrogenerated chemiluminescence biosensor
Authors: Chen Xiaojiao , He Yao , Zhang Youyu , Liu Meiling , Liu Yang , Li Jinghong
Published: August 2014

Multivalent recognition and enzyme-responsive aptamer electrogenerated chemiluminescence biosensor for the analysis of cancer cell and its surface glycan expression.
Well-dispersed lithium amidoborane nanoparticles through nanoreactor engineering for improved hydrogen release
Authors: Xia Guanglin , Chen Jie , Sun Weiwei , Tan Yingbin , Guo Zaiping , Liu Huakun , Yu Xuebin
Published: August 2014

Well-distributed lithium amidoborane (LiAB) nanoparticles were successfully fabricated via adopting carbon nanofibers (CNFs) with homogenous pores uniformly containing Li3N as the nanoreactor and reactant, for the subsequent interaction with AB.
Investigating the contribution of the active site environment to the slow reaction of hypoxia-inducible factor prolyl hydroxylase domain 2 with oxygen
Authors: Tarhonskaya Hanna , Chowdhury Rasheduzzaman , Leung Ivanhoe K. H. , Loik Nikita D. , McCullagh James S. O. , Claridge Timothy D. W. , Schofield Christopher J. , Flashman Emily
Published: August 2014

The prolyl hydroxylase domain proteins (PHDs) catalyse the post-translational hydroxylation of the hypoxia-inducible factor (HIF), a modification that regulates the hypoxic response in humans. The PHDs are Fe(II)/2-oxoglutarate (2OG) oxygenases; their catalysis is proposed to provide a link between cellular HIF levels and changes in O2 availability. Transient kinetic studies have shown that purified PHD2 reacts slowly with O2 compared with some other studied 2OG oxygenases, a property which may be related to its hypoxia-sensing role. PHD2 forms a stable complex with Fe(II) and 2OG; crystallographic and kinetic analyses indicate that an Fe(II)-co-ordinated water molecule, which must be displaced before O2 binding, is relatively stable in the active site of PHD2. We used active site substitutions to investigate whether these properties are related to the slow reaction of PHD2 with O2. While disruption of 2OG binding in a R383K variant did not accelerate O2 activation, we found that substitution of the Fe(II)-binding aspartate for a glutamate residue (D315E) manifested significantly reduced Fe(II) binding, yet maintained catalytic activity with a 5-fold faster reaction with O2. The results inform on how the precise active site environment of oxygenases can affect rates of O2 activation and provide insights into limiting steps in PHD catalysis.
Research on IT in China: A Call for Greater Contextualization
Authors: Li Liang , Gao Ping , Mao Ji-Ye
Published: August 2014

Research on information technologies (IT) in China has gained increasing attention in the international information systems (IS) community. This study systematically reviews papers on IT in China published in the ‘Senior Scholars’ Basket of Journals’ from 2000 to 2013. We have two specific objectives: to identify key research issues and trends, and to propose future directions for research on IT in China. This paper categorizes the global distribution of authors and their research methods. Five research streams are identified, including human behaviors in IS adoption and use, IS management, e-Business, social media, digital collaborations and group support, and industry and societal issues in IS. While each stream is examined in detail, we specifically pay attention to the effect of the Chinese context in each paper and the approaches to contextualizing the research. On the basis of our findings from the literature review, we propose a focus on the Chinese context as guidance for future research.
Optimization of ion-atomic beam source for deposition of GaN ultrathin films
Authors: Mach Jindřich , Šamořil Tomáš , Kolíbal Miroslav , Zlámal Jakub , Voborny Stanislav , Bartošík Miroslav , Šikola Tomáš
Published: August 2014

We describe the optimization and application of an ion-atomic beam source for ion-beam-assisted deposition of ultrathin films in ultrahigh vacuum. The device combines an effusion cell and electron-impact ion beam source to produce ultra-low energy (20–200 eV) ion beams and thermal atomic beams simultaneously. The source was equipped with a focusing system of electrostatic electrodes increasing the maximum nitrogen ion current density in the beam of a diameter of ≈15 mm by one order of magnitude (j ≈ 1000 nA/cm2). Hence, a successful growth of GaN ultrathin films on Si(111) 7 × 7 substrate surfaces at reasonable times and temperatures significantly lower (RT, 300 °C) than in conventional metalorganic chemical vapor deposition technologies (≈1000 °C) was achieved. The chemical composition of these films was characterized in situ by X-ray Photoelectron Spectroscopy and morphology ex situ using Scanning Electron Microscopy. It has been shown that the morphology of GaN layers strongly depends on the relative Ga-N bond concentration in the layers.
Improvement of the oil quality of the main oil crops.
Authors: Baldini M. , Ferfuia C. , Vischi M.
Published: August 2014

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.
Clinical Features of Malabsorptive Disorders, Small-Bowel Diseases, and Bacterial Overgrowth Syndromes
Authors: Oxentenko Amy S.
Published: August 2014

Malabsorption (defect in absorption of nutrients) and maldigestion (defect in hydrolysis of nutrients) both imply disordered physiologic mechanisms in the gastrointestinal system. Malabsorption and maldigestion of nutritional substrates can occur in multiple phases: the luminal phase, the mucosal phase, and the delivery phase. Small-bowel diseases include celiac disease, Whipple disease, tropical sprue, eosinophilic gastroenteritis, intestinal lymphangiectasia, and amyloidosis. Normally, the small-bowel flora contains a relatively small number of bacteria, with a predominance of gram-positive organisms. In contrast, the colonic flora has a significantly higher concentration of bacteria, which are largely gram-negative and anaerobic organisms. When there is stasis, altered motility, or loss of protective defenses in the proximal intestinal tract, bacteria that are more representative of colonic flora can overgrow in the small bowel and result in a syndrome of diarrhea and nutritional deficiencies known as small intestinal bacterial overgrowth.
Nonvariceal Gastrointestinal Tract Bleeding
Authors: Alexander Jeffrey A.
Published: August 2014

Upper gastrointestinal tract bleeding (“UGI bleeding”) constitutes 75% to 80% of all cases of acute gastrointestinal tract bleeding. The incidence has decreased, but the mortality rate from acute UGI bleeding, ranging from 3% to 10%, has not changed appreciably in the past 50 years. This lack of change in mortality rate likely is related to the increased age of patients who present with UGI bleeding and the increase in associated comorbid conditions. Peptic ulcers are the most common source of UGI bleeding, accounting for about 40% of cases. Other major causes are gastric erosions, bleeding varices, and Mallory-Weiss tears. The use of aspirin or nonsteroidal anti-inflammatory drugs is prevalent in 45% to 60% of all cases of acute bleeding. Moreover, the risk of UGI bleeding is increased in patients who take as few as one “baby aspirin” per day.
Cholestatic Liver Disease
Authors: Talwalkar Jayant A.
Published: August 2014

Cholestatic liver disease in adults without biliary obstruction encompasses a broad differential diagnosis. Drug-induced cholestasis may be the most common explanation for cholestasis in these patients. Primary biliary cirrhosis is the most common cholestatic liver disease in adults. Primary sclerosing cholangitis is about half as common as primary biliary cirrhosis. Other cholestatic conditions in adults include antimitochondrial antibody (AMA)-negative primary biliary cirrhosis, human immunodeficiency virus (HIV)-related cholangiopathy, and miscellaneous conditions.
Autoimmune Hepatitis
Authors: Watt Kymberly D. , Czaja Albert J.
Published: August 2014

Autoimmune hepatitis is a self-perpetuating inflammation of the liver of unknown cause that is associated with autoantibodies, hypergammaglobulinemia, and interface hepatitis seen on histologic examination. Autoimmune hepatitis afflicts 100,000 to 200,000 persons in the United States annually and accounts for 5.9% of liver transplants performed in the United States. The cause of autoimmune hepatitis is unknown. Multiple agents have been implicated as triggers of the disease, including certain viruses (hepatitis A, hepatitis B, hepatitis C, Epstein-Barr, herpes simplex, and measles viruses) and drugs (diclofenac, isoniazid, ?-methyldopa, minocycline, nitrofurantoin, atorvastatin, and propylthiouracil; recently, infliximab and adalimumab have been implicated). Hepatitis A virus infection and minocycline have been implicated most often worldwide. Most cases have no identifiable trigger.
Peptic Ulcer Disease
Authors: Hansel Stephanie L.
Published: August 2014

A peptic ulcer is a persistent 5 mm or larger break in the gastrointestinal mucosa of the stomach or duodenum that penetrates through the muscularis mucosa. At endoscopy, an ulcer should be readily apparent with perceivable depth. Smaller and more shallow mucosal breaks represent erosions. Most ulcers are due to infection with Helicobacter pylori or the administration of nonsteroidal anti-inflammatory drugs. The term peptic ulcer disease refers to ulceration that depends in part on the acid and peptic (pepsins) activity of gastric juice. Gastric malignancy is an example of ulceration that may occur in the absence of acid and peptic activity. Most peptic ulcer disease involves the stomach or duodenal bulb. Epidemiology, pathophysiology, diagnosis, testing, and treatment are discussed.
Preservation of Blueschist-facies Minerals along a Shear Zone by Coupled Metasomatism and Fast-flowing CO2-bearing Fluids
Authors: Kleine Barbara I. , Skelton Alasdair D. L. , Huet Benjamin , Pitcairn Iain K.
Published: August 2014

Two types of blue halo (types I and II) composed of blueschist-facies minerals are centered around a brittle, normal shear zone in greenschist-facies rocks on the island of Syros, Aegean Sea, Greece. The shear zone is steeply dipping and cuts a near-horizontal layer of greenschist-facies rocks (albite + epidote + actinolite + chlorite + quartz). Type I and II blue haloes are 0·3 m and c. 1 m wide respectively, and are seen on both sides of the shear zone. The inner type I haloes are composed of nearly pure glaucophane schist and were formed by metasomatic addition of Na2O and SiO2, and to a lesser extent of K2O and large ion lithophile elements (LILE), coupled with loss of CaO, Al2O3 and MnO. The outer type II haloes consist of a carbonated blueschist-facies assemblage (glaucophane + calcite + phengite + epidote + garnet + quartz). These experienced only slight metasomatic changes (i.e. addition of K2O and LILE), which cannot alone explain halo formation. We present petrological, geochemical and thermodynamic evidence that this assemblage was preserved at greenschist-facies conditions because XCO2 was elevated by flow of a CO2-bearing fluid along the shear zone, which was approximately contemporaneous with greenschist-facies hydration in the surrounding rocks. We further note that the flux of CO2-bearing fluid along the shear zone was rapid with respect to the fluid flux in the surrounding rocks. Mass-balance calculations reveal that the fluid flux within the shear zone was at least 100–2000 times greater than the fluid flux within the surrounding rocks. Mineral textures show greenschist-facies minerals replacing blueschist minerals in the type II haloes, supporting our interpretation that the blueschist-facies minerals were preserved during greenschist-facies retrogression. A simplified P–T vs XCO2 pseudosection confirms that preservation of carbonated blueschist can occur at greenschist-facies conditions in the presence of a CO2-bearing fluid.
Lack of Nephrotoxicity by 6% Hydroxyethyl Starch 130/0.4 during Hip Arthroplasty
Authors: Kancir Anne Sophie Pinholt , Pleckaitiene Lina , Hansen Torben Bæk , Ekeløf Niels Peter , Pedersen Erling Bjerregaard
Published: August 2014

Background:

Hydroxyethyl starch (HES) is commonly used as plasma expander during surgery but may be nephrotoxic as seen in studies in patients with sepsis. The authors hypothesized that the possible nephrotoxicity of 6% HES 130/0.4 could be revealed by measurements of urinary excretion of neutrophil gelatinase–associated lipocalin (u-NGAL) in patients with normal renal function during hip arthroplasty.

Methods:

In this randomized, double-blinded, placebo-controlled study, 40 patients referred for hip arthroplasty received either 6% HES 130/0.4 or isotonic saline 0.9%; 7.5 ml/kg during the first hour of surgery and 5 ml/kg during the following hours; 38 patients completed the study. U-NGAL, urine albumin, blood pressure, and plasma concentrations of creatinine, renin, NGAL, albumin, angiotensin-II, and aldosterone were measured before, during, and after surgery. U-NGAL was defined as primary outcome.

Results:

There were no significant differences in U-NGAL (mean difference and 95% CI), plasma creatinine, and urine albumin during the study. U-NGAL and urine albumin increased significantly in both groups the morning after surgery but was normalized at follow-up after 10 to 12 days. Mean arterial pressure was significantly higher during the recovery period in the HES group compared with that in the control group (91 [13] and 83 [6] mmHg, mean [SD], P < 0.03). Plasma renin and angiotensin-II were nonsignificantly different in both groups, whereas plasma aldosterone was significantly lower in the HES group. Plasma albumin was reduced in both groups, but to a significantly lower level in the HES group.

Conclusion:

The study showed no evidence of a harmful effect of intraoperative infusion of 6% HES 130/0.4 on renal function in patients during hip arthroplasty.
A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36
Authors: Cheng Zhongjun , Cheung Peggie , Kuo Alex J. , Yukl Erik T. , Wilmot Carrie M. , Gozani Or , Patel Dinshaw J.
Published: August 2014

The dynamic reversible methylation of lysine residues on histone proteins is central to chromatin biology. Key components are demethylase enzymes, which remove methyl moieties from lysine residues. KDM2A, a member of the Jumonji C domain-containing histone lysine demethylase family, specifically targets lower methylation states of H3K36. Here, structural studies reveal that H3K36 specificity for KDM2A is mediated by the U-shaped threading of the H3K36 peptide through a catalytic groove within KDM2A. The side chain of methylated K36 inserts into the catalytic pocket occupied by Ni2+ and cofactor, where it is positioned and oriented for demethylation. Key residues contributing to K36me specificity on histone H3 are G33 and G34 (positioned within a narrow channel), P38 (a turn residue), and Y41 (inserts into its own pocket). Given that KDM2A was found to also bind the H3K36me3 peptide, we postulate that steric constraints could prevent α-ketoglutarate from undergoing an “off-line”-to-“in-line” transition necessary for the demethylation reaction. Furthermore, structure-guided substitutions of residues in the KDM2A catalytic pocket abrogate KDM2A-mediated functions important for suppression of cancer cell phenotypes. Together, our results deduce insights into the molecular basis underlying KDM2A regulation of the biologically important methylated H3K36 mark.