bluuebunny/crossref_metadata_2025 huggingface dataset:
mTOR complex 2-Akt signaling at mitochondria-associated endoplasmic reticulum membranes (MAM) regulates mitochondrial physiology
Authors: Betz Charles , Stracka Daniele , Prescianotto-Baschong Cristina , Frieden Maud , Demaurex Nicolas , Hall Michael N.
Published: July 2013

The target of rapamycin (TOR) is a highly conserved protein kinase and a central controller of growth. Mammalian TOR complex 2 (mTORC2) regulates AGC kinase family members and is implicated in various disorders, including cancer and diabetes. Here we report that mTORC2 is localized to the endoplasmic reticulum (ER) subcompartment termed mitochondria-associated ER membrane (MAM). mTORC2 localization to MAM was growth factor-stimulated, and mTORC2 at MAM interacted with the IP
3
receptor (IP3R)-Grp75–voltage-dependent anion-selective channel 1 ER-mitochondrial tethering complex. mTORC2 deficiency disrupted MAM, causing mitochondrial defects including increases in mitochondrial membrane potential, ATP production, and calcium uptake. mTORC2 controlled MAM integrity and mitochondrial function via Akt mediated phosphorylation of the MAM associated proteins IP3R, Hexokinase 2, and phosphofurin acidic cluster sorting protein 2. Thus, mTORC2 is at the core of a MAM signaling hub that controls growth and metabolism.
Reconstituting pancreas development from purified progenitor cells reveals genes essential for islet differentiation
Authors: Sugiyama Takuya , Benitez Cecil M. , Ghodasara Amar , Liu Lucy , McLean Graeme W. , Lee Jonghyeob , Blauwkamp Timothy A. , Nusse Roeland , Wright Christopher V. E. , Gu Guoqiang , Kim Seung K.
Published: July 2013

Developmental biology is challenged to reveal the function of numerous candidate genes implicated by recent genome-scale studies as regulators of organ development and diseases. Recapitulating organogenesis from purified progenitor cells that can be genetically manipulated would provide powerful opportunities to dissect such gene functions. Here we describe systems for reconstructing pancreas development, including islet β-cell and α-cell differentiation, from single fetal progenitor cells. A strict requirement for native genetic regulators of in vivo pancreas development, such as
Ngn3
,
Arx
, and
Pax4
, revealed the authenticity of differentiation programs in vitro. Efficient genetic screens permitted by this system revealed that
Prdm16
is required for pancreatic islet development in vivo
.
Discovering the function of genes regulating pancreas development with our system should enrich strategies for regenerating islets for treating diabetes mellitus.
RNA interference knockdown of
DNA methyl-transferase 3
affects gene alternative splicing in the honey bee
Authors: Li-Byarlay Hongmei , Li Yang , Stroud Hume , Feng Suhua , Newman Thomas C. , Kaneda Megan , Hou Kirk K. , Worley Kim C. , Elsik Christine G. , Wickline Samuel A. , Jacobsen Steven E. , Ma Jian , Robinson Gene E.
Published: July 2013

Studies of DNA methylation from fungi, plants, and animals indicate that gene body methylation is ancient and highly conserved in eukaryotic genomes, but its role has not been clearly defined. It has been postulated that regulation of alternative splicing of transcripts was an original function of DNA methylation, but a direct experimental test of the effect of methylation on alternative slicing at the whole genome level has never been performed. To do this, we developed a unique method to administer RNA interference (RNAi) in a high-throughput and noninvasive manner and then used it to knock down the expression of
DNA methyl-transferase 3
(
dnmt3
), which is required for de novo DNA methylation. We chose the honey bee (
Apis mellifera
) for this test because it has recently emerged as an important model organism for studying the effects of DNA methylation on development and social behavior, and DNA methylation in honey bees is predominantly on gene bodies. Here we show that
dnmt3
RNAi decreased global genomic methylation level as expected and in addition caused widespread and diverse changes in alternative splicing in fat tissue. Four different types of splicing events were affected by
dnmt3
gene knockdown, and change in two types, exon skipping and intron retention, was directly related to decreased methylation. These results demonstrate that one function of gene body DNA methylation is to regulate alternative splicing.
Self-Reporting Bias in Chinook Salmon Sport Fisheries in Idaho: Implications for Roving Creel Surveys
Authors: McCormick Joshua L. , Quist Michael C. , Schill Daniel J.
Published: July 2013

Self-reporting bias in sport fisheries of Chinook Salmon Oncorhynchus tshawytscha in Idaho was quantified by comparing observed and angler-reported data. A total of 164 observed anglers fished for 541 h and caught 74 Chinook Salmon. Fifty-eight fish were harvested and 16 were released. Anglers reported fishing for 604 h, an overestimate of 63 h. Anglers reported catching 66 fish; four less harvested and four less released fish were reported than observed. A Monte Carlo simulation revealed that when angler-reported data were used, total catch was underestimated by 14–15 fish (19–20%) using the ratio-of-means estimator to calculate mean catch rate. Negative bias was reduced to six fish (8%) when the means-of-ratio estimator was used. Multiple linear regression models to predict reporting bias in time fished had poor predictive value. However, actual time fished and a categorical covariate indicating whether the angler fished continuously during their fishing trip were two variables that were present in all of the top a priori models evaluated. Underreporting of catch and overreporting of time fished by anglers present challenges when managing Chinook Salmon sport fisheries. However, confidence intervals were near target levels and using more liberal definitions of angling when estimating effort in creel surveys may decrease sensitivity to bias in angler-reported data.

Received January 3, 2013; accepted May 20, 2013
Disinvestment, Farm Size, and Gradual Farm Exit: The Impact of Subsidy Decoupling in a European Context
Authors: Kazukauskas Andrius , Newman Carol , Clancy Daragh , Sauer Johannes
Published: July 2013

The recent reform of the Common Agricultural Policy, which decouples farm subsidies from production, is expected to impact on farmers' production decisions. We perform a cross‐country farm‐level empirical analysis of farmers' production responses to these reforms using a panel dataset for the EU15 countries for the period 2001–2007. We apply quasi‐experimental empirical methods and find that the probability of a farm disinvesting decreased due to the policy change for most farms. However, the policy change facilitated exit for farms engaged in livestock production and those that were already in the process of leaving the sector.
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming
Authors: Guziolowski Carito , Videla Santiago , Eduati Federica , Thiele Sven , Cokelaer Thomas , Siegel Anne , Saez-Rodriguez Julio
Published: July 2013

Motivation: Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data. The training can be performed using stochastic optimization procedures, but these are unable to guarantee a global optima or to report the complete family of feasible models. This, however, is essential to provide precise insight in the mechanisms underlaying signal transduction and generate reliable predictions.

Results: We propose the use of Answer Set Programming to explore exhaustively the space of feasible logic models. Toward this end, we have developed caspo, an open-source Python package that provides a powerful platform to learn and characterize logic models by leveraging the rich modeling language and solving technologies of Answer Set Programming. We illustrate the usefulness of caspo by revisiting a model of pro-growth and inflammatory pathways in liver cells. We show that, if experimental error is taken into account, there are thousands (11 700) of models compatible with the data. Despite the large number, we can extract structural features from the models, such as links that are always (or never) present or modules that appear in a mutual exclusive fashion. To further characterize this family of models, we investigate the input–output behavior of the models. We find 91 behaviors across the 11 700 models and we suggest new experiments to discriminate among them. Our results underscore the importance of characterizing in a global and exhaustive manner the family of feasible models, with important implications for experimental design.

Availability:  caspo is freely available for download (license GPLv3) and as a web service at http://caspo.genouest.org/.

Supplementary information:  Supplementary materials are available at Bioinformatics online.

Contact:  anne.siegel@irisa.fr or saezrodriguez@ebi.ac.uk
Diagnostic and prognostic value of osteopontin in patients with acute congestive heart failure
Authors: Behnes Michael , Brueckmann Martina , Lang Siegfried , Espeter Florian , Weiss Christel , Neumaier Michael , Ahmad‐Nejad Parviz , Borggrefe Martin , Hoffmann Ursula
Published: July 2013

Aims

To evaluate the diagnostic and prognostic value of osteopontin in patients with acute dyspnoea and/or peripheral oedema suspected of having acute congestive heart failure (aCHF).

Methods and results

A total of 401 patients presenting with acute dyspnoea and/or peripheral oedema to the emergency department were prospectively enrolled and followed up for up to 5 years. Blood samples for biomarker measurements were collected on admission to the emergency department. Osteopontin combined with NT‐proBNP vs. NT‐proBNP alone for diagnosis of aCHF was tested. Additionally, osteopontin vs. NT‐proBNP for prognostic outcomes (i.e. all‐cause mortality, aCHF‐related rehospitalization, and both in combination) was tested. The diagnostic and prognostic capacity of osteopontin was tested by C‐statistics, reclassification indices, and multivariable Cox prediction models. Osteopontin plus NT‐proBNP improved the diagnostic capacity for aCHF diagnosis [accuracy 76%, 95% confidence interval (CI) 72–80%; specificity 74%, 95% CI 69–79%, net reclassification improvement (NRI) +0.10] compared with NT‐proBNP alone in the emergency department (P = 0.0001). Osteopontin independently predicted all‐cause mortality and aCHF‐related rehospitalization after 1 and 5 years. Compared with NT‐proBNP, osteopontin was of superior prognostic value, specifically in aCHF patients and for the prognostic outcome of aCHF‐related rehospitalization.

Conclusion

Osteopontin improves aCHF diagnosis when combined with NT‐proBNP. Osteopontin identifies aCHF patients with high 1‐ and 5‐year mortality and rehospitalization risk, and adds prognostic value to NT‐proBNP.

Trial registration

NCT00143793
Condition for the formation of micron-sized dust grains in dense molecular cloud cores
Authors: Hirashita Hiroyuki , Li Zhi-Yun
Published: July 2013

We investigate the condition for the formation of micron-sized grains in dense cores of molecular clouds. This is motivated by the detection of mid-infrared emission from deep inside a number of dense cores, the so-called ‘coreshine,’ which is thought to come from scattering by micron (μm)-sized grains. Based on numerical calculations of coagulation starting from the typical grain-size distribution in the diffuse interstellar medium, we obtain a conservative lower limit to the time t to form μm-sized grains: t/tff > 3(5/S)(nH/105 cm−3)−1/4 (where tff is the free-fall time at hydrogen number density nH in the core and S the enhancement factor of the grain–grain collision cross-section to account for non-compact aggregates). At the typical core density nH = 105 cm−3, it takes at least a few free-fall times to form the μm-sized grains responsible for coreshine. The implication is that those dense cores observed in coreshine are relatively long-lived entities in molecular clouds, rather than dynamically transient objects that last for one free-fall time or less.
Celerinatantimonas yamalensis sp. nov., a cold-adapted diazotrophic bacterium from a cold permafrost brine
Authors: Shcherbakova Viktoria , Chuvilskaya Nataliya , Rivkina Elizaveta , Demidov Nikita , Uchaeva Victoria , Suetin Stanislav , Suzina Nataliya , Gilichinsky David
Published: July 2013

A facultatively anaerobic nitrogen-fixing bacterium, strain C7T, was isolated from a permafrost cryopeg on the Yamal Peninsula, Russia. Comparative analysis of 16S rRNA gene sequences revealed that this bacterium was closely related toCelerinatantimonas diazotrophicaS-G2-2Twith a similarity of 95.5 %. Strain C7Tdiffered fromCelerinatantimonas diazotrophicain its ability to hydrolyse gelatin and inability to used-mannose, melibiose,l-rhamnose,myo-inositol, lactose, lactulose,d-mannitol, trehalose,dl-lactate, glycogen orl-proline as sole carbon sources. In addition, strain C7Tgrew over a temperature range of 0–34 °C with optimum growth at 18–22 °C. The whole-cell fatty acid profile included C16 : 0, C16 : 1ω7, C18 : 1ω7, C17cyclo and summed feature 2 [comprising C12 : 0aldehyde and/or unknown fatty acid 10.913 (MIDI designation) and/or iso-C16 : 1/C14 : 03-OH]. The DNA G+C content was 44.7 mol%. Strain C7Tis thus considered to represent a novel species, for which the nameCelerinatantimonas yamalensissp. nov. is proposed. The type strain is C7T( = VKM B-2511T = DSM 21888T).
Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum
Authors: Carro Lorena , Flores-Félix José David , Cerda-Castillo Eugenia , Ramírez-Bahena Martha-Helena , Igual José M. , Tejedor Carmen , Velázquez Encarna , Peix Alvaro
Published: July 2013

A bacterial strain, designated PECAE04T, was isolated from root nodules of Cicer arietinum in Spain. Phylogenetic analysis based on 16S rRNA gene sequence placed the isolate into the genus

Paenibacillus

with its closest relative being

Paenibacillus castaneae

Ch-32T with 98.4 % 16S rRNA gene sequence similarity followed by

Paenibacillus glycanilyticus

DS-1T,

Paenibacillus prosopidis

PW21T,

Paenibacillus xinjiangensis

B538T and

Paenibacillus catalpae

D75T with similarities ranging from 97.9 to 96.8 %. DNA–DNA hybridization measurements showed values lower than 20 % between the strain PECAE04T and any of these species. The isolate was a Gram-stain-positive, motile, sporulating rod. Catalase and oxidase activities were positive. Aesculin was hydrolysed but casein and gelatin were not. Acetoin production, H2S production, nitrate reduction and urease and caseinase production were negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the predominant menaquinone and anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, three phospholipids and an unidentified lipid. Meso-diaminopimelic acid was not detected in the peptidoglycan. The DNA G+C content was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PECAE04T should be considered to be a representative of a novel species of the genus

Paenibacillus

, for which the name Paenibacillus endophyticus sp. nov. is proposed. The type strain is PECAE04T ( = LMG 27297T = CECT 8234T).
Pontibacter toksunensis sp. nov., isolated from soil, and emended descriptions of Pontibacter roseus and Pontibacter akesuensis
Authors: Zhang Lei , Zhu Lingfang , Wei Linfang , Li Changfu , Wang Yao , Shen Xihui
Published: July 2013

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented bacterial strain, designated ZLD-7T, was isolated from a soil sample collected from an arid area in Xinjiang Province in north-west China, and characterized by using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that strain ZLD-7T was a member of the genus

Pontibacter

in the family

Cytophagaceae

, with sequence similarities of 93.7–96.2 % to type strains of other

Pontibacter

species. The only isoprenoid quinone of strain ZLD-7T was MK-7, and its major cellular fatty acids were summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I), iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profile consisted of phosphatidylethanolamine, one unidentified aminolipid and four unidentified polar lipids. The DNA G+C content was 47.8 mol%. On the basis of the evidence presented, it is proposed that strain ZLD-7T represents a novel species of the genus

Pontibacter

, for which the name Pontibacter toksunensis sp. nov. is proposed. The type strain is ZLD-7T ( = CCTCC AB 208003T = KCTC 23984T). Emended descriptions of

Pontibacter roseus

and

Pontibacter akesuensis

are also proposed.
Algimonas ampicilliniresistens sp. nov., isolated from the red alga Porphyra yezoensis, and emended description of the genus Algimonas
Authors: Fukui Youhei , Kobayashi Masahiro , Saito Hiroaki , Oikawa Hiroshi , Yano Yutaka , Satomi Masataka
Published: July 2013

Three strains (14A-2-7T, 14A-3-1 and 14A-3) of Gram-stain-negative, prosthecate, motile bacteria were isolated from an algal medium supplemented with 10 mg ampicillin l−1 (w/v), in which the red alga Porphyra yezoensis had been cultured. Based on the 16S rRNA gene sequence analysis, the three isolates formed a cluster with the genus

Algimonas

of the family

Hyphomonadaceae

. The sequences of the three isolates had high similarity with those of

Algimonas porphyrae

0C-2-2T (97.6 % similarity) and

Litorimonas taeanensis

G5T (95.6 % similarity). The DNA G+C contents of the three isolates ranged from 54.3 to 55.0 mol%, which were more similar to that of

A. porphyrae

0C-2-2T (58.5 mol%) than to that of

L. taeanensis

G5T (47.1 mol%). The DNA–DNA relatedness showed that the three isolates were representatives of the same species (88.1–94.0 % relatedness) and that strain 14A-2-7T was a representative of a different species from

A. porphyrae

0C-2-2T and

L. taeanensis

G5T (1.2–8.6 % relatedness). The phenotypic characteristics of strain 14A-2-7T differed by 20 results and 30 results from

A. porphyrae

0C-2-2T and

L. taeanensis

G5T, respectively. The three isolates contained ubiquinone-10 as the predominant quinone and C18 : 1ω7c as the major fatty acid. Based on the polyphasic taxonomic analysis, the three isolates represent a novel species of the genus

Algimonas

, for which the name Algimonas ampicilliniresistens sp. nov. is proposed. The type strain is 14A-2-7T ( = LMG 26421T = NBRC 108219T). An emended description of the genus

Algimonas

is also proposed.
Identification and genomic characterization of a novel fish reovirus, Hubei grass carp disease reovirus, isolated in 2009 in China
Authors: Fan Yuding , Rao Shujing , Zeng Lingbing , Ma Jie , Zhou Yong , Xu Jin , Zhang Hui
Published: July 2013

A novel fish reovirus, Hubei grass carp disease reovirus (HGDRV; formerly grass carp reovirus strain 104, GCRV104), was isolated from diseased grass carp in China in 2009 and the full genome sequence was determined. This reovirus was propagated in a grass carp kidney cell line with a typical cytopathic effect. The total size of the genome was 23 706 bp with a 51 mol% G+C content, and the 11 dsRNA segments encoded 12 proteins (two proteins encoded by segment 11). A nucleotide sequence similarity search using blastn found no significant matches except for segment 2, which partially matched that of the RNA-dependent RNA polymerase (RdRp) from several viruses in the genera Aquareovirus and Orthoreovirus of the family Reoviridae. At the amino acid level, seven segments (Seg-1 to Seg-6, and Seg-8) matched with species in the genera Aquareovirus (15–46 % identities) and Orthoreovirus (12–44 % identities), while for four segments (Seg-7, Seg-9, Seg-10 and Seg-11) no similarities in these genera were found. Conserved terminal sequences, 5′-GAAUU----UCAUC-3′, were found in each HGDRV segment at the 5′ and 3′ ends, and the 5′-terminal nucleotides were different from any known species in the genus Aquareovirus. Phylogenetic analysis based on RdRp amino acid sequences from members of the family Reoviridae showed that HGDRV clustered with aquareoviruses prior to joining a branch common with orthoreoviruses. Based on these observations, we propose that HGDRV is a new species in the genus Aquareovirus that is distantly related to any known species within this genus.
Natural infection of cynomolgus monkeys with dengue virus occurs in epidemic cycles in the Philippines
Authors: Kato Fumihiro , Ishida Yuki , Kawagishi Takahiro , Kobayashi Takeshi , Hishiki Takayuki , Miura Tomoyuki , Igarashi Tatsuhiko
Published: July 2013

To investigate the potential role of non-human primates (NHPs) in a dengue virus (DENV) epidemic, we conducted serological and genomic studies using plasma samples collected from 100 cynomolgus monkeys (Macaca fascicularis) in an animal breeding facility in the Philippines. An ELISA revealed 21 monkeys with a positive IgM reaction and 19 positive for IgG. Five of the monkeys were positive for both IgM and IgG. Of the 21 IgM-positive samples, a neutralization assay identified seven containing DENV-specific antibodies. We amplified the viral non-structural 1 (NS1) gene in two and the envelope (E) gene in one of these seven samples by RT-PCR. Phylogenetic analyses revealed that these DENV genes belonged to the epidemic DENV-2 family, not the sylvatic DENV family. These results suggest that NHPs may serve as a reservoir of epidemic DENV; therefore, the ecology of the urban DENV infection cycle should be investigated in these animals in detail.
REVIEW: Refuges for fauna in fire‐prone landscapes: their ecological function and importance
Authors: Robinson Natasha M. , Leonard Steve W.J. , Ritchie Euan G. , Bassett Michelle , Chia Evelyn K. , Buckingham Sebastian , Gibb Heloise , Bennett Andrew F. , Clarke Michael F.
Published: July 2013

Rapid environmental change is placing increasing pressure on the survival of many species globally. Ecological refuges can mitigate the impacts of change by facilitating the survival or persistence of organisms in the face of disturbance events that would otherwise lead to their mortality, displacement or extinction. Refuges may have a critical influence on the successional trajectory and resilience of ecosystems, yet their function remains poorly understood.

We review and describe the role of refuges in faunal conservation in the context of fire, a globally important disturbance process.

Refuges have three main functions in relation to fire: they enhance immediate survival during a fire event, facilitate the persistence of individuals and populations after fire and assist in the re‐establishment of populations in the longer term. Refuges may be of natural or anthropogenic origin, and in each case, their creation can arise from deterministic or stochastic processes. The specific attributes of refuges that determine their value are poorly known, but include within‐patch attributes relating to vegetation composition and structure; patch‐scale attributes associated with their size and shape; and the landscape context and spatial arrangement of the refuge in relation to fire patterns and land uses.

Synthesis and applications. Refuges are potentially of great importance in buffering the effects of wildfire on fauna. There is an urgent need for empirical data from a range of ecosystems to better understand what constitutes a refuge for different taxa, the spatial and temporal dynamics of species' use of refuges and the attributes that most influence their value to fauna. Complementary research is also required to evaluate threats to naturally occurring refuges and the potential for management actions to protect, create and enhance refuges. Knowledge of the spatial arrangement of refuges that enhance the persistence of fire‐sensitive species will aid in making decisions concerning land and fire management in conservation reserves and large natural areas. Global change in the magnitude and extent of fire regimes means that refuges are likely to be increasingly important for the conservation of biodiversity in fire‐prone environments.
Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing
Authors: Wang X. Q. , Zhao L. , Eaton D. A. R. , Li D. Z. , Guo Z. H.
Published: July 2013

Phylogenetic relationships among temperate species of bamboo are difficult to resolve, owing to both the challenge of detecting sufficiently variable markers and their polyploid history. Here, we use restriction site–associated DNA sequencing to identify candidate loci with fixed allelic differences segregating between and within two temperate species of bamboos: Arundinaria faberi and Yushania brevipaniculata. Approximately 27 million paired‐end sequencing reads were generated across four samples. From pooled data, we assembled 67 685 and 70 668 de novo contigs from partial overlap among paired‐end reads, with an average length of 240 and 241 bp for the two species, respectively, which were used to investigate functional classification of RAD tags in a blastx search. Analysed separately by population, we recovered 29 443 putatively orthologous RAD tags shared across the four sampled populations, containing 28 023 sequence variants, of which c. 13 000 are segregating between species, and c. 3000 segregating between populations within each species. Analyses based on these RAD tags yielded robust phylogenetic inferences, even with data set constructed from surprisingly few loci. This study illustrates the potential for reduced‐representation genome data to resolve difficult phylogenetic relationships in temperate bamboos.
Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all‐taxa biotic surveys
Authors: Geller J. , Meyer C. , Parker M. , Hawk H.
Published: July 2013

DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO2198 and LCO1490 (‘Folmer primers’) designed by Folmer et al. (Molecular Marine Biology and Biotechnology, 3, 1994, 294). Analysis of sequences published since 1994 has revealed mismatches in the Folmer primers to many metazoans. These sequences also show that an extremely high level of degeneracy would be necessary in updated Folmer primers to maintain broad taxonomic utility. In primers jgHCO2198 and jgLCO1490, we replaced most fully degenerated sites with inosine nucleotides that complement all four natural nucleotides and modified other sites to better match major marine invertebrate groups. The modified primers were used to amplify and sequence cytochrome c oxidase subunit I from 9105 specimens from Moorea, French Polynesia and San Francisco Bay, California, USA representing 23 phyla, 42 classes and 121 orders. The new primers, jgHCO2198 and jgLCO1490, are well suited for routine DNA barcoding, all‐taxon surveys and metazoan metagenomics.
Avian functional group responses to rainfall across four vegetation types in theSimpsonDesert, centralAustralia
Authors: Tischler Max , Dickman Christopher R. , Wardle Glenda M.
Published: July 2013

Temporal and spatial variability in rainfall and subsequent resource flows often drive large changes in bird demography and the structure of avian assemblages in arid regions. Here, we describe broad avian functional group responses to rainfall across four vegetation classes in theSimpsonDesert, centralAustralia, over a period when both dry and wet conditions prevailed. Birds were surveyed in eucalypt woodlands, gidyea woodlands, mixedAcacia(mulga) shrublands and spinifex‐dominated hummock grasslands in this region between 2006 and 2008 using a spatially nested hierarchical sampling design with fixed radius point counts as replicates. Predictably, the composition of bird communities varied across vegetation classes as well as over time. Generalist feeders and insectivorous birds dominated assemblages during dry periods, whereas granivorous species were most abundant and widespread following heavy rains. Carnivores and specialist nectarivores responded variably throughout the sampling period regardless of habitat. The dynamics of granivores were especially interesting; large numbers of nomadic species moved into the study area in response to rainfall, highlighting a key role for this group in shaping community structure. This study represents the first attempt to investigate avian functional group dynamics across differing vegetation types in a variable but low productivity landscape. The findings confirm that community composition is spatially and temporally dynamic, and prompt further investigation into the roles that habitat and resource limitation play in defining bird communities in aridAustralia.
Soft scale insects (Hemiptera: Coccoidea: Coccidae) on grapevines in Australia
Authors: Rakimov Adrian , Ben‐Dov Yair , White Vanessa , Hoffmann Ary A.
Published: July 2013

There is little information on the distribution and pest status of soft scale insects (Hemiptera: Coccoidea: Coccidae) in vineyards in Australia despite the potential of this group to spread ampeloviruses and directly damage vines. A survey of coccid species in the main vineyard regions was therefore undertaken. Parthenolecanium persicae (62% of sites), Part. pruinosum (46%) and Coccus hesperidum (8%) were the most common species collected, while Co. longulus, Parasaissetia nigra and Saissetia species were also recorded. Rare male Part. persicae were collected from one location. A 385 base pair fragment of the cytochrome oxidase subunit I (CO1) region was sequenced to provide a species‐specific marker for identification applicable across live stages. CO1 detected reasonable levels of sequence variation within some species and high levels of variation between species. The phylogenetic tree based on CO1 was able to discriminate between all species and showed Part. pruinosum from Gumeracha (SA), Part. nigra from West Swan (WA) and Co. longulus to be quite unique. These findings indicate that Part. pruinosum is much more common than previously appreciated and may include multiple species but also highlights the dominant pest status of Part. persicae in Australian vineyards and provides support for the application of CO1 to future molecular studies of Coccidae within Australia.
Technology and the future bioeconomy
Authors: Zilberman David , Kim Eunice , Kirschner Sam , Kaplan Scott , Reeves Jeanne
Published: July 2013

New discoveries in life sciences and the challenge of climate change are leading to the emergence of the bioeconomy where basic methods of advanced biology are applied to produce a wide array of products while also improving environmental quality. The emergence of the bioeconomy is a continuing evolutionary process of transition from systems of mining nonrenewable resources to farming renewable ones. This transition benefits from the modern tools of molecular biology that have expanded the human capacity to breed new organisms and utilize them to increase productivity in agriculture and fisheries as well as produce a wide array of products that were extracted in the past. This transition is leading to the integration of the agricultural sector with the energy and mineral sectors. The introduction of biotechnology has already improved the productivity of medicine as well as agriculture but, in the case of agriculture, has encountered resistance and regulatory constraints. The evolution of the bioeconomy requires continuous public investment in research and innovation as well as the establishment of a regulatory framework and financial incentives and institutions that would lead to continuous private sector investment in the development and commercialization of new products. One of the biggest challenges is the development of a regulatory framework that would control possible human and environmental externalities from new biotechnology products and, at the same time, not stifle innovation.
Serum Autoantibodies in Mice Immunized with Syngeneic Testicular Germ Cells Alone
Authors: Hirai Shuichi , Naito Munekazu , Terayama Hayato , Hatayama Naoyuki , Qu Ning , Musha Muhetaerjiang , Itoh Masahiro
Published: July 2013

Problem

The aim of this study was to identify the characteristics of serum autoantibodies in experimental autoimmune orchitis (EAO) induced by immunization with syngeneic testicular germ cells (TGC) alone in mice.

Method of study

The serum autoantibodies were analyzed by enzyme‐linked immunosorbent assay (ELISA), Western blotting, and immunohistochemical staining.

Results

Serum autoantibody titers against TGC and epididymal spermatozoa (ES) gradually increased with the development of EAO. At the initial stage of EAO, serum autoantibodies reacted with only a few antigens of TGC and ES, while in the later stage, the reactions with various antigens of TGC and ES occurred. However, the autoantibodies were specific to the testis and epididymis but not to other organs.

Conclusion

These results indicate that titers and kinds of autoantibodies in TGC‐immunized mice increase with EAO development and they are specific to TGC and ES.
The Conditionality of Vote‐Buying Norms: Experimental Evidence from Latin America
Authors: Gonzalez Ocantos Ezequiel , de Jonge Chad Kiewiet , Nickerson David W.
Published: July 2013

Anti‐vote‐buying campaigns led by NGOs and political elites denounce the practice as a crass economic transaction detrimental to democracy. Do potential clients stigmatize vote buying to the same degree, or does the mass public have a more conditional view of the acceptability of vote buying? We theorize that normative evaluations of vote buying vary based on individuals’ understanding of the transaction itself and abstract societal costs associated with the practice. We assess this perspective using survey experiments conducted in several Latin American countries that present hypothetical vote‐buying situations for evaluation by respondents, varying the socioeconomic status of the hypothetical client and the client's political predispositions. We find that the disapproval of vote buying is highly conditional on the attributes of the hypothetical client and that evaluations of vote buying depend on conceptions of the concrete benefits and abstract costs of vote buying as a part of electoral politics.
Reason for the increasing use of vacuum extraction in Sweden: a population‐based study
Authors: Elvander Charlotte , Ekéus Cecilia , Gemzell‐Danielsson Kristina , Cnattingius Sven
Published: July 2013

Objective

To explain the increasing rates of vacuum extraction in Sweden.

Design

Population‐based register study.

Setting

Nationwide study in Sweden.

Population

A total of 589 108 primiparous women with singleton, term live births in 1992–2010.

Methods

Odds ratios with 95% confidence intervals were estimated for potential risk factors for vacuum extraction and emergency cesarean. To explain the increase in vacuum extraction over time, we successively adjusted for maternal and infant characteristics in four different models.

Main outcome measures

Vacuum extraction.

Results

Rates of vacuum extraction increased from 11.5% in 1992 to 14.8% in 2010. The risk of vacuum extraction increased with maternal age and gestational length, but decreased with increasing maternal height. The increased use of vacuum extraction over time was partly explained by increasing maternal age and increased use of epidural anesthesia. Among women with and without epidural analgesia, the increase in vacuum extraction over time was confined to vacuum extraction due to signs of fetal distress.

Conclusions

Depending on risk factors, the odds of being delivered by vacuum extraction can vary immensely from one woman to another. Increasing maternal age explains a substantial fraction of the increase in vacuum extraction use since 1992. Whether the increase in vacuum extractions due to fetal distress reflects a true increase in fetal distress during labor remains to be explained.
Transepithelial corneal collagen cross‐linking by iontophoresis of riboflavin
Authors: Bikbova Guzel , Bikbov Mukharram
Published: July 2013

Purpose:  To evaluate the effectiveness of transepithelial cornea impregnation with riboflavin 0.1% by iontophoresis for collagen cross‐linking.

Material and methods:  Transepithelial collagen cross‐linking by iontophoresis of riboflavin was performed in a series of 22 eyes of 19 patients with progressive keratoconus I–II of Amsler classification. The riboflavin solution was administered by iontophoresis for 10 min in total, after which standard surface UVA irradiation (370 nm, 3 mW/cm2) was performed at a 5‐cm distance for 30 min.

Results:  The riboflavin/UVA treatment resulted in a decrease in the average keratometry level from 46.47 ± 1.03 to 44.12 ± 1.12 D 1 year after the procedure. Corneal astigmatism decreased from 3.44 ± 0.48 to 2.95 ± 0.23 D. Uncorrected distance visual acuity improved from 0.61 ± 0.44 up to 0.48 ± 0.41 (LogMAR). Preoperative and postoperative endothelial cell density remained unchanged at 2765 ± 21.15 cells/mm2.

Conclusion:  Transepithelial collagen cross‐linking by iontophoresis might become an effective method for riboflavin impregnation of the corneal stroma reducing the duration of the procedure and being more comfortable for the patients. Further long‐term studies are necessary to complete the evaluation of the efficacy and risk spectrum of the modified cross‐linking technique.
Effect of Danofloxacin on Reactive Oxygen Species Production, Lipid Peroxidation and Antioxidant Enzyme Activities in Kidney Tubular Epithelial Cell Line, LLC‐PK1
Authors: Yu Chun‐Hong , Liu Zhao‐Ying , Sun Lei‐Sheng , Li Yu‐Juan , Zhang Da‐Sheng , Pan Ren‐Tao , Sun Zhi‐Liang
Published: July 2013

The purpose of this study was to investigate the possibility that oxidative stress was involved in danofloxacin‐induced toxicity in renal tubular cells epithelial cell line (LLC‐PK1). Confluent LLC‐PK1 cells were incubated with various concentrations of danofloxacin. The extent of oxidative damage was assessed by measuring the reactive oxygen species (ROS) level, lipid peroxidation, cell apoptosis and antioxidative enzyme activities. Danofloxacin induced a concentration‐dependent increase in the ROS production, not even cytotoxic conditions. Similarly, danofloxacin caused an about 4 times increase in the level of thiobarbituric acid reactive substances at the concentration of 400 μM for 24 hr, but it did not induce cytotoxicity and apoptosis. Antioxidant enzymes activities, such as superoxide dismutase (SOD) and catalase (CAT), were increased after treatment with 100, 200 and 400 μM of danofloxacin for 24 hr. The activity of glutathione peroxidase (GPX) was significantly decreased in a concentration‐dependent manner. In addition, ROS production, lipid peroxidation and GPX decline were inhibited by additional glutathione and N‐acetyl cysteine. These data suggested that danofloxacin could not induce oxidative stress in LLC‐PK1 cells at the concentration (≤400 μM) for 24 hr. The increase levels of ROS and lipid peroxidation could be partly abated by the increase activities of SOD and CAT.
Efficacy and safety of pegylated‐interferon α‐2a in myelofibrosis: a study by the FIM and GEM French cooperative groups
Authors: Ianotto Jean‐Christophe , Boyer‐Perrard Françoise , Gyan Emmanuel , Laribi Kamel , Cony‐Makhoul Pascale , Demory Jean‐Loup , De Renzis Benoit , Dosquet Christine , Rey Jerome , Roy Lydia , Dupriez Brigitte , Knoops Laurent , Legros Laurence , Malou Mohamed , Hutin Pascal , Ranta Dana , Schoenwald Michele , Andreoli Annalisa , Abgrall Jean‐François , Kiladjian Jean‐Jacques
Published: July 2013

Myeloproliferative neoplasm‐related myelofibrosis is associated with cytopenic or proliferative phases, splenomegaly and constitutional symptoms. Few effective treatments are available and small series suggested that interferon could be an option for myelofibrosis therapy. We performed a retrospective study of pegylated‐interferon α‐2a (Peg‐IFNα‐2a) therapy in myelofibrosis. Sixty‐two patients treated with Peg‐IFNα‐2a at 17 French and Belgian centres were included. Responses were determined based on the criteria established by the International Working Group for Myelofibrosis Research and Treatment. Mean follow‐up was 26 months. Sixteen of 25 anaemic patients (64%) (eight concomitantly receiving recombinant erythropoietin) achieved a complete response and transfusion‐independence was obtained in 5/13 patients (38·5%). Constitutional symptoms resolved in 82% of patients. All five leucopenic patients normalized their leucocyte counts, whereas a normal platelet count was obtained in 5/8 thrombocytopenic patients. Splenomegaly was reduced in 46·5% of patients, and complete resolution of thrombocytosis and leucocytosis were observed in 82·8% and 68·8% of patients, respectively. Side effects (mostly haematological) were mainly of grade 1–2. The only factor independently associated with treatment failure was a spleen enlargement of more than 6 cm below the costal margin. In conclusion, Peg‐IFNα‐2a induced high response rates with acceptable toxicity in a large proportion of patients with primary and secondary myelofibrosis, especially in early phases.
Catheter‐related thrombosis in cancer patients
Authors: Murray Jim , Precious Elizabeth , Alikhan Raza
Published: July 2013

Central venous catheters are commonly used in haematology departments for the administration of chemotherapy, blood products and parenteral nutrition in patients with haematological malignancy. Thrombosis is a recognized complication of such devices especially in oncology patients. Catheter‐related thrombi (CRT) may lead to pulmonary embolism and infection, as well as catheter failure and potential delays in treatment. The vast majority of CRT are asymptomatic, thus a high index of suspicion is required in making the diagnosis. Doppler ultrasound or venography may be employed to identify CRT. Once confirmed, the initiation of treatment is a balance between the risks of anticoagulation against potential complications of CRT. A number of risk factors for CRT are discussed along with an overview of catheter types, their appropriate choice and intravascular positioning.
Clinical outcome and predictors of survival in patients with pneumocystis jirovecii pneumonia – results of a tertiary referral centre
Authors: Roembke Felicitas , Heinzow Hauke Sebastian , Gosseling Thomas , Heinecke Achim , Domagk Dirk , Domschke Wolfram , Meister Tobias
Published: July 2013

Background and Aims

Pneumocystis jirovecii pneumonia also known as pneumocystis pneumonia (PCP) is an opportunistic respiratory infection in human immunodeficiency virus (HIV) patients that may also develop in non‐HIV immunocompromised persons. The aim of our study was to evaluate mortality predictors of PCP patients in a tertiary referral centre.

Methods

Fifty‐one patients with symptomatic PCP were enrolled in the study. The patients had either HIV infection (n = 21) or other immunosuppressive conditions (n = 30). Baseline characteristics (e.g. age, sex and underlying disease) were retrieved. Kaplan–Meier analysis was employed to calculate survival. Comparisons were made by log‐rank test. A multivariate analysis of factors influencing survival was carried out using the Cox regression model. Chi‐squared test and Wilcoxon–Mann–Whitney test was applied as appropriate.

Results

The median survival time for the HIV group was >120 months compared with 3 months for the non‐HIV group (P = 0.009). Three‐month survival probability was also significantly greater in the HIV group compared with the non‐HIV group (90% vs 41%, P = 0.002). In univariate log‐rank test, intensive care unit (ICU) necessity, HIV negativity, age >50 years, haemoglobin <10g/dl, C‐reactive protein >5 mg/dL and multiple comorbidities were significant negative predictors of survival. In the Cox regression model, ICU and HIV statuses turned out to be independent prognostic factors of survival.

Conclusion

PCP is a serious problem in non‐HIV immunocompromised patients in whom survival outcomes are worse than those in HIV patients.
Providing Access to Engagement in Learning: The Potential of Universal Design for Learning in Museum Design
Authors: Rappolt‐Schlichtmann Gabrielle , Daley Samantha G.
Published: July 2013

Following passage of the Americans with Disabilities Act of 1990 (ADA), many museums improved the accessibility of their facilities. Even so, individuals with disabilities still lag behind in participation and engagement in museum experiences. Universal Design for Learning (UDL) provides an alternate model for the design of museum programs and exhibit spaces, one that is more aligned to progressive concepts of disability, providing not only physical access but also access to engagement in learning. In this article we argue that UDL has the potential to substantially improve the design of informal learning environments. Through two illustrative examples, we describe how the UDL design guidelines can be used to improve the probability that engagement will occur as individuals interact with exhibits, programs, and people in museums.
Improving the Museum Experiences of Children with Autism Spectrum Disorders and Their Families: An Exploratory Examination of Their Motivations and Needs and Using Web‐based Resources to Meet Them
Authors: Langa Lesley A. , Monaco Pino , Subramaniam Mega , Jaeger Paul T. , Shanahan Katie , Ziebarth Beth
Published: July 2013

Through a partnership with a local school, the Smithsonian Institution and the Information Policy and Access Center at the University of Maryland conducted an exploratory study to examine the motivations and needs of families visiting museums with children with Autism Spectrum Disorders (ASDs). This study represents one of the first undertakings to study visitors with ASDs, especially children, through a primarily qualitative data collection. Interest‐driven enjoyment emerged as a primary motivation, though to relax and to socialize outside of the family boundaries were not ranked as important motives for visiting museums. Children, who were directly interviewed, gave positive assessments of their museum experiences, while parents commented that challenges, both museum‐ and family‐related (crowds, loud noise, not feeling welcome, and a child's unpredictable behavior) surfaced in public settings like museums. Parents desired a “typical family outing” with their ASDs child, stating that manageable and safe environments helped families experience a museum.
Play For All at Chicago Children's Museum: A History and Overview
Authors: Golden Tamara , Walsh Lynn
Published: July 2013

In 2004, Chicago Children's Museum founded the Play For All initiative, which creates a community where play and learning connect for visitors of all abilities. The Play For All team discovered that families with children with disabilities were looking for an opportunity to explore and enjoy the museum without limitations and the fear of being judged. CCM also learned that being ADA compliant was not enough; being accessible and inclusive meant going above and beyond the ADA. Children's museums are a rare treat where almost everything should be interactive and ready to be played with. The Play For All team has made significant changes to the exhibits, staff training, and programming at Chicago Children's Museum by working with local families with disabilities and partner organizations. A culture shift has taken place within CCM. Play For All is now a top priority when decisions are being made.
A more comprehensive overview of executive dysfunction in children with cerebral palsy: theoretical perspectives and clinical implications
Authors: Roy Arnaud
Published: July 2013

This commentary is on the original article by Bodimeade et al. on pages 926–933 of this issue.