bluuebunny/crossref_metadata_2025 huggingface dataset:
Enlightenment Geisha: The Sex Trade, Education, and Feminine Ideals in Early Meiji Japan
Authors: Stanley Amy
Published: September 2013

During the mid-1870s, fearing the legal innovations of a “civilized” state, geisha and their employers recast Tokugawa-era practices of civic engagement and educational attainment in the language of enlightenment. Proprietors built schools intended to transform geisha into productive and moral mothers, and geisha donated to local educational institutions and suggested that their own studies would lead to self-sufficiency and freedom. These efforts associated geisha with the values of productivity and enlightenment, although similar strategies proved less successful for prostitutes. However, by the 1880s, both geisha and prostitutes were increasingly denied access to education and excluded from ideals of enlightened femininity that were predicated on marriage. This article considers how a group of unlikely actors deployed the Tokugawa past to become civilized, and in the process promoted ideas about the purpose of women's education that would later be expressed by an icon of Meiji modernity: the “good wife, wise mother.”
Asymmetric oscillatory expansion of a cylindrical plasma
Authors: KARIMOV A.R. , YU M.Y. , STENFLO L.
Published: September 2013

Asymmetric oscillatory expansion of a cylindrical plasma layer into vacuum is investigated analytically by solving the fluid equations of the electrons and ions together with the Maxwell's equations. For the problem considered, it is found that the asymmetrical flow components are strongly affected by the symmetrical components, but not the vice versa.
“I Kind of Got Dragged into Global History”: An Interview with Jan de Vries
Authors: Kemper Simon , Pucek Kaspar , Toivanen Mikko
Published: September 2013

On the morning of 30 May, freshly arrived from Wageningen, Professor Jan de Vries arrives at Leiden University. Later this day, he will be giving a lecture, to a full room, on his take on the so-called Great Divergence debate, but beforehand he has kindly agreed to an interview with Itinerario. Apart from him, present are three graduate students, the authors of this piece, and Professor Jos Gommans of Leiden University, in whose office we are, and whose grandmother's stately chair serves as the interviewee's place of honour. Over fresh cups of coffee, an amiable but wide-ranging conversation unfolds.

Professor Jan de Vries, of the University of California, Berkeley, is a respected economic historian with a long career reaching back to the 1970s. His work has taken on such diverse topics as Dutch rural economy in the Golden Age, European urbanisation and, in his widely influential book The Industrious Revolution, the developments that in his view paved the way to industrialisation in Europe. Lately his work has also taken a global turn, as he has addressed topics such as the Great Divergence and globalisation in history.

There are so many people named Jan de Vries. Helped by Wikipedia, we first thought we had somehow overlooked your early career as a motor driver! Yes, even in Berkeley there is more than one of us. If you look at the telephone book, you'll find three of us. One was even at the university [University of California, Berkeley]. He was an electrical engineer who worked in the space science laboratory which was affiliated with the university. Many years ago I had a telephone call in my office from a Dutchman who said, “Jan, I am waiting here for you.” And after a little bit he said, “you are Jan de Vries the electronicus [electronic engineer], right?” I answered “no, I am Jan de Vries the historicus [historian].” Later I met my name-sake and we still see each other periodically.
Craft and Small Scale Production in the Global Economy: Gujarat and Kachchh in the Eighteenth and Twenty-first Centuries
Authors: Berg Maxine
Published: September 2013

India's production of fine luxury and craft goods for world markets was discovered and exploited by Europeans in the seventeenth and eighteenth centuries. Textile producers in Gujarat, the Coromandel Coast, and Bengal applied fine craft skills to European designs, colour codes, and textile lengths and widths. Through the intervention of the East India Companies and private traders as well as their intermediaries, brokers and local merchants, weavers, and printers produced the goods to satisfy Western markets just as they had done for Eastern and African markets in the centuries before.

Today Indian craftspeople are engaging in a new phase of production for global markets. They are using traditional techniques of the kind that attracted Western buyers in the seventeenth and eighteenth centuries: hand weaving, hand block printing, and natural dyes. Accessing the niche national and international markets needed to provide a future for these crafts is a major challenge. This article focuses on the artisans, skills and markets in one area of India—the region of Kachchh in northern Gujarat, even now considered a remote part of the new global India. It sets this within a wider context of Gujarat and the earlier and more recent history of its textile industries. Douglas Haynes's recent book, Small Town Capitalism in Western India (2012) provides a framework for the study of small-scale industry, and the article will address his subject and methods. The new sources used are a collection of oral histories of craftspeople in a range of industries. These oral histories address skills and training across generations, and how these crafts have adapted and continue to adapt to the demands of national and world markets.
Re-examining Subject Making in the Netherlands East Indies Legal Education: Pedagogy, Curriculum, and Colonial State Formation
Authors: Djalins Upik
Published: September 2013

“Above all, we will put on record, that the Rechtsschool has not missed its target: the creation of independent (native) lawyers, who are aware of their position as independent judicial officers in the indigenous social relations.”

C.C. van Helsdingen,

Gedenkboek Rechtsschool 1929

When the Dutch introduced peace and order as the governing doctrine in the East Indies at the turn of the twentieth century, the network of colonial state institutions needed to project themselves as a unified, legitimate state with an authority to enforce justice. This state required a corps of jurists who embodied specific forms of subjectivity in order to maintain the projected authority. Educating natives as jurists offered the most economical means to staff the judiciary. This essay looks at legal education for Native elites as a colonial project of subject formation that was inseparable from colonial state formation. It does so by surveying three institutions in the Indies and the Netherlands between 1909 and 1939: the Batavia Rechtsschool, the Leiden United Faculty of Law and Letters, and the Batavia Rechtshoogeschool. Drawing on Foucauldian notions of disciplinary power and biopower in education and concepts from state theory, I argue that the pedagogical strategies and the legal education curricula in the Indies were deliberately designed to produce independent and critical Native jurists who were at the same time loyal to the Netherlands. The argument, thus, stands in contrast to literature that relies on early Foucault to construct education as a strictly normalising institution. I further suggest that although various state institutions did not unanimously agree on this ideal vision of Native jurists, they nevertheless tolerated it due to the urgent need to project the presence of a just state.

Using a variety of sources I focus my attention on two arenas of investigation: the vision of the ideal subjectivity to be embodied by Native jurists, and the technologies employed to achieve it. With this focus, I do not attempt to represent a comprehensive native point of view. Instead, I limit myself to examining the debates among Dutch educators and policy makers regarding proper legal education for the Native elites, the resulting policies as decreed in various ordinances, and the policies' implementation in the schools' curricula and pedagogy.
Source identification through social networks in an epidemiological investigation of a hepatitis A outbreak at an elementary school in Anhui province, China
Authors: WU J. B. , LI X. L. , ZHANG J. , XU D. , ZHU J. J. , ZHOU B. S.
Published: September 2013

In May 2011, the Center for Disease Control and Prevention of a Chinese county found a rapid increase in the number of hepatitis A case notification; these were traced to an outbreak in an elementary school. Twenty-eight cases aged between 7 and 13 years with onset between 7 May and 8 June were serologically confirmed. Network method was conducted to reconstruct an outbreak network and to quantify the relative importance of those involved in the outbreak. A case-control study was used to study the association between the outbreak and putative risk factors. The network analysis suggested this was a disseminated outbreak originating from a 4-year-old boy with propagated spread. Evidence from the case-control study supported consumption of well water as a potential risk factor; however, this was unable to be established through field investigation. Outbreak networks can be used to identify the possible source of infectious disease outbreak, especially when the environmental investigation information is negative or not available.
Statistical analyses and correlation between tropospheric temperature and humidity at Dome C, Antarctica
Authors: Ricaud P. , Carminati F. , Courcoux Y. , Pellegrini A. , Attié J.-L. , El Amraoui L. , Abida R. , Genthon C. , August T. , Warner J.
Published: September 2013

The Dome C (Concordia) station in Antarctica (75°06′S, 123°21′E, 3233 m above mean sea level) has a unique opportunity to test the quality of remote-sensing measurements and meteorological analyses because it is situated well inside the Eastern Antarctic Plateau and is less affected by local phenomena. Measurements of tropospheric temperature and water vapour (H2O) together with the integrated water vapour (IWV) performed in 2010 are statistically analysed to assess their quality and to study the yearly correlation between temperature and H2O over the entire troposphere. The statistical tools include yearly evolution, seasonally-averaged mean and bias, standard deviation and linear Pearson correlation. The datasets are made of measurements from the ground-based microwave radiometer H2O Antarctica Microwave Stratospheric and Tropospheric Radiometer (HAMSTRAD), radiosonde, in situ sensors, the space-borne infrared sensors Infrared Atmospheric Sounding Interferometer (IASI) on the MetOp-A platform and the Atmospheric InfraRed Sounder (AIRS) on the Aqua platform, and the analyses from the European Centre for Medium-Range Weather Forecast (ECMWF). Despite some obvious biases within all these datasets, our study shows that temperature and IWV are generally measured with high quality whilst H2O measurement quality is slightly worse. The AIRS and IASI measurements do not have the vertical resolution to correctly probe the lowermost troposphere, whilst HAMSTRAD loses sensitivity in the upper troposphere-lower stratosphere. Within the entire troposphere over the whole year, it is found that the time evolution of temperature and H2O is highly correlated (> 0.8). This suggests that, in addition to the variability of solar radiation producing an obvious diurnal cycle in the planetary boundary layer in summer and an obvious seasonal cycle over the year, the H2O and temperature intra-seasonal variabilities are affected by the same processes, e.g. related to the long-range transport of air masses.
TOUCH ME – ‘Touch’ genes in the micropylar endosperm
Authors: Nonogaki Hiroyuki
Published: September 2013

The micropylar region of endosperm (ME) is a physical barrier to radicle emergence in seeds of many different species, including tomato (Solanum lycopersicum) and Arabidopsis thaliana. ME is thought to be weakened through cell wall-modifying proteins, and this is supported by transcriptome data showing enrichment of cell wall-associated genes in ME. Gibberellin and ethylene have been suggested to be involved in induction of these genes in ME. However, mechanisms underlying this critical event for germination still remain elusive. In addition to hormonal regulation of ME weakening, recent data from high-throughput analyses suggested that it might be important for the radicle tip to ‘touch’ ME (or mechanosensing), in terms of ME-specific gene induction. This emerging hypothesis can be integrated with previous hypotheses about hormonal regulation of ME-specific gene expression in seeds.
Autobiographical Memory in Children with Temporal Lobe Epilepsy
Authors: Gascoigne Michael B. , Smith Mary Lou , Webster Richard , Barton Belinda , Gill Deepak , Lah Suncica
Published: September 2013

Autobiographical memory involves the recall of personal facts (semantic memory) and re-experiencing of specific personal events (episodic memory). Although impairments in autobiographical memory have been found in adults with unilateral temporal lobe epilepsy (TLE) and attributed to compromised hippocampal integrity, it is not yet known whether this occurs in children with TLE. In the current study, 21 children with TLE and 24 healthy controls of comparable age, sex, and socioeconomic status were administered the Children's Autobiographical Interview. Compared to controls, children with TLE recalled fewer episodic details, but only when no retrieval prompts were provided. There was no difference between the groups for semantic autobiographic details. Interestingly, the number of episodic details recalled increased significantly from 6 to 16 years of age in healthy control children, but not in children with TLE. Exploratory analyses revealed that, within the group of children with TLE, epilepsy factors, including presence or absence of structural hippocampal abnormalities, did not relate to the richness of episodic recall. Our results provide first evidence of autobiographical episodic memory deficits in children with TLE. (JINS, 2013, 19, 1–12)
Possible unintended consequences of Basel III and Solvency II ‐ Abstract of the Edinburgh discussion
Authors: Kemp Malcolm
Published: September 2013

This abstract relates to the following paper:

Al-DarwishA., HafemanM., ImpavidoG., KempM. and O'MalleyP.Possible Unintended Consequences of Basel III and Solvency II.British Actuarial Journal, doi:10.1017/S1357321713000391
Oestrogen levels in serum and urine of premenopausal women eating low and high amounts of meat
Authors: Harmon Brook E , Morimoto Yukiko , Beckford Fanchon , Franke Adrian A , Stanczyk Frank Z , Maskarinec Gertraud
Published: September 2013

Objective

Based on the hypothesis that high-meat diets may increase breast cancer risk through hormonal pathways, the present analysis compared oestrogens in serum and urine by meat-eating status.

Design

Intervention with repeated measures.

Setting

Two randomized soya trials (BEAN1 and BEAN2) among premenopausal healthy women.

Subjects

BEAN1 participants completed seven unannounced 24 h dietary recalls and donated five blood and urine samples over 2 years. BEAN2 women provided seven recalls and three samples over 13 months. Serum samples were analysed for oestrone (E1) and oestradiol (E2) using RIA. Nine oestrogen metabolites were measured in urine by LC–MS. Semi-vegetarians included women who reported consuming <30 g of red meat, poultry and fish daily, and pescatarians those who reported consuming <20 g of meat/poultry but >10 g of fish daily. All other women were classified as non-vegetarians. We applied mixed models to compute least-square means by vegetarian status adjusted for potential confounders.

Results

The mean age of the 272 participants was 41·9 (sd4·5) years. Serum E1(85v.100 pg/ml,P= 0·04) and E2(140v.154 pg/ml,P= 0·04) levels were lower in the thirty-seven semi-vegetarians than in the 235 non-vegetarians. The sum of the nine urinary oestrogen metabolites (183v.200 pmol/mg creatinine,P= 0·27) and the proportions of individual oestrogens and pathways did not differ by meat-eating status. Restricting the models to the samples collected during the luteal phase strengthened the associations.

Conclusions

Given the limitations of the study, the lower levels of serum oestrogens in semi-vegetarians than non-vegetarians need confirmation in larger populations.
Grower perceptions of native pollinators and pollination strategies in the lowbush blueberry industry
Authors: Hanes Samuel P. , Collum Kourtney K. , Hoshide Aaron K. , Asare Eric
Published: September 2013

Pollinator declines and dependence on insect pollination, particularly in fruit and vegetable crops, creates a pressing need to understand growers' interactions with pollinators and factors affecting pollination strategies. At present, many growers are dependent on commercial honey bees (Apis mellifera), but diversified strategies may be necessary to secure adequate crop pollination in the future. As of yet, little social science research exists on pollination practices. This article presents the results of a survey of lowbush blueberry growers in Maine. The survey was part of a five-year pollination security study focusing on four fruit and vegetables crops in the Northeast US. The survey assesses grower perceptions of native pollinators' effectiveness and their perceptions of native pollinators' contribution to fruit set. Results indicate a widespread perception among growers of native pollinators' importance. While native pollinators are not effective enough to replace rented honey bees for three-quarters of the industry, they are broadly seen as an important form of insurance in poor weather when honey bees' effectiveness is reduced. The main obstacle to greater utilization of native pollinators found in this study was uncertainty over native pollinators' contribution to yield and the associated difficulty monitoring native pollinators' population size. Scientists and extension experts must work to reduce these obstacles before more widespread use of native pollinators will occur.
The Genetic and Environmental Structure of Reproduction-Related Variables: The Case of Fertility and Breastfeeding
Authors: Colodro-Conde Lucía , Rijsdijk Frühling , Ordoñana Juan R.
Published: September 2013

Life history theory studies the evolution of traits related to reproductive fitness. Fertility and parental investment are key life history traits which, from an evolutionary standpoint, appear strongly interrelated. The aim of this work was to analyze the genetic and environmental structure and relationship of two behaviors associated with reproductive fitness: total number of offspring and mean duration of breastfeeding. A total of 1,347 women distributed in 239 monozygotic pairs, 236 dizygotic pairs, and 393 individual twins from opposite sex pairs provided information about their reproductive history. We conducted separate univariate analyses to study the sources of variance of both variables; and a bivariate analysis, with threshold liability models. The sources of variance for number of children and breastfeeding were best explained by a model including familial and unique environmental factors, being E = 0.54 (CI 95%: 0.44, 0.66) and E = 0.46 (CI 95%: 0.34, 0.61), respectively. The phenotypic correlation between number of children and breastfeeding was low but significant (r = 0.16, CI 95%: 0.07, 0.25). Familial correlation between these variables did not reach significance, but unique environmental correlation did (re = 0.20, CI 95%: 0.02, 0.37). In conclusion, results do not support the existence of a clear common structure for the number of children a woman has and the time she spends breastfeeding them, at least in modern societies. The relationship found was mainly due to unique environmental factors. More research on these and related phenotypes is needed to better understand women's reproductive decisions and how natural selection acts on the life history traits.
Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales
Authors: Youssef Noha H , Savage-Ashlock Kristen N , McCully Alexandra L , Luedtke Brandon , Shaw Edward I , Hoff Wouter D , Elshahed Mostafa S
Published: September 2013

We investigated the mechanisms of osmoadaptation in the order Halobacteriales, with special emphasis on Haladaptatus paucihalophilus, known for its ability to survive in low salinities. H. paucihalophilus genome contained genes for trehalose synthesis (trehalose-6-phosphate synthase/trehalose-6-phosphatase (OtsAB pathway) and trehalose glycosyl-transferring synthase pathway), as well as for glycine betaine uptake (BCCT family of secondary transporters and QAT family of ABC transporters). H. paucihalophilus cells synthesized and accumulated ∼1.97–3.72 μmol per mg protein of trehalose in a defined medium, with its levels decreasing with increasing salinities. When exogenously supplied, glycine betaine accumulated intracellularly with its levels increasing at higher salinities. RT-PCR analysis strongly suggested that H. paucihalophilus utilizes the OtsAB pathway for trehalose synthesis. Out of 83 Halobacteriales genomes publicly available, genes encoding the OtsAB pathway and glycine betaine BCCT family transporters were identified in 38 and 60 genomes, respectively. Trehalose (or its sulfonated derivative) production and glycine betaine uptake, or lack thereof, were experimentally verified in 17 different Halobacteriales species. Phylogenetic analysis suggested that trehalose synthesis is an ancestral trait within the Halobacteriales, with its absence in specific lineages reflecting the occurrence of gene loss events during Halobacteriales evolution. Analysis of multiple culture-independent survey data sets demonstrated the preference of trehalose-producing genera to saline and low salinity habitats, and the dominance of genera lacking trehalose production capabilities in permanently hypersaline habitats. This study demonstrates that, contrary to current assumptions, compatible solutes production and uptake represent a common mechanism of osmoadaptation within the Halobacteriales.
A computational approach to chemical etiologies of diabetes
Authors: Audouze Karine , Brunak Søren , Grandjean Philippe
Published: September 2013

Computational meta-analysis can link environmental chemicals to genes and proteins involved in human diseases, thereby elucidating possible etiologies and pathogeneses of non-communicable diseases. We used an integrated computational systems biology approach to examine possible pathogenetic linkages in type 2 diabetes (T2D) through genome-wide associations, disease similarities and published empirical evidence. Ten environmental chemicals were found to be potentially linked to T2D, the highest scores were observed for arsenic, 2,3,7,8-tetrachlorodibenzo-p-dioxin, hexachlorobenzene and perfluorooctanoic acid. For these substances we integrated disease and pathway annotations on top of protein interactions to reveal possible pathogenetic pathways that deserve empirical testing. The approach is general and can address other public health concerns in addition to identifying diabetogenic chemicals and offers thus promising guidance for future research in regard to the etiology and pathogenesis of complex diseases.
A degree formula for equivariant cohomology
Authors: Lynn Rebecca
Published: September 2013

The primary theorem of this paper concerns the Poincaré (Hilbert) series for the cohomology ring of a finite groupGGwith coefficients in a prime field of characteristicpp. This theorem is proved using the ideas of equivariant cohomology whereby one considers more generally the cohomology ring of the Borel constructionH∗(EG×GX)H^*(EG \times _G X), whereXXis a manifold on whichGGacts. This work results in a formula that computes the “degree” of the Poincaré series in terms of corresponding degrees of certain subgroups of the groupGG. In this paper, we discuss the theorem and the method of proof.
Boundary behavior of infinitesimal generators in the unit ball
Authors: Bracci Filippo , Shoikhet David
Published: September 2013

We prove a Julia-Wolff-Carathéodory type theorem for infinitesimal generators on the unit ball in

C

n

\mathbb {C}^{n}

. Moreover, we study jets expansions at the boundary and give necessary and sufficient conditions on such jets for an infinitesimal generator to generate a group of automorphisms of the ball.
Bves and NDRG4 regulate directional epicardial cell migration through autocrine extracellular matrix deposition
Authors: Benesh Emily C. , Miller Paul M. , Pfaltzgraff Elise R. , Grega-Larson Nathan E. , Hager Hillary A. , Sung Bong Hwan , Qu Xianghu , Baldwin H. Scott , Weaver Alissa M. , Bader David M.
Published: September 2013

Directional cell movement is universally required for tissue morphogenesis. Although it is known that cell/matrix interactions are essential for directional movement in heart development, the mechanisms governing these interactions require elucidation. Here we demonstrate that a novel protein/protein interaction between blood vessel epicardial substance (Bves) and N-myc downstream regulated gene 4 (NDRG4) is critical for regulation of epicardial cell directional movement, as disruption of this interaction randomizes migratory patterns. Our studies show that Bves/NDRG4 interaction is required for trafficking of internalized fibronectin through the “autocrine extracellular matrix (ECM) deposition” fibronectin recycling pathway. Of importance, we demonstrate that Bves/NDRG4-mediated fibronectin recycling is indeed essential for epicardial cell directional movement, thus linking these two cell processes. Finally, total internal reflectance fluorescence microscopy shows that Bves/NDRG4 interaction is required for fusion of recycling endosomes with the basal cell surface, providing a molecular mechanism of motility substrate delivery that regulates cell directional movement. This is the first evidence of a molecular function for Bves and NDRG4 proteins within broader subcellular trafficking paradigms. These data identify novel regulators of a critical vesicle-docking step required for autocrine ECM deposition and explain how Bves facilitates cell-microenvironment interactions in the regulation of epicardial cell–directed movement.
Optimizing a global alignment of protein interaction networks
Authors: Chindelevitch Leonid , Ma Cheng-Yu , Liao Chung-Shou , Berger Bonnie
Published: September 2013

Motivation: The global alignment of protein interaction networks is a widely studied problem. It is an important first step in understanding the relationship between the proteins in different species and identifying functional orthologs. Furthermore, it can provide useful insights into the species’ evolution.

Results: We propose a novel algorithm, PISwap, for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other intractable problems. PISwap can begin with different types of network alignment approaches and then iteratively adjust the initial alignments by incorporating network topology information, trading it off for sequence information. In practice, our algorithm efficiently refines other well-studied alignment techniques with almost no additional time cost. We also show the robustness of the algorithm to noise in protein interaction data. In addition, the flexible nature of this algorithm makes it suitable for different applications of network alignment. This algorithm can yield interesting insights into the evolutionary dynamics of related species.

Availability: Our software is freely available for non-commercial purposes from our Web site, http://piswap.csail.mit.edu/.

Contact:  bab@csail.mit.edu or csliao@ie.nthu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
miREval 2.0: a web tool for simple microRNA prediction in genome sequences
Authors: Gao Dadi , Middleton Robert , Rasko John E. J. , Ritchie William
Published: September 2013

Result: We have developed miREval 2.0, an online tool that can simultaneously search up to 100 sequences for novel microRNAs (miRNAs) in multiple organisms. miREval 2.0 uses multiple published in silico approaches to detect miRNAs in sequences of interest. This tool can be used to discover miRNAs from DNA sequences or to validate candidates from sequencing data.

Availability:  http://mimirna.centenary.org.au/mireval/.

Contact: w.ritchie@centenary.org.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pre-activation of the genome integrity checkpoint increases DNA damage tolerance
Authors: Tsaponina Olga , Chabes Andrei
Published: September 2013

The genome integrity checkpoint is a conserved signaling pathway that is regulated in yeast by the Mec1 (homologous to human ATR) and Rad53 (homologous to human Chk1) kinases. The pathway coordinates a multifaceted response that allows cells to cope with DNA damage and DNA replication stress. The full activation of the checkpoint blocks origin firing, stabilizes replication forks, activates DNA repair proteins and may lead to senescence or apoptosisin higher eukaryotes. We have recently demonstrated that endogenous replication stress can activate the genome integrity checkpoint in budding yeast at a low level that does not go so far as to interfere with cell cycle progression, but it does activate DNA damage-inducible proteins. Here we demonstrate that the low level pre-activation of the checkpoint, either by endogenous replication stress or by the nucleotide-depleting drug hydroxyurea, can increase damage tolerance to multiple DNA-damaging agents. These results may provide new strategies for using the checkpoint to protect normal cells from genotoxic stress.
The telomere resolvase of the Lyme disease spirochete, Borrelia burgdorferi, promotes DNA single-strand annealing and strand exchange
Authors: Mir Taskia , Huang Shu Hui , Kobryn Kerri
Published: September 2013

Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming the ‘end-replication problem’ for the linear replicons. Hairpin telomeres are formed from inverted repeat replicated telomere junctions by the telomere resolvase, ResT. ResT uses a reaction mechanism similar to that of the type IB topoisomerases and tyrosine recombinases. We report here that ResT also possesses single-strand annealing activity and a limited ability to promote DNA strand exchange reactions on partial duplex substrates. This combination of activities suggests ResT is a nexus between the seemingly distinct processes of telomere resolution and homologous recombination. Implications for hairpin telomere replication and linear plasmid recombination, including antigenic variation, are discussed.
ERK phosphorylation of MED14 in promoter complexes during mitogen-induced gene activation by Elk-1
Authors: Galbraith Matthew D. , Saxton Janice , Li Li , Shelton Samuel J. , Zhang Hongmei , Espinosa Joaquin M. , Shaw Peter E.
Published: September 2013

The ETS domain transcription factor Elk-1 stimulates expression of immediate early genes (IEGs) in response to mitogens. These events require phosphorylation of Elk-1 by extracellular signal-regulated kinase (ERK) and phosphorylation-dependent interaction of Elk-1 with co-activators, including histone acetyltransferases and the Mediator complex. Elk-1 also recruits ERK to the promoters of its target genes, suggesting that ERK phosphorylates additional substrates in transcription complexes at mitogen-responsive promoters. Here we report that MED14, a core subunit of the Mediator, is a bona fide ERK substrate and identify serine 986 (S986) within a serine-proline rich region of MED14 as the major ERK phosphorylation site. Mitogens induced phosphorylation of MED14 on S986 at IEG promoters; RNAi knockdown of MED14 reduced CDK8 and RNA polymerase II (RNAPII) recruitment, RNAPII C-terminal domain phosphorylation and impaired activation of IEG transcription. A single alanine substitution at S986 reduced activation of an E26 (ETS)-responsive reporter by oncogenic Ras and mitogen-induced, Elk-1-dependent transcription, whereas activities of other transcriptional activators were unaffected. We also demonstrate that Elk-1 can associate with MED14 independently of MED23, which may facilitate phosphorylation of MED14 by ERK to impart a positive and selective impact on mitogen-responsive gene expression.
Comparison of the Potency of Different Propofol Formulations
Authors: Le Guen Morgan , Grassin-Delyle Stanislas , Cornet Camille , Genty Antoine , Chazot Thierry , Dardelle Dominique , Liu Ngai , Dreyfus Jean-François , Mazoit Jean-Xavier , Devillier Philippe , Alvarez Jean-Claude , Sessler Daniel I. , Fischler Marc
Published: September 2013

Background

Several commercial formulations of propofol are available. The primary outcome of this study was the required dose of propofol alone or combined with lidocaine to achieve induction of general anesthesia.

Methods

This multicenter, double-blinded trial randomized patients (American Society of Anesthesiologists physical status I–III) just before elective surgery with the use of a computer-generated list. Three different propofol 1% formulations—Diprivan® (Astra-Zeneca, Cheshire, United Kingdom), Propofol® (Fresenius-Kabi AG, Bad Homburg, Germany), and Lipuro® (B-Braun, Melshungen AG, Germany)—were compared with either placebo (saline solution) or lidocaine 1% mixed to the propofol solution. Depth of anesthesia was automatically guided by bispectral index and by a computerized closed-loop system for induction, thus avoiding dosing bias. The authors recorded the total dose of propofol and duration of induction and the patient’s discomfort through a behavioral scale (facial expression, verbal response, and arm withdrawal) ranging from 0 to 6. The authors further evaluated postoperative recall of pain using a Visual Analog Scale.

Results

Of the 227 patients enrolled, 217 were available for analysis. Demographic characteristics were similar in each group. Propofol® required a higher dose for induction (2.2 ± 0.1 mg/kg) than Diprivan® (1.8 ± 0.1 mg/kg) or Lipuro® (1.7 ± 0.1 mg/kg; P = 0.02). However, induction doses were similar when propofol formulations were mixed with lidocaine. Patient discomfort during injection was significantly reduced with lidocaine for every formulation: Diprivan® (0.5 ± 0.3 vs. 2.3 ± 0.3), Propofol® (0.4 ± 0.3 vs. 2.4 ± 0.3), and Lipuro® (1.1 ± 0.3 vs. 1.4 ± 0.3), all differences significant, with P < 0.0001. No adverse effect was reported.

Conclusion

Plain propofol formulations are not equipotent, but comparable doses were required when lidocaine was concomitantly administered.
Lynch Syndrome
Authors: Huang Sherry C. , Durno Carol A. , Erdman Steven H.
Published: September 2013

Colorectal cancer is a rare disease in the pediatric age group and, when present, suggests an underlying genetic predisposition. The most common hereditary colon cancer susceptibility condition, Lynch syndrome (LS), previously known as hereditary nonpolyposis colorectal cancer, is an autosomal dominant condition caused by a germline mutation in 1 of 4 DNA mismatch repair (MMR) genes: MLH1, MSH2, MSH6, or PMS2. The mutation‐prone phenotype of this disorder is associated with gastrointestinal, endometrial, and other cancers and is now being identified in both symptomatic adolescents with malignancy as well in asymptomatic mutation carriers who are at risk for a spectrum of gastrointestinal and other cancers later in life. We review the DNA MMR system, our present understanding of LS in the pediatric population, and discuss the newly identified biallelic form of the disease known as constitutional mismatch repair deficiency syndrome. Both family history and tumor characteristics can help to identify patients who should undergo genetic testing for these cancer predisposition syndromes. Patients who carry either single allele (LS) or double allele (constitutional mismatch repair deficiency syndrome) mutations in the MMR genes benefit from cancer surveillance programs that target both the digestive and extraintestinal cancer risk of these diseases. Because spontaneous mutation in any one of the MMR genes is extremely rare, genetic counseling and testing are suggested for all at‐risk family members.
Challenges in Meeting Fellowship Procedural Guidelines in Pediatric Therapeutic Endoscopy and Liver Biopsy
Authors: Lerner Diana G. , Li B.U. , Mamula Petar , Fishman Douglas S. , Kramer Robert , Goh Vi Lier , El‐Chammas Khalil , Pentiuk Scott P. , Rothbaum Robert , Gurrum Bhaskar , Rahhal Riad M. , Goday Praveen S. , Vitola Bernadette
Published: September 2013

Objective:

The aims of this study were to assess the opportunities for therapeutic endoscopy, liver biopsies, and percutaneous endoscopic gastrostomy (PEG) placements available to fellows during a 3‐year pediatric gastroenterology fellowship, and to evaluate access to ancillary procedural‐training opportunities.

Methods:

Data were collected from 12 pediatric gastroenterology fellowship programs in the United States. Procedures completed in the years 2009–2011 were queried using CPT codes and endoscopy databases. The maximal opportunity for procedures was based on the total procedures performed by the institution in 3 years divided by the total number of fellows in the program. The centers completed a questionnaire regarding ancillary opportunities for endoscopic training.

Results:

There is significant variability in pediatric endoscopic training opportunities in specialized gastrointestinal (GI) procedures. Under the 1999 guidelines, no centers were able to meet the thresholds for polypectomy and control of nonvariceal bleeding. The 2013 guidelines allowed the number of programs reaching polypectomy thresholds to increase by 67% but made no difference for control of bleeding despite a decrease in the threshold. Training in PEG placement was not available in 42% of the surveyed centers. Elective ancillary procedural training is offered by 92% of the surveyed centers.

Conclusions:

Most training programs do not have the volume of therapeutic endoscopy procedures for all of the fellows to meet the training guidelines. Training in therapeutic endoscopy, PEG placement, and liver biopsy in pediatric GI fellowships should be supplemented using all of the possible options including rotations with adult GI providers and hands‐on endoscopy courses. A shift toward evaluating competency via quality measures may be more appropriate.
Baseline Retinal Nerve Fiber Layer Thickness and Macular Volume Quantified by OCT in the North American Phase 3 Fingolimod Trial for Relapsing–Remitting Multiple Sclerosis
Authors: Winges Kimberly M. , Werner John S. , Harvey Danielle J. , Cello Kimberly E. , Durbin Mary K. , Balcer Laura J. , Calabresi Peter A. , Keltner John L.
Published: September 2013

Background:

Patients with multiple sclerosis (MS) demonstrate thinning of peripapillary retinal nerve fiber layer (RNFL) and decreased macular volume as measured by optical coherence tomography (OCT). To our knowledge, there are no previous reports from a large MS OCT database with strict quality control measures that quantitate RNFL and macula in patients with relapsing–remitting multiple sclerosis.

Methods:

The University of California Davis OCT Reading Center gathered OCT data at baseline as part of the North American phase 3 trial of fingolimod (Gilenya). Average RNFL thickness (RNFLT) and macular volume (TMV) were measured using time domain OCT (TD-OCT). RNFL quadrants, clock hours, and macular subfields were included. With strict quality control and accounting for signal strength differences, scans were categorized as “reduced” or “not reduced” for each field, based on being less than 5th percentile for age-matched controls derived from the normative database in the scanner software. Patients were deemed “abnormal” if at least 1 eye had reduced values for a given parameter. Patients with abnormalities in corresponding RNFL and macular subfields were compared by cross-tabulation.

Results:

The TD-OCT data were prospectively collected from 939 of the 1,083 trial patients, 712 of whom met all final quality and data inclusion criteria. Of the final cohort, 242 (34.0%) demonstrated reduced (less than 5th percentile) average RNFLT in at least 1 eye. One hundred seventy-eight (25.0%) patients had reduced TMV. One hundred twenty-eight (18.0%) demonstrated both reduced TMV and RNFLT in the same eye, whereas 42 (5.8%) had reduced TMV and RNFLT in both eyes. Of the 242 patients with reduced average RNFL thickness, 128 (52.9%) also had reduced TMV. Fifty patients had reduced TMV in the absence of reduced RNFLT in at least 1 eye, a cohort prevalence of 7.0%. Quadrant and subfield analysis showed a predominance of temporal and inferior RNFL thinning, with inferior macular thinning corresponding best to RNFL thinning.

Conclusion:

RNFL and macular thinning/volume loss is common at baseline in relapsing–remitting multiple sclerosis, as measured by TD-OCT. When the RNFL is thin, the macular volume is reduced in more than half of the patients. There is a population of reduced TMV without any reduction in RNFLT. Documenting the prevalence and distribution of these structural abnormalities supports recent reports and suggests new retinal areas to probe for functional vision changes in MS.
Nocardiopsis fildesensis sp. nov., an actinomycete isolated from soil
Authors: Xu Shanshan , Yan Lien , Zhang Xuan , Wang Chao , Feng Ge , Li Jing
Published: September 2013

A filamentous actinomycete strain, designated GW9-2T, was isolated from a soil sample collected from the Fildes Peninsula, King George Island, West Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew slowly on most media tested, producing small amounts of aerial mycelia and no diffusible pigments on most media tested. The strain grew in the presence of 0–12 % (w/v) NaCl (optimum, 2–4 %), at pH 9.0–11.0 (optimum, pH 9.0) and 10–37 °C (optimum, 28 °C). The isolate contained meso-diaminopimelic acid, no diagnostic sugars and MK-9(H4) as the predominant menaquinone. The major phospholipids were phosphatidylglycerol, phosphatidylcholine and phosphatidylmethylethanolamine. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, C18 : 1ω9c, iso-C15 : 0 and iso-C17 : 0. DNA–DNA relatedness was 37.6 % with

Nocardiopsis lucentensis

DSM 44048T, the nearest phylogenetic relative (97.93 % 16S rRNA gene sequence similarity). On the basis of the results of a polyphasic study, a novel species,

Nocardiopsis

fildesensis sp. nov., is proposed. The type strain is GW9-2T ( = CGMCC 4.7023T = DSM 45699T = NRRL B-24873T).
Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils
Authors: Crowe M. A. , Power J. F. , Morgan X. C. , Dunfield P. F. , Lagutin K. , Rijpstra W. I. C. , Vyssotski M. , Sinninghe Damste J. S. , Houghton K. M. , Ryan J. L. J. , Stott M. B.
Published: September 2013

An aerobic, thermophilic, moderately acidophilic non-spore-forming bacterium, strain K22T, was isolated from geothermally heated soil at Mount Ngauruhoe, New Zealand. On the basis of 16S rRNA gene sequence similarity, K22T was shown to belong to subdivision 4 of the phylum

Acidobacteria

and to be most closely related to ‘Candidatus Chloracidobacterium thermophilum’ (86 %) and

Blastocatella fastidiosa

(86 %). Cells stained Gram-negative and were catalase and oxidase-positive. The major fatty acids detected were iso-C15 : 0, iso-C17 : 0, iso-C19 : 0 and iso-C21 : 0 when standard lipid extraction protocols were employed. Analysis of the total cell lipid acid hydrolysate also detected membrane-spanning and ether lipids, which made up approximately 40 % of the total membrane composition. These lipids included dicarboxylic (iso-diabolic) acid and the glyceryl ether of alkyl analogues of iso-C15 : 0 and iso-diabolic acid. The G+C content of the genomic DNA was 59.6 mol% and the primary respiratory quinone was MK-8. Strain K22T grew at 50–69 °C with an optimum temperature of 65 °C and at pH 4.1–7.8 with an optimum growth pH of 6.5. NaCl tolerance was up to 1 % (w/v). Cells displayed a chemoheterotrophic and obligately aerobic metabolism. Cells grew on nutrient broth, alginate, arabinose, Casamino acids, glucose, lactate, formate, mannose, sodium alginate, peptone, sucrose, tryptone, xanthan, xylan, xylose and yeast extract. Nitrogen sources included nitrate, ammonium, urea, yeast extract and Casamino acids, but not dinitrogen gas. The distinct phylogenetic position and the phenotypic characteristics separate strain K22T from all other members of the class

Acidobacteria

and indicate that it represents a novel species and genus, for which the name Pyrinomonas methylaliphatogenes gen. nov., sp. nov. is proposed. The type strain of the type species is K22T ( = DSM 25857T = ICMP 18710T).
Thermoactinomyces daqus sp. nov., a thermophilic bacterium isolated from high-temperature Daqu
Authors: Yao Su , Liu Yang , Zhang Mingjuan , Zhang Xin , Li Hong , Zhao Ting , Xin Chunhui , Xu Ling , Zhang Bolin , Cheng Chi
Published: September 2013

Daqu is a fermentation starter used in the production of Chinese liquors. A thermophilic bacterium, designated strain H-18T, was isolated from a high-temperature Daqu sample collected from the manufacturing process of a sesame-flavoured liquor in Shandong province, China. It was investigated in a taxonomic study using a polyphasic approach. Strain H-18T formed white aerial mycelium and greyish-yellow substrate mycelium, bearing single endospores on aerial and substrate hyphae or on unbranched short sporophores. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major fatty acids were iso-C15 : 0 and iso-C17 : 0. The predominant menaquinone was MK-7. These chemotaxonomic properties are similar to those of members of the genus

Thermoactinomyces

. The G+C content of the genomic DNA was 49.1 mol%. 16S rRNA gene sequence comparisons indicated that strain H-18T was most closely related to

Thermoactinomyces vulgaris

KCTC 9076T (96.42 % similarity),

Thermoactinomyces intermedius

KCTC 9646T (96.06 %),

Laceyella putida

KCTC 3666T (96.32 %) and

Laceyella sacchari

KCTC 9790T (95.55 %). Strain H-18T showed low DNA–DNA relatedness (40.8, 33.4, 20.0 and 14.4 %) with the above strains. Based on morphological and chemotaxonomic characteristics, DNA–DNA hybridization data and physiological properties, strain H-18T represents a novel species of the genus

Thermoactinomyces

, for which the name

Thermoactinomyces

daqus sp. nov. is proposed. The type strain is H-18T ( = DSM 45914T = CICC 10681T).