bluuebunny/crossref_metadata_2025 huggingface dataset:
A Critical Assessment of RIN Price Behavior and the Implications for Corn, Ethanol, and Gasoline Price Relationships
Authors: Whistance Jarrett , Thompson Wyatt
Published: June 2014

This study observationally and statistically assesses theories put forth regarding expected price behavior of Renewable Identification Numbers (RINs) using a dataset of daily RIN price observations from January 2009 through May 2013. RIN price behavior tends to follow theoretical expectations, but some notable exceptions occur, the causes of which remain uncertain. Information provided by RIN prices is used to test the implications of a binding renewable fuel standard (RFS) versus a nonbinding RFS on ethanol‐gasoline and corn‐gasoline price relationships. In certain cases, cointegration tests provide evidence that the relationships are weaker when the RFS mandates are believed to be binding.
SMaSH: a benchmarking toolkit for human genome variant calling
Authors: Talwalkar Ameet , Liptrap Jesse , Newcomb Julie , Hartl Christopher , Terhorst Jonathan , Curtis Kristal , Bresler Ma’ayan , Song Yun S. , Jordan Michael I. , Patterson David
Published: June 2014

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers.

Results: We propose SM a SH, a benchmarking methodology for evaluating germline variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on these benchmarking data. Moreover, we illustrate the utility of SM a SH to evaluate the performance of some leading single-nucleotide polymorphism, indel and structural variant calling algorithms.

Availability and implementation: We provide free and open access online to the SM a SH tool kit, along with detailed documentation, at smash.cs.berkeley.edu

Contact:  ameet@cs.berkeley.edu or pattrsn@cs.berkeley.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Tedna: a transposable element
de novo
assembler
Authors: Zytnicki Matthias , Akhunov Eduard , Quesneville Hadi
Published: June 2014

Motivation : Recent technological advances are allowing many laboratories to sequence their research organisms. Available de novo assemblers leave repetitive portions of the genome poorly assembled. Some genomes contain high proportions of transposable elements, and transposable elements appear to be a major force behind diversity and adaptation. Few de novo assemblers for transposable elements exist, and most have either been designed for small genomes or 454 reads.

Results : In this article, we present a new transposable element de novo assembler, Tedna, which assembles a set of transposable elements directly from the reads. Tedna uses Illumina paired-end reads, the most widely used sequencing technology for de novo assembly, and forms full-length transposable elements.

Availability and implementation : Tedna is available at http://urgi.versailles.inra.fr/Tools/Tedna , under the GPLv3 license. It is written in C++11 and only requires the Sparsehash Package, freely available under the New BSD License. Tedna can be used on standard computers with limited RAM resources, although it may also use large memory for better results. Most of the code is parallelized and thus ready for large infrastructures.

Contact : matthias.zytnicki@toulouse.inra.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Dizziness, Vertigo, and Syndromes of the Medulla
Authors: Wray Shirley H.
Published: June 2014

reviews the medulla’s vestibular components (the vestibular, perihypoglossal, and inferior olivary nuclei ), and the components of the vestibular labyrinth (the semicircular canals and the otolith receptors) preparatory to a full discussion of dizziness and vertigo as diagnostic symptoms. The model used for history-taking is extensive and allows for clear distinction to be made between the two symptoms and their implications for risk of stroke. Direction- changing nystagmus as a localizing sign is discussed in depth, and provocative tests to elicit nystagmus by suppression of fixation are presented in clinical detail. The head-thrust (head impulse) test is also described as a simple way to identify a complete unilateral or bilateral loss of vestibular function at the bedside. Medullary syndromes illustrated by case studies include oculopalatal tremor, benign paroxysmal positional vertigo, upbeat and apogeotropic nystagmus, Wallenberg’s syndrome due to infarction of the medulla, and a case of intractable hiccups.
Severe Morbidity and Mortality Risk From Malaria in the United States, 1985–2011
Authors: Hwang Jimee , Cullen Karen A. , Kachur S. Patrick , Arguin Paul M. , Baird J. Kevin
Published: May 2014

Background.  Recent reports of Plasmodium vivax associated with severe syndromes and mortality from malaria endemic areas questions the “benign” course of non-falciparum malarias.

Methods.  We retrospectively analyzed data from patients reported to the US Centers for Disease Control and Prevention with a diagnosis of malaria parasite single-species infection between 1985 and 2011. Patients classified as having severe illness were further classified according to outcome (survival versus death) and clinical syndrome.

Results.  Among all cases, .9% of Plasmodium falciparum cases resulted in death and 9.3% were classified as severe, whereas .09% of P. vivax cases resulted in death and 1.3% were classified as severe. The odds ratios for severe illness among 15 272 diagnoses of P. falciparum relative to patients diagnosed with P. vivax (n = 12 152), Plasmodium malariae (n = 1254), or Plasmodium ovale (n = 903) was 7.5, 5.7, and 5.0, respectively (P < .0001 for all); in contrast, the corresponding odds ratios for death among those severely ill was 1.6, 1.1, and .8 (P > .1 for all), respectively. Compared with P. vivax (n = 163), the odds of P. falciparum cases classified as severely ill (n = 1416) were 1.9 (P = .0006), .5 (P = .001), and 1.3 times (P = .1) as likely to present as cerebral, acute respiratory distress, and renal syndromes, respectively.

Conclusions.  Although less common, patients presenting with non-falciparum even in the United States can develop severe illness, and severe illness in patients having malaria of any species threatens life.
See-saw rocking: an
in vitro
model for mechanotransduction research
Authors: Tucker R. P. , Henningsson P. , Franklin S. L. , Chen D. , Ventikos Y. , Bomphrey R. J. , Thompson M. S.
Published: June 2014

In vitro
mechanotransduction studies, uncovering the basic science of the response of cells to mechanical forces, are essential for progress in tissue engineering and its clinical application. Many varying investigations have described a multitude of cell responses; however, as the precise nature and magnitude of the stresses applied are infrequently reported and rarely validated, the experiments are often not comparable, limiting research progress. This paper provides physical and biological validation of a widely available fluid stimulation device, a see-saw rocker, as an
in vitro
model for cyclic fluid shear stress mechanotransduction. This allows linkage between precisely characterized stimuli and cell monolayer response in a convenient six-well plate format. Models of one well were discretized and analysed extensively using computational fluid dynamics to generate convergent, stable and consistent predictions of the cyclic fluid velocity vectors at a rocking frequency of 0.5 Hz, accounting for the free surface. Validation was provided by comparison with flow velocities measured experimentally using particle image velocimetry. Qualitative flow behaviour was matched and quantitative analysis showed agreement at representative locations and time points. Maximum shear stress of 0.22 Pa was estimated near the well edge, and time-average shear stress ranged between 0.029 and 0.068 Pa. Human tenocytes stimulated using the system showed significant increases in collagen and GAG secretion at 2 and 7 day time points. This
in vitro
model for mechanotransduction provides a versatile, flexible and inexpensive method for the fluid shear stress impact on biological cells to be studied.
Identification of functional parameters for the classification of older female fallers and prediction of ‘first-time’ fallers
Authors: König N. , Taylor W. R. , Armbrecht G. , Dietzel R. , Singh N. B.
Published: June 2014

Falls remain a challenge for ageing societies. Strong evidence indicates that a previous fall is the strongest single screening indicator for a subsequent fall and the need for assessing fall risk without accounting for fall history is therefore imperative. Testing in three functional domains (using a total 92 measures) were completed in 84 older women (60–85 years of age), including muscular control, standing balance, and mean and variability of gait. Participants were retrospectively classified as fallers (
n
= 38) or non-fallers (
n
= 42) and additionally in a prospective manner to identify first-time fallers (FTFs) (
n
= 6) within a 12-month follow-up period. Principal component analysis revealed that seven components derived from the 92 functional measures are sufficient to depict the spectrum of functional performance. Inclusion of only three components, related to mean and temporal variability of walking, allowed classification of fallers and non-fallers with a sensitivity and specificity of 74% and 76%, respectively. Furthermore, the results indicate that FTFs show a tendency towards the performance of fallers, even before their first fall occurs. This study suggests that temporal variability and mean spatial parameters of gait are the only functional components among the 92 measures tested that differentiate fallers from non-fallers, and could therefore show efficacy in clinical screening programmes for assessing risk of first-time falling.
Detection of anen masseand reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation
Authors: Whelan Donna R. , Hiscox Thomas J. , Rood Julian I. , Bambery Keith R. , McNaughton Don , Wood Bayden R.
Published: June 2014

The role that DNA conformation plays in the biochemistry of cells has been the subject of intensive research since DNA polymorphism was discovered. B-DNA has long been considered the native form of DNA in cells although alternative conformations of DNA are thought to occur transiently and along short tracts. Here, we report the first direct observation of a fully reversibleen masseconformational transition between B- and A-DNA within live bacterial cells using Fourier transform infrared (FTIR) spectroscopy. This biospectroscopic technique allows for non-invasive and reagent-free examination of the holistic biochemistry of samples. For this reason, we have been able to observe the previously unknown conformational transition in all four species of bacteria investigated. Detection of this transition is evidence of a previously unexplored biological significance for A-DNA and highlights the need for new research into the role that A-DNA plays as a cellular defence mechanism and in stabilizing the DNA conformation. Such studies are pivotal in understanding the role of A-DNA in the evolutionary pathway of nucleic acids. Furthermore, this discovery demonstrates the exquisite capabilities of FTIR spectroscopy and opens the door for further investigations of cell biochemistry with this under-used technique.
Novel biopesticide based on a spider venom peptide shows no adverse effects on honeybees
Authors: Nakasu Erich Y. T. , Williamson Sally M. , Edwards Martin G. , Fitches Elaine C. , Gatehouse John A. , Wright Geraldine A. , Gatehouse Angharad M. R.
Published: June 2014

Evidence is accumulating that commonly used pesticides are linked to decline of pollinator populations; adverse effects of three neonicotinoids on bees have led to bans on their use across the European Union. Developing insecticides that pose negligible risks to beneficial organisms such as honeybees is desirable and timely. One strategy is to use recombinant fusion proteins containing neuroactive peptides/proteins linked to a ‘carrier’ protein that confers oral toxicity. Hv1a/GNA (
Galanthus nivalis
agglutinin), containing an insect-specific spider venom calcium channel blocker (ω-hexatoxin-Hv1a) linked to snowdrop lectin (GNA) as a ‘carrier’, is an effective oral biopesticide towards various insect pests. Effects of Hv1a/GNA towards a non-target species,
Apis mellifera
, were assessed through a thorough early-tier risk assessment. Following feeding, honeybees internalized Hv1a/GNA, which reached the brain within 1 h after exposure. However, survival was only slightly affected by ingestion (LD
50
> 100 µg bee
−1
) or injection of fusion protein. Bees fed acute (100 µg bee
−1
) or chronic (0.35 mg ml
−1
) doses of Hv1a/GNA and trained in an olfactory learning task had similar rates of learning and memory to no-pesticide controls. Larvae were unaffected, being able to degrade Hv1a/GNA. These tests suggest that Hv1a/GNA is unlikely to cause detrimental effects on honeybees, indicating that atracotoxins targeting calcium channels are potential alternatives to conventional pesticides.
Trophic interactions of fish communities at midwater depths enhance long-term carbon storage and benthic production on continental slopes
Authors: Trueman C. N. , Johnston G. , O'Hea B. , MacKenzie K. M.
Published: June 2014

Biological transfer of nutrients and materials between linked ecosystems influences global carbon budgets and ecosystem structure and function. Identifying the organisms or functional groups that are responsible for nutrient transfer, and quantifying their influence on ecosystem structure and carbon capture is an essential step for informed management of ecosystems in physically distant, but ecologically linked areas. Here, we combine natural abundance stable isotope tracers and survey data to show that mid-water and bentho-pelagic-feeding demersal fishes play an important role in the ocean carbon cycle, bypassing the detrital particle flux and transferring carbon to deep long-term storage. Global peaks in biomass and diversity of fishes at mid-slope depths are explained by competitive release of the demersal fish predators of mid-water organisms, which in turn support benthic fish production. Over 50% of the biomass of the demersal fish community at depths between 500 and 1800 m is supported by biological rather than detrital nutrient flux processes, and we estimate that bentho-pelagic fishes from the UK–Irish continental slope capture and store a volume of carbon equivalent to over 1 million tonnes of CO
2
every year.
Rhizocola hellebori gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae containing 3,4-dihydroxydiaminopimelic acid in the cell-wall peptidoglycan
Authors: Matsumoto Atsuko , Kawaguchi Yoko , Nakashima Takuji , Iwatsuki Masato , Ōmura Satoshi , Takahashi Yōko
Published: June 2014

An actinomycete strain, K12-0602T, was isolated from the root of a Helleborus orientalis plant in Japan. The 16S rRNA gene sequence of strain K12-0602T showed that it had a close relationship with members of the family

Micromonosporaceae

and the 16S rRNA gene sequence similarity values between strain K12-0602T and type strains of type species of 27 genera belonging to the family

Micromonosporaceae

were below 96.2 %. MK-9 (H4) and MK-9 (H6) were detected as major menaquinones, and galactose, xylose, mannose and ribose were present in the whole-cell hydrolysate. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were iso-C15 : 0, iso-C16 : 0, C17 : 1ω9c and anteiso-C17 : 0. Phosphatidylethanolamine was detected as the phospholipid corresponding to phospholipid type II. The G+C content of the genomic DNA was 67 mol%. Analyses of the cell-wall peptidoglycan by TLC and LC/MS showed that it was composed of alanine, glycine, hydroxylglutamic acid and an unknown amino acid, which was subsequently determined to be 3,4-dihydroxydiaminopimelic acid using instrumental analyses, including NMR and mass spectrometry. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strain K12-0602T represents a novel species of a new genus in the family

Micromonosporaceae

, for which the name Rhizocola hellebori gen. nov., sp. nov. is proposed. The type strain of the type species is K12-0602T ( = NBRC 109834T = DSM 45988T). This is the first report, to our knowledge, of 3,4-dihydroxydiaminopimelic acid being found as a diamino acid in bacterial cell-wall peptidoglycan.
Generation of an infectious Negev virus cDNA clone
Authors: Gorchakov Rodion V. , Tesh Robert B. , Weaver Scott C. , Nasar Farooq
Published: May 2014

The genus Negevirus consists of insect-only viruses isolated from mosquitoes and sandflies. Here, we report the successful construction of a full-length infectious cDNA clone of Negev virus (NEGV) strain M30957. Viral RNA was transcribed in vitro and virus was readily rescued with or without the use of a cap analogue. These results strongly suggest that NEGV, and likely other members within the genus, is a non-segmented, single-stranded, positive-sense RNA virus.
Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements
Authors: Turelli Priscilla , Castro-Diaz Nathaly , Marzetta Flavia , Kapopoulou Adamandia , Raclot Charlène , Duc Julien , Tieng Vannary , Quenneville Simon , Trono Didier
Published: May 2014

Reverse transcription-derived sequences account for at least half of the human genome. Although these retroelements are formidable motors of evolution, they can occasionally cause disease, and accordingly are inactivated during early embryogenesis through epigenetic mechanisms. In the mouse, at least for endogenous retroviruses, important mediators of this process are the tetrapod-specific KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor TRIM28. The present study demonstrates that KRAB/TRIM28-mediated regulation is responsible for controlling a very broad range of human-specific endogenous retroelements (EREs) in human embryonic stem (ES) cells and that it exerts, as a consequence, a marked effect on the transcriptional dynamics of these cells. It further reveals reciprocal dependence between TRIM28 recruitment at specific families of EREs and DNA methylation. It finally points to the importance of persistent TRIM28-mediated control of ERE transcriptional impact beyond their presumed inactivation by DNA methylation.
A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis inArabidopsisIntraspecific Hybrids
Authors: Ng Danny W.-K. , Miller Marisa , Yu Helen H. , Huang Tien-Yu , Kim Eun-Deok , Lu Jie , Xie Qiguang , McClung C. Robertson , Chen Z. Jeffrey
Published: June 2014

Hybrid plants and animals often show increased levels of growth and fitness, a phenomenon known as hybrid vigor or heterosis. Circadian rhythms optimize physiology and metabolism in plants and animals. In plant hybrids and polyploids, expression changes of the genes within the circadian regulatory network, such as CIRCADIAN CLOCK ASSOCIATED1 (CCA1), lead to heterosis. However, the relationship between allelic CCA1 expression and heterosis has remained elusive. Here, we show a parent-of-origin effect on altered circadian rhythms and heterosis in Arabidopsis thaliana F1 hybrids. This parent-of-origin effect on biomass heterosis correlates with altered CCA1 expression amplitudes, which are associated with methylation levels of CHH (where H = A, T, or C) sites in the promoter region. The direction of rhythmic expression and hybrid vigor is reversed in reciprocal F1 crosses involving mutants that are defective in the RNA-directed DNA methylation pathway (argonaute4 and nuclear RNA polymerase D1a) but not in the maintenance methylation pathway (methyltransferase1 and decrease in DNA methylation1). This parent-of-origin effect on circadian regulation and heterosis is established during early embryogenesis and maintained throughout growth and development.
Colour in a new light: a spectral perspective on the quantitative genetics of carotenoid colouration
Authors: Evans Simon R. , Sheldon Ben C.
Published: May 2014

Carotenoid‐based colours are model traits for research on animal signalling and sexual selection but, whereas the consequences of variable expression have been extensively studied, its causes are rarely quantified. This issue is complicated by the composite nature of carotenoid‐based colour patches, which combine pigments and a reflective background. Ultimately, the evolution of such colours will be determined by the processes that govern variable expression of these mechanisms.

We present a novel approach to assessing the quantitative genetics of colour expression, in which reflectance spectra are analysed directly, thereby avoiding the data loss and inherent subjectivity of summary colour variables. Further, the influence of the component mechanisms can be distinguished in spectral analyses due to their contrasting wavelength‐dependencies.

Using data from a 6‐year study of carotenoid‐based plumage reflectance in wild great tits (Parus major), we employ a multi‐parallel ‘animal modelling’ approach to estimate sources of variance for narrow (2 nm) wavebands across the visible spectrum.

Moderate heritability estimates were limited to the violet‐blue region of the spectrum, diagnostic of the carotenoid content of plumage being heritable. The natal environment effect was limited entirely to the violet‐blue, again indicating that it relates to variation in carotenoid content of feathers. Other wavelengths were sensitive to annual and permanent environmental variation but only marginally influenced by additive genetic variation. Hence, background reflectance is the component that is more sensitive to the environment.

Analysing reflectance spectra directly provided an objective perspective of the dynamics of colour expression that is not apparent when relying on summary colour scores. In this case, our results suggest that carotenoid deposition may be an effective target of selection and hence could explain the important role carotenoids frequently play in intraspecific signalling.
Specific detection of the floodwater mosquitoes Aedes sticticus and Aedes vexans DNA in predatory diving beetles
Authors: Vinnersten Thomas Z. Persson , Halvarsson Peter , Lundström Jan O.
Published: June 2014

Floodwater mosquitoes (Diptera: Culicidae) are associated with periodically flooded wet meadows, marshes, and swamps in floodplains of major rivers worldwide, and their larvae are abundant in the shallow parts of flooded areas. The nuisance caused by the blood‐seeking adult female mosquitoes motivates mosquito control. Larviciding with Bacillus thuringiensis israelensis is considered the most environmentally safe method. However, some concern has been raised whether aquatic predatory insects could be indirectly affected by this reduction in a potential vital prey. Top predators in the temporary wetlands in the River Dalälven floodplains are diving beetles (Coleoptera: Dytiscidae), and Aedes sticticus and Ae. vexans are the target species for mosquito control. For detailed studies on this aquatic predator–prey system, we developed a polymerase chain reaction (PCR) assay for detection of mosquito DNA in the guts of medium‐sized diving beetles. Primers were designed for amplifying short mitochondrial DNA fragments of the cytochrome C oxidase subunit I (COI) gene in Ae. sticticus and Ae. vexans, respectively. Primer specificity was confirmed and half‐life detectability of Ae. sticticus DNA in diving beetle guts was derived from a feeding and digestion experiment. The Ae. sticticus DNA within diving beetle guts was detected up to 12 h postfeeding, and half‐life detectability was estimated to 5.6 h. In addition, field caught diving beetles were screened for Ae. sticticus and Ae. vexans DNA and in 14% of the diving beetles one or both mosquito species were detected, showing that these mosquito species are utilized as food by the diving beetles.
Efficient Extraction of Olive Pulp and Stone Proteins by using an Enzyme‐Assisted Method
Authors: Vergara‐Barberán María , Lerma‐García María Jesús , Herrero‐Martínez José Manuel , Simó‐Alfonso Ernesto Francisco
Published: June 2014

An efficient protein extraction protocol for proteins from olive pulp and stone by using enzymes was developed. For this purpose, different parameters that affect the extraction process, such as enzyme type and content, pH, and extraction temperature and time, were tested. The influence of these factors on protein recovery was examined using the standard Bradford assay, while the extracted proteins were characterized by sodium dodecyl sulfate‑polyacrylamide gel electrophoresis (SDS‐PAGE). The best extraction conditions were achieved at pH 7.0 and 5% (v/v) Palatase® 20000 L (lipase) for pulp and Lecitase® Ultra (phospholipase) for stone proteins. The optimal extraction temperature and time were 30 and 40 °C for 15 min for pulp and stone tissues, respectively. Under these conditions, several protein extracts coming from olive fruits of different genetic variety were analyzed, their profiles being compared by SDS‐PAGE. The developed enzyme‐assisted extraction method showed faster extraction, higher recovery, and reduced solvent usage than the nonenzymatic methods previously described in the literature. In the case of stone proteins, different electrophoretic profiles and band intensities were obtained that could be helpful to distinguish samples according to their genetic variety.
Development of High‐Performance Liquid Chromatographic for Quality and Authenticity Control of Chinese Propolis
Authors: Cui‐ping Zhang , Shuai Huang , Wen‐ting Wei , Shun Ping , Xiao‐ge Shen , Ya‐jing Li , Fu‐liang Hu
Published: June 2014

A RP‐high‐performance liquid chromatography (HPLC) method was developed for quality control of Chinese propolis by simultaneous analysis of 12 flavonoids and 8 phenolic acids. The results showed that vanillic acid, rutin, myricetin, and luteolin were not detected in all of the analyzed propolis and poplar tree gum samples. The caffeic acid, ferulic acid and p‐coumaric acid were not detected in poplar tree gum but were detected in propolis, which suggest that they are practical indexes of distinguishing propolis from poplar tree gum. The flavonoid profiles of poplar tree gum were found to be similar to those of propolis, which are dominated by pinobanksin, pinocembrin, 3‐O‐acetylpinobanksin, chrysin, and galangin. Therefore, the proposed method could be applied to exclude poplar tree gum from propolis with cafferic acid, ferulic acid, and p‐coumaric acid as qualitative markers, and distinguish poplar source resin from other illegal substances, and evaluate the quality grading of poplar‐type propolis with pinobanksin, pinocembrin, 3‐O‐acetylpinobanksin, chrysin, and galangin as qualitative and quantitative markers.
Complementary substrate‐selectivity of metabolic adaptive convergence in the lignocellulolytic performance by Dichomitus squalens
Authors: Bak Jin Seop
Published: June 2014

The lignocellulolytic platform of the wood‐decaying organism Dichomitus squalens is important for production of biodegradable elements; however, the system has not yet been fully characterized. In this study, using statistical target optimization, we analysed substrate selectivity based on a variety of D. squalens metabolic pathways using combined omics tools. As compared with the alkali‐lignin (AL) programme, the rice straw (RS) programme has the advantage of multilayered signalling to regulate cellulolytic‐related genes or to connect their pathways. The spontaneous instability of the AL programme was accelerated by harsh starvation as compared with that of the RS programme. Therefore, the AL programme converged on cellular maintenance much easier and more rapidly. However, regardless of external substrate/concentration type, the compensatory pattern of the major targets (especially peroxidases and growth regulators) was similar, functioning to maintain cellular homeostasis. Interestingly, ligninolytic‐mediated targets under non‐kaleidoscopic conditions were induced by a substrate‐input‐control, and especially this mechanism had an important effect on the early stages of the biodegradation process. This optimized target analysis could be used to understand lignocellulolytic network and to improve downstream efficiency.
Ring‐Hydroxylating Oxygenase database: a database of bacterial aromatic ring‐hydroxylating oxygenases in the management of bioremediation and biocatalysis of aromatic compounds
Authors: Chakraborty Joydeep , Jana Tanmoy , Saha Sudipto , Dutta Tapan K.
Published: June 2014

Bacterial Rieske‐type aromatic ring‐hydroxylating oxygenases (RHOs) constitute a large family of enzymes, primarily involved in bioremediation of diverse aromatic compounds in the environment. In the present study, we have designed a manually curated database, Ring‐Hydroxylating Oxygenase database (RHObase), which provides comprehensive information on all biochemically characterized bacterial RHOs. It consists of ∼ 1000 entries including 196 oxygenase α‐subunits, 153 oxygenase β‐subunits, 92 ferredoxins and 110 reductases, distributed among 131 different bacterial strains implementing a total of 318 oxygenation reactions. For each protein, users can get detailed information about its structure and conserved domain(s) with motif signature. RHObase allows users to search a query, based on organism, oxygenase, substrate, or protein structure. In addition, this resource provides analysis tools to perform blast search against RHObase for prediction of putative substrate(s) for the query oxygenase and its phylogenetic affiliation. Furthermore, there is an integrated cheminformatics tool to search for structurally similar compound(s) in the database vis‐a‐vis RHO(s) capable of transforming those compound(s). Resources in the RHObase and multiple search/display options therein are intended to provide oxygenase‐related requisite information to researchers, especially working in the field of environmental microbiology and biocatalysis to attain difficult chemistry of biotechnological importance.
Genetic and environmental regulation of plant architectural traits and opportunities for pest control in raspberry
Authors: Graham J. , Hackett C.A. , Smith K. , Karley A.J. , Mitchell C. , Roberts H. , O'Neill T.
Published: May 2014

Part of the reason for the under‐exploitation of physical resistance traits in plant breeding is that the genetic basis and heritability of these traits is poorly characterised, and any associations of particular traits with pest and disease resistances have yet to be determined. In raspberry, some associations between architectural traits and disease resistances have been demonstrated, for example cane hairs and resistance to cane diseases. The aim of this work is to examine a range of traits, including leaf trichomes, leaf density, cane density, bush density, lateral length and lateral numbers, to determine the heritability and therefore breeding potential of these traits. The effect of these traits against aphids and spider mites, two important pests in raspberry, was examined. Chromosomal regions with candidate genes regulating these traits were identified as the first step to understanding the genetic control.
Medical care and organisation at the 2012 Roskilde Music Festival: a prospective observational study
Authors: STAGELUND S. , JANS Ø. , NIELSEN K. , JANS H. , WILDGAARD K.
Published: June 2014

Background

Music festivals, with a mix of music, alcohol and camping at the festival site combined with low hygiene, have become an integral part of society and attracts large numbers of guests. Our study was performed in order to increase the very limited knowledge on health‐care issues and organisation of major music festivals.

Method

Pre‐defined illness and injury categories were constructed based on categories previously reported from music festivals. We prospectively recorded patient presentations to the Medical Health Care Organisation (MHCO) at the 2012 Roskilde Festival.

Results

During 10 days, more than 130,000 guests and volunteers attended the 2012 Roskilde Festival. Ten thousand six hundred thirty patient presentations were registered between the 30th of June and 9th of July 2012 by the MHCO. The majority of patient presentations, 6919, could be handled by first‐aid volunteers with different levels of training. The remaining 3473 patient presentations were assessed to require further health‐care competencies or additional resources such as prescriptions, medication or suturing. Two hundred thirty‐eight patient presentations were triaged to a designated observation area. Two hundred sixty patients were referred to a local hospital, a general practitioner or a dentist. The overall patient presentation rate was 72/1000 attendees, and the transport‐to‐hospital rate was 1.8/1000 attendees.

Conclusion

Our study demonstrates that illnesses and injuries are frequent, although mostly minor, in this normally low‐risk population consisting of primarily young and healthy guests. However, comparison with other recent events was difficult as only limited data have been published from other music festivals. Future festivals should publish similar data.
Insightful Insiders? Insider Trading and Stock Return around Debt Covenant Violation Disclosures
Authors: Griffin Paul A. , Lont David H. , McClune Kate
Published: June 2014

This study asks whether insider trading associates with an information advantage around first‐time debt covenant violation disclosures in SEC filings, which potentially results from early access to information about the debt covenant violation disclosure. We document two results. First, we find net insider selling up to 12 months before a debt covenant violation disclosure, which precedes investors' negative returns before disclosure; and net insider buying up to 12 months after disclosure, which precedes investors' positive returns after disclosure. Second, we show that net insider trading one to two months before and after the violation disclosure associates predictably with investors' short‐term reaction to the covenant violation announcement.
Mild cognitive impairment diagnosed with the new DSM‐5 criteria: prevalence and associations with non‐cognitive psychopathology
Authors: Lopez‐Anton R. , Santabárbara J. , De‐la‐Cámara C. , Gracia‐García P. , Lobo E. , Marcos G. , Pirez G. , Saz P. , Haro J. M. , Rodríguez‐Mañas L. , Modrego P. J. , Dewey M. E. , Lobo A.
Published: June 2014

Objective

To contrast the prevalence of mild cognitive impairment (MCI) as diagnosed using DSM‐5 criteria (DSM5‐MCI) with MCI as diagnosed using Petersen's criteria (P‐MCI) and to explore the association of both with non‐cognitive psychopathological symptoms (NCPS).

Method

A two‐phase epidemiological screening was implemented in a population‐based sample of individuals aged 55+ (n = 4803). The Geriatric Mental State (GMS) was the main psychopathological instrument used, and AGECAT was used to make psychiatric diagnoses. Research psychiatrists diagnosed DSM5‐MCI and P‐MCI using operational criteria. Logistic regression models were then used to investigate the association of MCI with anxiety and depression and with NCPS.

Results

Weighted prevalence of DSM5‐MCI and P‐MCI was, respectively, 3.72% and 7.93% for the aged 65+. NCPS were common in both MCI categories, but negative‐type symptoms such as ‘anergia’ and ‘observed slowness’ were considerably more frequent among persons with DSM5‐MCI. Anxiety and depression diagnostic categories were associated with both P‐MCI and DSM5‐MCI, but affective‐type symptoms were mainly associated with P‐MCI. Some negative‐type symptoms were inversely associated with P‐MCI, and no association was observed with DSM5‐MCI.

Conclusion

The prevalence of DSM5‐MCI was half that of P‐MCI. Negative‐type NCPS were more frequently and typically associated with DSM5‐MCI.
Estimating occupancy using spatially and temporally replicated snow surveys
Authors: Whittington J. , Heuer K. , Hunt B. , Hebblewhite M. , Lukacs P. M.
Published: June 2014

Occupancy modelling is increasingly used to monitor changes in the spatial distribution of rare and threatened species. Occupancy methods have traditionally relied upon temporally replicated surveys to estimate detection probability. Recently, occupancy models with spatial replication have been used to estimate detection probabilities over large geographical areas that are difficult to survey repeatedly. We developed occupancy models that combine spatially and temporally replicated data and applied them to snow‐tracking surveys of six species, including wolverine Gulo gulo and Canadian lynx Lynx canadensis. We surveyed thirty‐nine 100‐km2 cells and used 1‐km trail segments within cells as spatial replicates. We surveyed 56% of the cells once and 44% of the cells between 2 and 14 times, resulting in a total of 872 km surveyed. We compared four occupancy models that incorporated spatial correlation in detection probability and hierarchically estimated occupancy at two spatial scales: cell occupancy and segment presence. We detected strong serial correlation in probability of detection for all species. Our models with serial correlation had higher occupancy estimates with larger confidence intervals than models assuming segments were independent and exchangeable. Spatial and temporal replicates have identical power to detect decreases in occupancy when survey segments are independent, but spatial correlation in detection probability can reduce the power of spatial replicates. The effects of spatial correlation are more pronounced when detection probability is low. Application of temporal replicates to spatial replicated surveys increases the precision of occupancy estimates, but sampling design trade‐offs between number of sites and spatial versus temporal replicates need to balance levels of spatial correlation in detection probability with costs to visit sites.
Prevalence and risk factors for retinopathy in persons without diabetes: the Singapore Indian Eye Study
Authors: Bhargava Mayuri , Cheung Carol Yim‐lui , Sabanayagam Charumathi , Huang Lei , Lamoureux Ecosse L. , Wang Jie Jin , Tai E.‐S. , Heng C.‐K. , Ikram Mohammad Kamran , Mitchell Paul , Wong Tien Yin
Published: June 2014

Purpose

To describe prevalence and risk factors for retinopathy in an Asian Indian population without diabetes.

Methods

A population‐based cross‐sectional study of 3400 Indians aged 40–80 years residing in Singapore was conducted. Retinopathy was assessed from retinal photographs by trained graders using modified Airlie House Classification System. Risk factors were assessed from standardized interviews, clinical examinations and laboratory investigations. Diabetes mellitus was defined as glycosylated haemoglobin ≥6.5%, use of diabetic medication or physician diagnosis of diabetes.

Results

Among the 1900 individuals without diabetes, mean HbA1c was 5.7% and mean systolic blood pressure was 132.4 mmHg. Age‐standardized prevalence of retinopathy was 5.05% (n = 98; 95% confidence interval [CI], 4.07–6.21), with no significant difference in retinopathy prevalence between males (6.15%) and females (4.13%). Among non‐diabetic persons with retinopathy, 96.9% (n = 95) had signs of minimal‐to‐mild retinopathy while 3.06% (n = 3) had moderate‐to‐severe retinopathy. After adjusting for multiple covariables, retinopathy signs were associated with higher levels of HbA1c (odds ratio [OR], 2.4; 95% CI, 1.3–4.5; per% increase), systolic blood pressure (OR, 1.02; 95% CI, 1.01–1.03; per mmHg increase) and serum creatinine (OR, 1.005; 95% CI, 1.002–1.009; per mm increase), but not C‐reactive protein, cigarette smoking or lipid levels.

Conclusion

One in 20 Asian Indian persons without diabetes had retinopathy signs. Risk factors for these signs include higher glycosylated haemoglobin, systolic blood pressure and serum creatinine.
Feminist geographies of new spatial media
Authors: Leszczynski Agnieszka , Elwood Sarah
Published: June 2014

Critical GIS emphasized the ways in which social, political, and economic inequalities are (re)produced through spatial information technologies and attendant practices. In the mid‐1990s through the early 2000s, feminist interventions challenged the presumed gender neutrality and universality of GIS and brought gender to the fore of Critical GIS concerns. However, the rise of nascent web‐based spatial information technologies—or new spatial media—signals the need to extend this work to determine how it is that gender matters differently in this newly diversified, pervasive, and public context of geographic information technologies. Building on an analysis of online commentaries and an assessment of the functions and promotional material of several illustrative applications, we argue that gender continues to “matter” vis‐à‐vis new spatial media in three key dimensions: i) new practices of data creation and curation; ii) affordances of new technologies; and iii) new digital spatial mediations of everyday life.
Isocitrate dehydrogenase mutation is frequently observed in giant cell tumor of bone
Authors: Kato Kaneko Mika , Liu Xing , Oki Hiroharu , Ogasawara Satoshi , Nakamura Takuro , Saidoh Noriko , Tsujimoto Yuta , Matsuyama Yuka , Uruno Akira , Sugawara Masato , Tsuchiya Takashi , Yamakawa Mitsunori , Yamamoto Masayuki , Takagi Michiaki , Kato Yukinari
Published: June 2014

Giant cell tumors of bone (GCTB) are benign and locally destructive tumors that include osteoclast‐type multinuclear giant cells. No available treatment is definitively effective in curing GCTB, especially in surgically unresectable cases. Isocitrate dehydrogenase (IDH) mutations have been reported not only in gliomas and acute myeloid leukemias, but also in cartilaginous tumors and osteosarcomas. However, IDH mutations in GCTB have not been investigated. The IDH mutations are remarkably specific to arginine 132 (R132) in IDH1 and arginine 172 (R172) or arginine 140 (R140) in IDH2; IDH1/2 mutations are known to convert α‐ketoglutarate to oncometabolite R(‐)‐2‐hydroxyglutarate. We recently reported that the most frequent IDH mutation in osteosarcomas is IDH2‐R172S, which was detected by MsMab‐1, a multispecific anti‐IDH1/2 mAb. Herein, we newly report the IDH mutations in GCTB, which were stained by MsMab‐1 in immunohistochemistry. DNA direct sequencing and subcloning identified IDH mutations of GCTB as IDH2‐R172S (16 of 20; 80%). This is the first report to describe IDH mutations in GCTB, and MsMab‐1 can be anticipated for use in immunohistochemical determination of IDH1/2 mutation‐bearing GCTB.
Magnetic resonance imaging in zirconia‐based dental implantology
Authors: Duttenhoefer Fabian , Mertens Marianne E. , Vizkelety Josef , Gremse Felix , Stadelmann Vincent A. , Sauerbier Sebastian
Published: June 2014

Objectives

X‐ray‐based planning and post‐implantation assessment of titanium implants is the commonly accepted standard to date. However, new implant materials such as zirconia (ZrO2) have become available, and magnetic resonance imaging may be a valuable alternative with these implants. The present in vitro study investigated artifacts produced by titanium and zirconia implants in magnetic resonance imaging (MRI) and assessed the accuracy of pre‐implant planning and post‐implantation assessment comparing MRI to standard X‐ray‐based imaging modalities: Orthopantomogram (OPT), cone beam (CBCT), and computed tomography (CT).

Materials and methods

Twelve porcine mandibles were prepared and scanned (MRI, OPT, CBCT, μCT), and bone height above the nerve canal was measured. Specimens were implanted with either two titanium or zirconia implants and rescanned to investigate the influence of implant materials on post‐implantation assessment. MRI and μCT artifacts were quantified with implants embedded in gelatin phantoms and porcine specimens.

Results

Compared with CBCT set as standard, μCT, OPT, and MRI showed similar accuracy in pre‐op bone height measurements. Post‐implantation, while titanium implants induced a strong B0‐field distortion resulting in extensive signal voids, zirconia implants were clearly depictable with only minor distortions.

Conclusions

Excellent contrast, limited artifacts, radiation‐free and accurate implant assessment may indicate that MRI is a valuable imaging alternative for zirconia‐based implant dentistry.
The impact of diabetes mellitus and glycemic control on clinical outcomes following liver transplant for hepatitis C
Authors: Morbitzer Kathryn A. , Taber David J. , Pilch Nicole A. , Meadows Holly B. , Fleming James N. , Bratton Charles F. , McGillicuddy John W. , Baliga Prabhakar K. , Chavin Kenneth D.
Published: June 2014

Hepatitis C is the leading indication for liver transplantation in the USA and recurrence is universal. The impact of preexisting diabetes, new‐onset diabetes after transplant (NODAT), and glycemic control on fibrosis progression has not been studied. This retrospective longitudinal cohort study included adult liver recipients with hepatitis C transplanted between 2000 and 2011. Patients were divided into three groups: preexisting diabetes (n = 41), NODAT (n = 59), and no diabetes (n = 103). Patients with preexisting diabetes (70%) or NODAT (59%) were more likely to develop hepatitis C recurrence (≥stage 1 fibrosis), as compared to non‐diabetics (36%, p = 0.006). There was also a trend toward a higher incidence of at least Stage 2 fibrosis (36% and 48% vs. 23%, respectively; p = 0.063). Patients with tight glycemic control had a lower rate of Stage 2 fibrosis development (78% vs. 60%, p = 0.027), while those with good control (<150 mg/dL) also had lower rates of Stage 2 fibrosis (84% vs. 62%, p = 0.004). Multivariable analysis verified a decreased rate of recurrence for patients with blood glucose <138 mg/dL (p = 0.021), after controlling for confounders. These results demonstrate that diabetes is strongly associated with an increased risk of hepatitis C virus‐related fibrosis development and glycemic control may reduce the risk and severity of recurrence.