bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sardars, Jobbers, Kanganies: The Labour Contractor and Indian Economic History
Authors: ROY TIRTHANKAR 
Published: September 2007

AbstractA figure in part a foreman, in part a headman, and in part a recruiting contractor, formed an indispensable part of labour organization in mills, mines, ports and plantations in nineteenth-century India, and in the tropical colonies where Indian emigrants went for work. Historians have explained the presence of such a figure by the needs of capital for intermediaries, or needs of labour for familiar relationships in an unfamiliar environment. The significance of the labour agent for economic history, however, seems to go beyond these needs. The universal presence of a worker who embodied a variable blend of roles prompts several larger questions. Was the labour agent an institutional response to an economic problem? Were modern forms of agency rooted in older modes of labour organization? The scholarship discussed the gains for employers. Were there costs too? This paper is a preliminary attempt at framing these larger issues. I suggest here that the agent had roots in the traditional economy, and represented an incorporation of putting out and the authority of the headman inside modern work sites, and that this incorporation of traditional authority in a modern setting gave rise to contradictions.
Metalloproteases and egg-hatching in Pediculus humanus, the body (clothes) louse of humans (Phthiraptera: Insecta)
Authors: BOWLES V. M. , YOUNG A. R. , BARKER S. C. 
Published: September 2007

SUMMARYTo investigate the biochemical components of egg-hatch in the body louse, Pediculus humanus, egg-shell-washings (ESW) were collected during the first 2 h post-hatching and analysed by gelatin SDS-PAGE. These ESW contained proteases with molecular mass in the range of 25–100 kDa; the most abundant proteases were ~25 kDa. The 3 main regions of protease activity in the one-dimensional gelatin SDS-PAGE gels resolved to at least 23 distinct regions of protease activity when analysed by two-dimensional gelatin SDS-PAGE, with iso-electric points spread over the entire 3 to 10 pH range. Mechanistic characterization indicated that the ESW contained proteases of the metallo-class, inhibited by both 1,10-phenanthroline and EDTA. Several protease inhibitors were tested for their ability to inhibit louse egg-hatch in vitro. The metalloprotease inhibitor 1,10-phenanthroline and the aminopeptidase inhibitor bestatin significantly inhibited (P<0·05) louse egg-hatch (100% and 58%, respectively). The presence of metalloproteases at the time of egg-hatch and the inhibition of egg-hatch in P. humanus by metalloprotease inhibitors suggests a crucial role for these proteases in the hatching of this medically important parasite.
A rapid and sensitive intracellular flow cytometric assay to identifyTheileria parvainfection within target cells
Authors: ROCCHI M. S. , BALLINGALL K. T. , NGUGI D. , MacHUGH N. D. , McKEEVER D. J. 
Published: September 2007

SUMMARYTheileria parvais an intracellular protozoan parasite transmitted by ticks that causes a fatal lymphoproliferative disease of cattle known as East Coast Fever. Vaccination against the disease currently relies on inoculation of the infective sporozoite stage of the parasite and simultaneous treatment with long-acting formulations of oxytetracycline. Sporozoites are maintained as frozen stabilates of triturated infected ticks and the method requires accurate titration of stabilates to determine appropriate dose rates. Titration has traditionally been undertaken in cattle and requires large numbers of animals because of individual variation in susceptibility to infection. An alternative tissue culture-based method is laborious and time consuming. We have developed a flow cytometric method for quantifying the infectivity of sporozoite stabilatesin vitrobased on the detection of intracellular parasite antigen. The method allows clear identification of parasitized cells with a high degree of sensitivity and specificity. Analysis of infected cells between 48 and 72 h post-infection clearly defines the potential transforming capability of different stabilates.
Depression and common mental disorders in lone parents: results of the 2000 National Psychiatric Morbidity Survey
Authors: Cooper C. , Bebbington P. E. , Meltzer H. , Bhugra D. , Brugha T. , Jenkins R. , Farrell M. , King M. 
Published: September 2007

BackgroundLone mothers experience higher rates of psychiatric morbidity, while rates in lone fathers have never been studied. We aimed to determine the relative contributions of financial strain and decreased social support to the excess of depression and common mental disorders (CMD) in lone parents.MethodWe investigated whether parent status (lone parent, partnered parent, others) was associated with psychiatric morbidity measured using the revised Clinical Interview Schedule, after controlling for self-reported financial strain (income and debt) and social support.ResultsLone mothers were twice as likely to have a CMD (OR 1.8, 95% CI 1.4–2.3) as other women. This was not significant after controlling for financial strain or social support. Lone fathers were nearly four times more likely to have a CMD than other men (OR 3.9, 95% CI 2.3–6.8), and this risk remained undiminished by controlling for age, income, debt and levels of social support.ConclusionDebt management would be a rational strategy to reduce psychiatric morbidity in lone mothers. More studies are needed to inform prevention strategies in lone fathers.
Cigarette smoking and suicidal behaviour: results from a 25-year longitudinal study
Authors: Boden J. M. , Fergusson D. M. , Horwood L. J. 
Published: September 2007

BackgroundThis study examined the associations between cigarette smoking and suicidal ideation and suicide attempts, both before and after control for potentially confounding using fixed effects regression models.MethodData were gathered during the Christchurch Health and Development Study, a 25-year longitudinal study of a birth cohort of New Zealand children (635 males, 630 females). The analysis was based on a sample of 1041 participants with available data on cigarette smoking and suicidal behaviour from ages 16 to 25 years. The main outcome measures were suicidal ideation and suicide attempts, ages 16–18, 18–21, and 21–25.ResultsThere were significant bivariate associations between the frequency of cigarette smoking and both suicidal ideation and suicide attempts. Cohort members who smoked 20 or more cigarettes per day had odds of suicidal ideation that were 3.39 times (95% CI 2.06–5.59) those of non-smokers, and odds of suicide attempt that were 4.39 (95% CI 2.18–8.85) times those of non-smokers. Control for non-observed fixed confounding factors reduced the association between cigarette smoking and suicidal ideation and suicide attempts to statistical non-significance. After adjustment, those smoking more than 20 cigarettes per day had odds of suicidal ideation that were 1.00 times (95% CI 0.46–2.18) those of non-smokers, and odds of suicide attempt that were 1.84 (95% CI 0.81–4.18) times those of non-smokers.ConclusionsThe findings suggest that the associations between frequency of cigarette smoking and suicidal behaviour may largely be explained by the non-observed background factors and life circumstances that are associated with both cigarette smoking and suicidal behaviour.
Chronic fatigue syndrome and related disorders in UK veterans of the Gulf War 1990–1991: results from a two-phase cohort study
Authors: Ismail K. , Kent K. , Sherwood R. , Hull L. , Seed P. , David A. S. , Wessely S. 
Published: September 2007

BackgroundThe aim was to determine the prevalence of chronic fatigue syndrome (CFS), chronic fatigue and fibromyalgia in UK military personnel after the Gulf War 1990–1991.MethodA two-phase cohort study was used. Three randomly selected subsamples identified from a population-based cross-sectional postal survey of over 10 000 current and ex-service UK military personnel (Gulf veterans were those deployed to the Gulf War 1990–1991; non-Gulf veterans were Bosnia peacekeepers 1992–1997 and those on active duty during the Gulf War 1990–1991 but not deployed) were recruited. Their disability status was assessed using the Short Form 36 physical functioning scale; Gulf veterans who reported physical disability (n=111) were compared with non-Gulf (n=133) veterans who reported similar levels of physical disability. Screening for known medical and psychiatric conditions was conducted to exclude medical explanations for disability and symptomatic distress. Standardised criteria for CFS, chronic fatigue and fibromyalgia were used.ResultsDisabled Gulf veterans were more likely to be overweight, have elevated γ-glutamyl transferase levels and screen positive for hypertension. There were no other clinically significant differences in clinical markers for medically explainable conditions. Disabled Gulf veterans were more likely than similarly disabled Bosnia and Era veterans (adjusted odds ratio 7.8, 95% confidence interval 2.5–24.5) to meet the criteria for CFS. Rates for other medically unexplained conditions were not significantly increased.ConclusionsSymptoms in keeping with CFS account for a significant part of the symptomatic distress in Gulf veterans.
Declining incidence of meningococcal disease in Denmark, confirmed by a capture–recapture analysis for 1994 and 2002
Authors: HOWITZ M. F. , SAMUELSSON S. , MØLBAK K. 
Published: September 2007

SUMMARYDenmark has in the past 10 years experienced a decrease in the number of notified cases of meningococcal disease. In 1994 the completeness of the Notification System for Meningococcal Disease (NSMD) was estimated as 96% (95% CI 93–98). To answer the question whether the observed decrease reflects a real decrease in the incidence; we estimated the completeness of the notification system in 2002. We estimated the completeness of registration by a capture–recapture analysis. As the first data source, we used the national NSMD, which is an integrated surveillance system between the Department of Epidemiology and the Neisseria Reference Laboratory. The second independent source was the National Patient Registry (NPR). In 2002, the completeness of the NSMD was estimated as 96% (95% CI 95–98) and for the NPR as 84% (95% CI 82–85). The ‘real’ incidence rate was 1·9/100 000 population, which compared to 4·4/100 000 population in 1994. We concluded that the observed decrease in incidence rate is real. The NSMD in Denmark functions well and captures almost all cases of meningococcal disease. The complete registration which includes a unique personal identification number serves as an outstanding source for nationwide registry linkage studies.
Acinetobacterinfections: a growing threat for critically ill patients
Authors: FALAGAS M. E. , KARVELI E. A. , SIEMPOS I. I. , VARDAKAS K. Z. 
Published: September 2007

SUMMARYThere has been increasing concern regarding the rise ofAcinetobacterinfections in critically ill patients. We extracted information regarding the relative frequency ofAcinetobacterpneumonia and bacteraemia in intensive-care-unit (ICU) patients and the antimicrobial resistance ofAcinetobacterisolates from studies identified in electronic databases.Acinetobacterinfections most frequently involve the respiratory tract of intubated patients andAcinetobacterpneumonia has been more common in critically ill patients in Asian (range 4–44%) and European (0–35%) hospitals than in United States hospitals (6–11%). There is also a gradient in Europe regarding the proportion of ICU-acquired pneumonias caused byAcinetobacterwith low numbers in Scandinavia, and gradually rising in Central and Southern Europe. A higher proportion ofAcinetobacterisolates were resistant to aminoglycosides and piperacillin/tazobactam in Asian and European countries than in the United States. The data suggest thatAcinetobacterinfections are a growing threat affecting a considerable proportion of critically ill patients, especially in Asia and Europe.
Large Q fever outbreak due to sheep farming near residential areas, Germany, 2005
Authors: GILSDORF A. , KROH C. , GRIMM S. , JENSEN E. , WAGNER-WIENING C. , ALPERS K. 
Published: September 2007

SUMMARYIn June 2005 Coxiella burnetii-infected sheep, grazing and lambing on a meadow bordering a residential area, caused a large Q fever outbreak (331 cases) in Germany. Our outbreak investigation provided attack rates (AR) by distance between residence and meadow, sex and age groups. The AR of people living within 50 m of the meadow was 11·8%. It decreased the further the residence was from the meadow, falling to 1·3% at 350–400 m distance (RR 8·7, 95% CI 4·5–17·1). The AR was higher in men (RR 1·4, 95% CI 1·1–1·8). In the 25–64 years age group, the AR was 2·3 times higher compared to other age groups (95% CI 1·7–3·0). The distance-related AR showed a relationship between risk of infection and living close to the meadow. Ongoing urbanization will probably lead to further Q fever outbreaks, hence prevention activities undertaken by animal and public health practitioners should be aligned and strengthened.
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
Authors: Hijikata Atsushi , Kitamura Hiroshi , Kimura Yayoi , Yokoyama Ryo , Aiba Yuichi , Bao Yanyuan , Fujita Shigeharu , Hase Koji , Hori Shohei , Ishii Yasuyuki , Kanagawa Osami , Kawamoto Hiroshi , Kawano Kazuya , Koseki Haruhiko , Kubo Masato , Kurita-Miki Ai , Kurosaki Tomohiro , Masuda Kyoko , Nakata Mitsumasa , Oboki Keisuke , Ohno Hiroshi , Okamoto Mariko , Okayama Yoshimichi , O-Wang Jiyang , Saito Hirohisa , Saito Takashi , Sakuma Machie , Sato Katsuaki , Sato Kaori , Seino Ken-ichiro , Setoguchi Ruka , Tamura Yuki , Tanaka Masato , Taniguchi Masaru , Taniuchi Ichiro , Teng Annabelle , Watanabe Takeshi , Watarai Hiroshi , Yamasaki Sho , Ohara Osamu 
Published: September 2007

AbstractMotivation: Although a huge amount of mammalian genomic data does become publicly available, there are still hurdles for biologists to overcome before such data can be fully exploited. One of the challenges for gaining biological insight from genomic data has been the inability to cross-reference transcriptomic and proteomic data using a single informational platform. To address this, we constructed an open-access database that enabled us to cross-reference transcriptomic and proteomic data obtained from immune cells.Results: The database, named RefDIC (Reference genomics Database of Immune Cells), currently contains: (i) quantitative mRNA profiles for human and mouse immune cells/tissues obtained using Affymetrix GeneChip technology; (ii) quantitative protein profiles for mouse immune cells obtained using two-dimensional gel electrophoresis (2-DE) followed by image analysis and mass spectrometry and (iii) various visualization tools to cross-reference the mRNA and protein profiles of immune cells. RefDIC is the first open-access database for immunogenomics and serves as an important information-sharing platform, enabling a focused genomic approach in immunology.Availability: All raw data and information can be accessed from http://refdic.rcai.riken.jp/. The microarray data is also available at http://cibex.nig.ac.jp/ under CIBEX accession no. CBX19, and http://www.ebi.ac.uk/pride/ under PRIDE accession numbers 2354–2378 and 2414.Contact: hijikata@rcai.riken.jpSupplementary information: Supplementary data are available at Bioinformatics online.
Efficient parameter estimation for spatio-temporal models of pattern formation: case study ofDrosophila melanogaster
Authors: Fomekong-Nanfack Yves , Kaandorp Jaap A. , Blom Joke 
Published: September 2007

AbstractMotivation: Diffusable and non-diffusable gene products play a major role in body plan formation. A quantitative understanding of the spatio-temporal patterns formed in body plan formation, by using simulation models is an important addition to experimental observation. The inverse modelling approach consists of describing the body plan formation by a rule-based model, and fitting the model parameters to real observed data. In body plan formation, the data are usually obtained from fluorescent immunohistochemistry or in situ hybridizations. Inferring model parameters by comparing such data to those from simulation is a major computational bottleneck. An important aspect in this process is the choice of method used for parameter estimation. When no information on parameters is available, parameter estimation is mostly done by means of heuristic algorithms.Results: We show that parameter estimation for pattern formation models can be efficiently performed using an evolution strategy (ES). As a case study we use a quantitative spatio-temporal model of the regulatory network for early development in Drosophila melanogaster. In order to estimate the parameters, the simulated results are compared to a time series of gene products involved in the network obtained with immunohistochemistry. We demonstrate that a (μ,λ)-ES can be used to find good quality solutions in the parameter estimation. We also show that an ES with multiple populations is 5–140 times as fast as parallel simulated annealing for this case study, and that combining ES with a local search results in an efficient parameter estimation method.Supplementary information and availability: Bioinformatics online; software: http://www.science.uva.nl/research/scs/3D-RegNet/fly_eaContact: jaapk@science.uva.nl
Extending assembly of short DNA sequences to handle error
Authors: Jeck William R. , Reinhardt Josephine A. , Baltrus David A. , Hickenbotham Matthew T. , Magrini Vincent , Mardis Elaine R. , Dangl Jeffery L. , Jones Corbin D. 
Published: September 2007

AbstractInexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illumina's Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (∼30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error.Availability: http://152.2.15.114/~labweb/VCAKEContact: william.jeck@gmail.com
DNA Barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae).
Authors: Trewick Steven A. 
Published: September 2007

AbstractDNA barcoding has been touted as a program that will efficiently and relatively cheaply inform on biological diversity; yet many exemplars purporting to demonstrate the efficacy of the method have been undertaken by its principal proponents. Critics of DNA barcoding identify insufficient within‐taxon sampling coupled with the knowledge that levels of haplotypic paraphyly are rather high as key reasons to be sceptical of the value of an exclusively DNA‐based taxonomic. Here I applied a DNA barcoding approach using mtDNA sequences from the cytochrome oxidase I gene to examine diversity in a group of endemic New Zealand grasshoppers belonging to the genus Sigaus. The mtDNA data revealed high genetic distances among individuals of a single morpho‐species, but this diversity was geographically partitioned. Phylogenetic analysis supported at least four haplogroups within one species (Sigaus australis) but paraphyly of this species with respect to several others. In some instances two morphologically and ecologically distinct species shared identical mtDNA haplotypes. The mismatch of genealogy and taxonomy revealed in the Sigaus australis complex indicates that, if used in isolation, DNA barcoding data can be highly misleading about biodiversity. Furthermore, failure to take into account evidence from natural history and morphology when utilizing DNA barcoding will tend to conceal the underlying evolutionary processes associated with speciation.© The Willi Hennig Society 2007.
Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysis
Authors: Bayly Michael J. , Udovicic Frank , Gibbs Adele K. , Parra‐O. Carlos , Ladiges Pauline Y. 
Published: September 2007

AbstractPseudogenes from the 18S−5.8S−26S cistron of nuclear ribosomal DNA are reported in the eucalypt group (Myrtaceae), which includes seven genera. Putative pseudogenes are identified by a range of sequence comparisons including: the number of CpG and CpNpG methylation sites, GC content, estimated secondary structure stability of internal transcribed spacer transcripts, the presence of conserved motifs, patterns of sequence relationships and inferred substitution patterns. These comparisons indicate that pseudogenes are widespread, being evident in Eucalyptus (subgenera Eucalyptus and Eudesmia), Corymbia (extracodical sections Rufaria, Ochraria and Blakearia), Angophora, Stockwellia quadrifida and Arillastrum gummiferum. At least six sequences used in previous phylogenetic studies are identified as pseudogenes, and a further 10 pseudogenes are newly sequenced here. Gene trees place pseudogenes in a number of distinct lineages: pseudogenes from Eucalyptus group with other Eucalyptus sequences, those from Corymbia and Angophora group with other Corymbia/Angophora sequences, that from Stockwellia groups with other sequences from the Eucalyptopsis group, and that from Arillastrum is placed as sister to the other included sequence of Arillastrum. Some pseudogenes in Eucalyptus, Corymbia and Angophora represent “deep” ribosomal DNA paralogues that pre‐date species differentiation in these groups, and a recombination analysis shows no evidence of recombination between putative pseudogenes and their functional counterparts. The presence of divergent paralogues presents both challenges and opportunities for the reconstruction of eucalypt phylogenies using ribosomal DNA sequences. Phylogenetic data sets should include only orthologous sequences, but different paralogues potentially provide additional, independent, character sets for phylogenetic analyses.© The Willi Hennig Society 2007.
The chili pepper CaATL1: an AT‐hook motif‐containing transcription factor implicated in defence responses against pathogens
Authors: KIM SOO‐YONG , KIM YOUNG‐CHEOL , SEONG EUN SOO , LEE YONG‐HWAN , PARK JEONG MEE , CHOI DOIL 
Published: September 2007

SUMMARYUsing cDNA microarray analysis, we isolated a cDNA clone,CaATL1(Capsicum annuumL. BukangAT‐hook‐Likegene1), from a chili pepper plant incompatibly interacting with bacterial pathogens. The deduced amino acid sequence has a potential nuclear localization sequence and an AT‐hook DNA binding motif which can bind AT‐rich sequence elements. Expression ofCaATL1was specifically induced in host‐ and non‐host‐resistant responses against bacterial and viral pathogens in pepper plants. In addition,CaATL1transcripts also increased following salicylic acid and ethephone treatment but were only mildly induced by methyl‐jasmonate treatment. CaATL1::smGFP (soluble‐modified green fluorescent protein) fusion protein localized to nuclei in tobacco BY2 protoplasts. The C‐terminal region of the CaATL1 protein fused to the LexA DNA binding domain was able to activate reporter gene expression in yeast. To analyse further the role of theCaATL1in pathogen defence response, we generatedCaATL1‐over‐expressing transgenic tomato plants. These transgenic plants showed enhanced disease resistance against bacterial and oomycete pathogens. Taken together, these results provide the first evidence of a role for a plant AT‐hook motif‐containing transcription factor in pathogen defence response.