bluuebunny/crossref_metadata_2025_split huggingface dataset:
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 1929When 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

SUMMARYIn 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

AbstractThe 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

AbstractThe 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

AbstractAutobiographical 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

AbstractObjectiveBased 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.DesignIntervention with repeated measures.SettingTwo randomized soya trials (BEAN1 and BEAN2) among premenopausal healthy women.SubjectsBEAN1 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.ResultsThe 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.ConclusionsGiven 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

AbstractPollinator 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.
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

Abstract
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

AbstractComputational 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.
Optimizing a global alignment of protein interaction networks
Authors: Chindelevitch Leonid , Ma Cheng-Yu , Liao Chung-Shou , Berger Bonnie 
Published: September 2013

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.