bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hybrid military establishment of the East India Company in South Asia: 1750–1849
Authors: Roy Kaushik 
Published: June 2011

AbstractDuring the seventeenth century, the East India Company (EIC) was a minor power in South Asia, repeatedly defeated in battle. However, this changed rapidly, beginning in the 1750s, as the EIC started projecting power from its coastal enclaves into the interior. One after other, the indigenous powers were defeated and destroyed. This article argues that the EIC’s military success was not merely the result of importing the military institutions that emerged in western Europe: there was no military revolution in early modern South Asia. Rather, the EIC blended imported British military institutions and techniques with South Asia’s indigenous military traditions, creating a hybrid military establishment in which South Asian manpower, animals, and economic resources were crucial. The article focuses on the construction of the EIC’s military establishment by concentrating on three spheres: military technology, manpower management, and logistics.
Inherited mutations impair responses to environmental carcinogens: Cancer prevention in mutation carriers
Authors: Friedenson Bernard 
Published: June 2011

AbstractSome environmental carcinogens may be responsible for a modest increase in the numbers of cancers after years of exposure. Economic or political factors weigh against widespread bans of carcinogens. However, lists of chemicals and agents that cause cancer assume that everyone is equally susceptible to their carcinogenic effects.Hereditary cancer gene mutations can target specific tissues if they are exposed to a carcinogen and the hereditary deficit impairs normal protective responses. Mutation carriers should then have higher risks for specific cancers caused by specific carcinogens.For example, it can be predicted that BRCA1 or BRCA2 mutation carriers should be highly susceptible to the carcinogen formaldehyde. High formaldehyde levels can overwhelm normal enzyme detoxification systems or detoxification genes may be inadequate or missing. Formaldehyde that is not detoxified causes strands of DNA to cross-link to each other and to nearby proteins. Carriers of mutations in BRCA1/2 dependent pathways are deficient in the ability to undo these cross-links.Human myeloid leukemias are linked to formaldehyde. Inherited biallelic BRCA2 gene defects and other defects in BRCA1/2 mediated pathways dramatically increase risks for myeloid leukemia, even among infants. In 12 of 15 studies, heterozygous BRCA1 or BRCA2 mutations increase risks for myeloid leukemias. Moreover, chromosome arms lost in hereditary breast cancers encode enzymes essential for formaldehyde metabolism. BRCA1/2 mutation carriers may reduce their very high cancer risks by lowering their exposure to formaldehyde.Cancers associated with many other hereditary gene deficits can also be stimulated by distinct environmental hazards. Widespread education could prevent or delay some cancers in mutation carriers.
HOW CREDIT INSTITUTIONS LOOK AT SOCIETY
Authors: Lopes Daniel Seabra , Marques Rafael 
Published: June 2011

ABSTRACT
Twenty years ago, Anthony Giddens proclaimed that modernity was, inherently, deeply and intrinsically sociological in the sense that sociological knowledge tended to be rapidly assimilated by individuals and institutions and therefore incorporated into subsequent processes of change. Thus, it may seem relevant to question just how much sociology is actually being put into practice in economic institutions in general and in credit institutions in particular. Drawing on fieldwork conducted in the marketing, risk, and financial departments of two Portuguese retail banks, this article describes how these institutions use specific views of society which are predominantly statistical and bear little resemblance to more qualitative sociological or anthropological accounts. Hence, there is a clear need to reconsider the problem of social reflexivity and to grasp to what extent the social sciences are still important in providing a framework for perceiving the economy and society.
Dangerous Severe Personality Disordered (DSPD) Patients: Characteristics and Comparison with Other High-Risk Offenders
Authors: Burns Tom , Fazel Seena , Fahy Tom , Fitzpatrick Ray , Rogers Robert , Sinclair Julia , Linsell Louise , Doll Helen , Yiend Jenny , group IDEA 
Published: June 2011

England and Wales introduced the administrative category of Dangerous Severe Personality Disorder (DSPD) and established special units in prisons and high-secure psychiatric hospitals for their treatment. To examine their characteristics, we approached 202 patients admitted to DSPD units; 174 consented to participate in research. All were male, and the median age was 38 years. Most were white and born in the UK. Most patients (75%) met full DSPD criteria as suffering from severe personality disorder that caused them to be dangerous. With respect to personality disorder, most had elevated psychopathic traits and 40% met criteria for psychopathy on the Psychopathy Checklist-Revised (Hare, 2003). With respect to dangerousness, 25% of patients had a history of homicide; 28%, sexual offenses; and 41%, other violent offenses. Median time spent in prison was more than 12 years. According to standardized measures of violence risk, those admitted to DSPD units resembled other groups of high risk offenders described in the international literature. There were some significant differences between those admitted to prison- versus hospital-based units. The findings confirmed that DSPD units contain dangerous offenders with no evidence of preemptive incarceration.
vipR: variant identification in pooled DNA using R
Authors: Altmann Andre , Weber Peter , Quast Carina , Rex-Haffner Monika , Binder Elisabeth B. , Müller-Myhsok Bertram 
Published: June 2011

Abstract
Motivation: High-throughput-sequencing (HTS) technologies are the method of choice for screening the human genome for rare sequence variants causing susceptibility to complex diseases. Unfortunately, preparation of samples for a large number of individuals is still very cost- and labor intensive. Thus, recently, screens for rare sequence variants were carried out in samples of pooled DNA, in which equimolar amounts of DNA from multiple individuals are mixed prior to sequencing with HTS. The resulting sequence data, however, poses a bioinformatics challenge: the discrimination of sequencing errors from real sequence variants present at a low frequency in the DNA pool.
Results: Our method vipR uses data from multiple DNA pools in order to compensate for differences in sequencing error rates along the sequenced region. More precisely, instead of aiming at discriminating sequence variants from sequencing errors, vipR identifies sequence positions that exhibit significantly different minor allele frequencies in at least two DNA pools using the Skellam distribution. The performance of vipR was compared with three other models on data from a targeted resequencing study of the TMEM132D locus in 600 individuals distributed over four DNA pools. Performance of the methods was computed on SNPs that were also genotyped individually using a MALDI-TOF technique. On a set of 82 sequence variants, vipR achieved an average sensitivity of 0.80 at an average specificity of 0.92, thus outperforming the reference methods by at least 0.17 in specificity at comparable sensitivity.
Availability: The code of vipR is freely available via: http://sourceforge.net/projects/htsvipr/
Contact: altmann@mpipsykl.mpg.de
Sorting the nuclear proteome
Authors: Bauer Denis C. , Willadsen Kai , Buske Fabian A. , Lê Cao Kim-Anh , Bailey Timothy L. , Dellaire Graham , Bodén Mikael 
Published: June 2011

Abstract
Motivation: Quantitative experimental analyses of the nuclear interior reveal a morphologically structured yet dynamic mix of membraneless compartments. Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed.
Results: This study investigates determinants of associations between eight intra-nuclear compartments and their proteins in heterogeneous genome-wide data. We develop a model based on a range of candidate determinants, capable of mapping the intra-nuclear organization of proteins. The model integrates protein interactions, protein domains, post-translational modification sites and protein sequence data. The predictions of our model are accurate with a mean AUC (over all compartments) of 0.71.
We present a complete map of the association of 3567 mouse nuclear proteins with intra-nuclear compartments. Each decision is explained in terms of essential interactions and domains, and qualified with a false discovery assessment. Using this resource, we uncover the collective role of transcription factors in each of the compartments. We create diagrams illustrating the outcomes of a Gene Ontology enrichment analysis. Associated with an extensive range of transcription factors, the analysis suggests that PML bodies coordinate regulatory immune responses.
Contact: m.boden@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Possible effects of global warming on fish recruitment: shifts in spawning season and latitudinal distribution can alter growth of fish early life stages through changes in daylength
Authors: Shoji Jun , Toshito Shun-ichi , Mizuno Ken-ichiro , Kamimura Yasuhiro , Hori Masakazu , Hirakawa Koji 
Published: June 2011

Abstract
Shoji, J., Toshito, S., Mizuno, K., and Kamimura, Y., Hori, M., Hirakawa, K. 2011. Possible effects of global warming on fish recruitment: shifts in spawning season and latitudinal distribution can alter growth of fish early life stages through changes in daylength. – ICES Journal of Marine Science, 68: 1165–1169. Changes in growth rates, shifts in the spawning season, and shifts in the spawning area (latitude) are expected after an increase in sea temperature resulting from global warming. Fish can avoid higher temperatures by a poleward shift in the spawning area and a temporal shift in spawning timing. However, these shifts will include changes in daylength experienced during their early life stages. To understand comprehensively the possible effects of global warming on fish recruitment, effects of temperature and daylength on growth, daily ration, and growth efficiency of black rockfish, Sebastes cheni, a dominant species in coastal waters of the western North Pacific, were examined under wild and laboratory conditions. The growth rate was elevated at higher temperatures between 11.1 and 21.3°C. Growth efficiency was highest at 16°C. The effect of photoperiod on growth was also significant, with enhanced growth resulting from the longer daylength. The effect of shifts in spawning season and spawning area would differ among fish species and spawning season. Comparison of early growth under different daylength conditions between S. cheni and ayu, Plecoglossus altivelis altivelis, indicated that the shifts in spawning season and spawning area would have different effects on fish early life stages (FELSs) related to changes in daylength. Changes in daylength resulting from a poleward shift in the spawning area will have opposite effects for summer- and winter-growing FELSs, and the effects are more prominent at higher latitudes.
What ocean biogeochemical models can tell us about bottom-up control of ecosystem variability
Authors: Gnanadesikan A. , Dunne J. P. , John J. 
Published: June 2011

AbstractGnanadesikan, A., Dunne, J. P., and John, J. 2011. What ocean biogeochemical models can tell us about bottom-up control of ecosystem variability. – ICES Journal of Marine Science, 68: 1030–1044. Processes included in earth system models amplify the impact of climate variability on phytoplankton biomass and, therefore, on upper trophic levels. Models predict much larger relative interannual variability in large phytoplankton biomass than in total phytoplankton biomass, supporting the goal of better constraining size-structured primary production and biomass from remote sensing. The largest modelled variability in annually averaged large phytoplankton biomass is associated with changes in the areal extent of relatively productive regions. Near the equator, changes in the areal extent of the high-productivity zone are driven by large-scale shifts in nutrient fields, as well as by changes in currents. Along the poleward edge of the Subtropical Gyres, changes in physical mixing dominate. Finally, models indicate that high-latitude interannual variability in large phytoplankton biomass is greatest during spring. Mechanisms for producing such variability differ across biomes with internal ocean processes, such as convection complicating efforts to link ecosystem variability to climate modes defined using sea surface temperature alone. In salinity-stratified subpolar regions, changes in bloom timing driven by salinity can produce correlations between low surface temperatures and high productivity, supporting the potential importance of using coupled atmosphere–ocean reanalyses, rather than simple forced ocean reanalyses, for attributing past ecosystem shifts.
Physiological individual-based modelling of larval Atlantic herring (Clupea harengus) foraging and growth: insights on climate-driven life-history scheduling
Authors: Hufnagl Marc , Peck Myron A. 
Published: June 2011

AbstractHufnagl, M., and Peck, M. A. 2011. Physiological individual-based modelling of larval Atlantic herring (Clupea harengus) foraging and growth: insights on climate-driven life-history scheduling. – ICES Journal of Marine Science, 68: 1170–1188. A physiological individual-based model for the foraging and growth of Atlantic herring (Clupea harengus) larvae was constructed, validated using laboratory and field data, tested for parameter sensitivity, and used to examine climate-driven constraints on life-history scheduling. Model scenarios examined how natural (phenological and magnitude) changes in key environmental factors (temperature, prey, and photoperiod/daylength) affected the estimates of survival and growth of spring- and autumn-spawned larvae. The most suitable hatching seasons agreed well with the periods of larval abundance in Northeast Atlantic waters. Modelled survival is unlikely in June, July, and November. Mean annual temperature, prey concentration, and composition significantly influenced larval growth of both autumn and spring spawners. The model suggested that climate-driven changes in bottom-up factors will affect spring- and autumn-spawned larvae in different ways. It is unlikely that autumn-spawning herring will be able to avoid unfavourable conditions by delaying their spawning time or by utilizing more northern spawning grounds because of limitations in daylength to larval growth and survival. Conversely, earlier spawning in spring, or later, midsummer spawning will be tightly constrained by match–mismatch dynamics between larvae and zooplankton production.
Effects of climate change on fish and fisheries: forecasting impacts, assessing ecosystem responses, and evaluating management strategies
Authors: Hollowed Anne Babcock , Barange Manuel , Ito Shin-ichi , Kim Suam , Loeng Harald , Peck Myron A. 
Published: June 2011

Abstract
Hollowed, A. B., Barange, M., Ito, S-I., Kim, S., Loeng, H., and Peck, M. 2011. Effects of climate change on fish and fisheries: forecasting impacts, assessing ecosystem responses, and evaluating management strategies. – ICES Journal of Marine Science, 68: 984–985.
The potential use of a Gadget model to predict stock responses to climate change in combination with Bayesian networks: the case of Bay of Biscay anchovy
Authors: Andonegi Eider , Fernandes Jose Antonio , Quincoces Iñaki , Irigoien Xabier , Uriarte Andrés , Pérez Aritz , Howell Daniel , Stefánsson Gunnar 
Published: June 2011

AbstractAndonegi, E., Fernandes, J. A., Quincoces, I., Irigoien, X., Uriarte, A., Pérez, A., Howell, D., and Stefánsson, G. 2011. The potential use of a Gadget model to predict stock responses to climate change in combination with Bayesian networks: the case of Bay of Biscay anchovy. – ICES Journal of Marine Science, 68: 1257–1269. The European anchovy (Engraulis encrasicolus) is a short-lived pelagic species distributed in Atlantic European waters, with the Bay of Biscay being one of the main centres of abundance. Because it is a short-lived species, the state of the stock is determined largely by incoming recruitment. Recruitment is highly variable and depends on a variety of factors, such as the size of the spawning stock and environmental conditions in the area. The use of a coupled model that could serve to predict the evolution of the anchovy stock in the short, medium, and long term under several fishing-pressure scenarios and given climate scenarios is demonstrated. This coupled model consists of a Gadget (Globally Applicable Disaggregated General Ecosystem Toolbox) model that was used to analyse the status of the Bay of Biscay anchovy population and to simulate future scenarios based on the estimated recruitment levels, combined with a probabilistic Bayesian network model for recruitment estimation based on machine-learning methods and using climatic indices as potential forecasting factors. The results indicate that certain combinations of medium to high fishing pressure and adverse environmental conditions could force the stock outside its biological reference boundaries.
Review article: cyclic vomiting syndrome in adults – rediscovering and redefining an old entity
Authors: Hejazi R. A. , McCallum R. W. 
Published: June 2011

Aliment Pharmacol Ther 2011; 34: 263–273SummaryBackground  Cyclic vomiting syndrome is a disorder characterised by recurrent episodes of severe nausea and vomiting separated by symptom‐free periods.Aims  To review the history, epidemiology, clinical aspects, pathophysiology, diagnosis and treatments of adult cyclic vomiting syndrome as well as to identify areas for further clinical research and the unanswered questions in this field.Methods  We conducted a PubMed search using such keywords as cyclic vomiting syndrome; nausea; vomiting; pathophysiology; diagnosis; treatment; trigger factors; gastric emptying test; autonomic nerve function test; gastrointestinal hormones; outcome and natural history and combined this information with the knowledge and extensive clinical research and publications from the authors.Results  Available data show that in adult cyclic vomiting syndrome, severe epigastric and sometimes diffuse abdominal pain accompanies most cycles of nausea and vomiting interspersed with periods of symptomatic remission. Psychological disorders, specifically anxiety and depression are common, and gastric emptying is actually rapid in approximately 60% of patients and normal in the remainder. There is an impressive and sustained response to high‐dose tricyclic antidepressants. In up to 15% who are regarded as poor responders to tricyclic antidepressants, a predictable profile can be identified related to co‐existing psychological disorders, marijuana use, poorly controlled migraine headache or chronic narcotic use.Conclusions  Cyclic vomiting syndrome in adults is an entity that is being increasingly recognised, but the need to educate Internists, Gastroenterologists and Emergency Department staff remains an ongoing challenge.
What is the optimal type of fluid to be used for peri‐operative fluid optimisation directed by oesophageal Doppler monitoring?
Authors: Morris C. , Rogerson D. 
Published: June 2011

SummaryThe objective of this review was to determine the optimal type or class of intravenous fluid to be used during peri‐operative patient optimisation guided by oesophageal Doppler monitoring and to identify future directions for research. We undertook a literature review of patients undergoing major (general, colorectal, orthopaedic and urological) surgery, whose fluid therapy was managed using peri‐operative oesophageal Doppler monitoring. We identified 10 studies that included 891 randomised patients. A variety of regimens and types of fluid were used in association with oesophageal Doppler monitoring, including crystalloid, gelatin and hydroxyethyl starch. A wide variety of hydroxyethyl starch preparations were used, including high molecular weight and highly substituted hetastarches, and lower molecular weight tetrastarches. Most studies were of high quality, associated with reduced hospital stay, but underpowered to evaluate other outcomes. In units with established enhanced recovery facilities, the benefits of colloid based on oesophageal Doppler monitoring were not reproduced. There is little evidence to support preferential use of any particular type of fluid during oesophageal Doppler guided optimisation; however, routine use of colloids is associated with significantly higher costs and may increase hospital stay. Furthermore, many of these fluids have not been evaluated in patient populations in whom optimisation is being applied or proposed, and the potential for harm cannot be excluded. Recommendations for future studies are provided, including adequate power for primary end points beyond hospital stay and adequate follow‐up, and inclusion of a crystalloid comparison group.
‘Now I understand’: consulting parents on chart design and parental information for the UK‐WHO child growth charts
Authors: Sachs M. , Sharp L. , Bedford H. , Wright C. M. 
Published: June 2011

AbstractBackground  Regular assessment of growth is an important part of child health surveillance in the UK and most parents are very interested in their child's growth. UK parents are given a personal child health record (PCHR), including growth charts, which are plotted during baby clinic visits. Parents were consulted as part of the process of designing new UK charts to incorporate the World Health Organization growth standard. This paper describes the main themes that emerged and how they influenced the final design.Method  Three sets of consultations with 47 parents were conducted to collect preliminary information, and to evaluate proposed chart designs, instructions and written information for parents.Results  At every consultation, the impact of the depiction of the 50th centile line in bold was mentioned spontaneously by parents. They also found aspects of the charts unclear, including the implications of a recorded weight on any particular centile, the difficulty of understanding existing text about charts in the PCHR, their preference for using pounds and ounces rather than metric weights and confusion about how frequently babies should be weighed. This led to the production of parental information including explanation of these issues which were then tested in two further sets of focus groups.Conclusion  Involving parents in the process of designing growth charts and information influenced the finished design and the text in the PCHR. Ensuring information meets parents' needs is important to ensure successful growth monitoring.