bluuebunny/crossref_metadata_2025 huggingface dataset:
A lineage‐specific centromere retrotransposon in Oryza brachyantha
Authors: Gao Dongying , Gill Navdeep , Kim Hye‐Ran , Walling Jason G , Zhang Wenli , Fan Chuanzhu , Yu Yeisoo , Ma Jianxin , SanMiguel Phillip , Jiang Ning , Cheng Zhukuan , Wing Rod A. , Jiang Jiming , Jackson Scott A.
Published: August 2009

Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elements are highly concentrated in centromeres, and are likely to play a role in centromere function. In order to study centromere evolution in the Oryza (rice) genus, we sequenced the orthologous region to centromere 8 of Oryza sativa from a related species, Oryza brachyantha. We found that O. brachyantha does not have the canonical CRR (CR of rice) found in the centromeres of all other Oryza species. Instead, a new Ty3‐gypsy (Metaviridae) retroelement (FRetro3) was found to colonize the centromeres of this species. This retroelement is found in high copy numbers in the O. brachyantha genome, but not in other Oryza genomes, and based on the dating of long terminal repeats (LTRs) of FRetro3 it was amplified in the genome in the last few million years. Interestingly, there is a high level of removal of FRetro3 based on solo‐LTRs to full‐length elements, and this rapid turnover may have played a role in the replacement of the canonical CRR with the new element by active deletion. Comparison with previously described ChIP cloning data revealed that FRetro3 is found in CENH3‐associated chromatin sequences. Thus, within a single lineage of the Oryza genus, the canonical component of grass centromeres has been replaced with a new retrotransposon that has all the hallmarks of a centromeric retroelement.
CNI1/ATL31, a RING‐type ubiquitin ligase that functions in the carbon/nitrogen response for growth phase transition in Arabidopsis seedlings
Authors: Sato Takeo , Maekawa Shugo , Yasuda Shigetaka , Sonoda Yutaka , Katoh Etsuko , Ichikawa Takanari , Nakazawa Miki , Seki Motoaki , Shinozaki Kazuo , Matsui Minami , Goto Derek B. , Ikeda Akira , Yamaguchi Junji
Published: August 2009

Plants are able to sense and respond to changes in the balance between carbon (C) and nitrogen (N) metabolite availability, known as the C/N response. During the transition to photoautotrophic growth following germination, growth of seedlings is arrested if a high external C/N ratio is detected. To clarify the mechanisms for C/N sensing and signaling during this transition period, we screened a large collection of FOX transgenic plants, overexpressing full‐length cDNAs, for individuals able to continue post‐germinative growth under severe C/N stress. One line, cni1‐D (carbon/nitrogen insensitive 1‐dominant), was shown to have a suppressed sensitivity to C/N conditions at both the physiological and molecular level. The CNI1 cDNA encoded a predicted RING‐type ubiquitin ligase previously annotated as ATL31. Overexpression of ATL31 was confirmed to be responsible for the cni1‐D phenotype, and a knock‐out of this gene resulted in hypersensitivity to C/N conditions during post‐germinative growth. The ATL31 protein was confirmed to contain ubiquitin ligase activity using an in vitro assay system. Moreover, removal of this ubiquitin ligase activity from the overexpressed protein resulted in the loss of the mutant phenotype. Taken together, these data demonstrated that CNI1/ATL31 activity is required for the plant C/N response during seedling growth transition.
Allergic status of schoolchildren with food allergy to eggs, milk or wheat in infancy
Authors: Kusunoki Takashi , Morimoto Takeshi , Nishikomori Ryuta , Heike Toshio , Fujii Tatsuya , Nakahata Tatsutoshi
Published: August 2009

Although children allergic to eggs, milk or wheat in infancy tend to become tolerant by school age, the allergic status of these children at school age has not been well evaluated. To investigate the allergic status of schoolchildren who avoided eggs, milk or wheat because of an immediate‐type allergic reaction at <1‐yr‐old (food avoiders in infancy), we conducted a large‐scale questionnaire‐based survey of schoolchildren. A questionnaire on allergic diseases was distributed to the parents of 14,669 schoolchildren aged 7 to 15 yr in 30 schools in Kyoto, Japan. Of these, 13,215 responded (response rate, 90.1%). The rate of 7‐yr‐old children who were food avoiders in infancy was 5.4%. This rate decreased as the current age of the children increased, down to 3% in 15‐yr‐old children, indicating that food allergy in infancy tended to become more prevalent over the past 8 yr. Although more than 80% became tolerant to these foods by school age, the prevalence of bronchial asthma, atopic dermatitis, allergic rhinitis and allergic conjunctivitis were significantly higher in this group. Moreover, avoidance of other foods (buckwheat, shellfish, fruits and others) at school age was seen at much higher frequencies than in non‐food avoiders in infancy (adjusted odds ratio, 7.7; confidence interval, 5.9–10.2). This risk did not differ significantly between those who did and did not develop tolerance to eggs, milk and wheat by 3 yr old. In conclusion, food avoiders in infancy appear to have a higher risk of not only other allergic diseases (‘atopic march’) but also allergy to other foods (‘food allergen march’) at school age, indicating the need for continuous attention to food allergy.
Serological and clinical characteristics of children with peanut sensitization in an Asian community
Authors: Chiang Wen Chin , Pons Laurent , Kidon Mona Iancovici , Liew Woei Kang , Goh Anne , Wesley Burks A.
Published: August 2009

Chiang WC, Pons L, Kidon MI, Liew WK, Goh A, Wesley Burks A. Serological and clinical characteristics of children with peanut sensitization in an Asian community. Pediatr Allergy Immunol 2010: 21: e429–e438. © 2009 John Wiley & Sons A/S

In the past two decades, peanut allergy prevalence has increased in the West but has been perceived as having remained low in Asia. To review the clinical presentation of Asian children with peanut hypersensitivity and measure their IgE responses to major peanut allergens. We enrolled 31 children presenting with various allergies and a positive skin prick test to peanut from the Children’s hospital outpatient allergy clinic in Singapore. A detailed questionnaire was completed by parents. The children’s serum IgE specific to native Ara h 1, native Ara h 2, and recombinant Ara h 3 were detected using ELISA. Of the 31 patients, 19 had previously documented reactions to peanuts, while 12 had no previous clinical reaction. Most, 89.5% (17/19) of first reactions featured skin changes (urticaria, erythema, angioedema), but only 36.8% (7/19) involved skin symptoms alone. Respiratory symptoms and GI symptoms occurred in 42.1% and 26.3% of patients respectively and did not occur as the sole manifestation of reaction. The most common GI manifestation was emesis, present in 26.3% (5/19) of subjects. Two children experienced impaired consciousness with systemic, anaphylactic events. Although most sought treatment for their first peanut reaction only one patient received epinephrine. Half of our patients reported a subsequent accidental ingestion after the diagnosis of peanut allergy, with a median time from diagnosis to first accidental ingestion of 4 months and a reported increased severity of reaction in approximately half of the repeat exposures. Eighty‐seven percent of children had specific IgE directed against at least one of the major peanut allergens. Among all patients, 87.1% had IgE specific to both Ara h 1 and Ara h 2 and 54.8% to rAra h 3. Asian children with peanut sensitization have clinically similar presentations and respond to the same major allergenic proteins as their Western counterparts. The perceived differences between the populations in this context do not stem from divergent clinical or immunological responses.
Mineral classification from quantitative X‐ray maps using neural network: Application to volcanic rocks
Authors: Tsuji Takeshi , Yamaguchi Haruka , Ishii Teruaki , Matsuoka Toshifumi
Published: August 2009

We developed a mineral classification technique of electron probe microanalyzer (EPMA) maps in order to reveal the mineral textures and compositions of volcanic rocks. In the case of lithologies such as basalt that include several kinds of minerals, X‐ray intensities of several elements derived from EPMA must be considered simultaneously to determine the mineral map. In this research, we used a Kohonen self‐organizing map (SOM) to classify minerals in the thin‐sections from several X‐ray intensity maps. The SOM is a type of artificial neural network that is trained using unsupervised training to produce a two‐dimensional representation of multi‐dimensional input data. The classified mineral maps of in situ oceanic basalts of the Juan de Fuca Plate allowed us to quantify mineralogical and textural differences among the marginal and central parts of the pillow basalts and the massive flow basalt. One advantage of mineral classification using a SOM is that relatively many minerals can be estimated from limited input elements. By applying our method to altered basalt which contains multiple minerals, we successfully classify eight minerals in thin‐section.
Geophysical implications of Izu–Bonin mantle wedge hydration from chemical geodynamic modeling
Authors: Hebert Laura B. , Gurnis Michael
Published: August 2009

Using two‐dimensional dynamic models of the Northern Izu–Bonin (NIB) subduction zone, we show that a particular localized low‐viscosity (ηLV =  3.3 × 1019 − 4.0 × 1020 Pa s), low‐density (Δρ ∼ −10 kg/m3 relative to ambient mantle) geometry within the wedge is required to match surface observations of topography, gravity, and geoid anomalies. The hydration structure resulting in this low‐viscosity, low‐density geometry develops due to fluid release into the wedge within a depth interval from 150 to 350 km and is consistent with results from coupled geochemical and geodynamic modeling of the NIB subduction system and from previous uncoupled models of the wedge beneath the Japan arcs. The source of the fluids can be either subducting lithospheric serpentinite or stable hydrous phases in the wedge such as serpentine or chlorite. On the basis of this modeling, predictions can be made as to the specific low‐viscosity geometries associated with geophysical surface observables for other subduction zones based on regional subduction parameters such as subducting slab age.
Management of cow's milk protein allergy in infants and young children: An expert panel perspective
Authors: Allen Katrina J , Davidson Geoffrey P , Day Andrew S , Hill David J , Kemp Andrew S , Peake Jane E , Prescott Susan L , Shugg Albert , Sinn John KH , Heine Ralf G
Published: August 2009

Cow's milk protein allergy is a condition commonly managed by general practitioners and paediatricians. The diagnosis is usually made in the first 12 months of life. Management of immediate allergic reactions and anaphylaxis includes the prevention of accidental food ingestion and provision of an adrenaline autoinjector, if appropriate. By contrast, the clinical course of delayed food‐allergic manifestations is characterised by chronicity, and is often associated with nutritional or behavioural sequelae. Correct diagnosis of these non‐IgE‐mediated conditions may be delayed due to a lack of reliable diagnostic markers. This review aims to guide clinicians in the: (i) diagnostic evaluation (skin prick testing or measurement of food‐specific serum IgE levels; indications for diagnostic challenges for suspected IgE‐ and non‐IgE‐mediated food allergy), (ii) dietary treatment, (iii) assessment of response to treatment, (iv) differential diagnosis and further diagnostic work‐up in non‐responders, (v) follow‐up assessment of tolerance development and (vi) recommendations for further referral.
Parental awareness and attitudes of food marketing to children: A community attitudes survey of parents in New South Wales, Australia
Authors: Kelly Bridget , Chapman Kathy , Hardy Louise L , King Lesley , Farrell Louise
Published: August 2009

Aim:  To determine parents' attitudes and awareness of food marketing to children.

Method:  Computer‐assisted telephone interviews of a random sample of 400 parents of children aged 5–17 years and who were the main grocery buyers for that household, living in NSW, Australia. The main outcome measures included parental awareness and attitudes relating to food marketing to children, the perceived role of government versus industry in food marketing regulation and children's food purchasing requests as a result of exposure to food marketing.

Results:  The majority of parents were concerned about food marketing to children, with the highest level of concern registered for the positioning of food at supermarket checkouts (83% of parents concerned). Parental awareness of certain non‐broadcast media food marketing (e.g. print, radio and premium offers) to children was low. The majority of parents (91%) did not trust the industry to protect children from food marketing. Most parents (81%) believed that the government should restrict the use of non‐broadcast media marketing of unhealthy food to children. Parents of younger children were more likely to report that their child asked for advertised food products, compared with parents of adolescents (65% and 48% respectively, P < 0.0001).

Conclusions:  Reductions in point of sale food promotions would be welcomed by parents. Raising community awareness of the non‐broadcast media channels used to market food to children is important as part of building family and policy efforts to limit exposure to this otherwise relatively unregulated media environment.
Evaluation of a national resource to identify and study rare diseases: The Australian Paediatric Surveillance Unit
Authors: He Suwen , Zurynski Yvonne A , Elliott Elizabeth J
Published: August 2009

Aims:  To evaluate the Australian Paediatric Surveillance Unit (APSU).

Methods:  We used criteria recommended by the Centres for Disease Control and Prevention (CDC) for evaluating surveillance systems and reviewed productivity, response rates, completeness of the mailing list and impacts of APSU studies. Anonymous evaluation questionnaires were sent to 1260 reporting clinicians, 42 researchers and 86 public health professionals to seek their feedback as users of the APSU.

Results:  APSU provides national epidemiological and clinical data about rare childhood conditions that inform public health policy and clinical practice. Between 2000 and 2007, APSU data were disseminated in 106 journal articles, 207 scientific presentations and 85 media items. Of paediatricians and paediatric sub‐specialists actively practicing in Australia and listed as Fellows of the Royal Australasian College of Physicians, 92% participate in APSU surveillance. An average 96% of monthly report cards were returned per annum since 2000. Sensitivity of case ascertainment was difficult to calculate for many conditions because alternative sources of ascertainment do not exist. Evaluation questionnaires were returned by 818 (65%) reporting clinicians, who believe APSU is valuable for generating knowledge 665 (81%), identifying research priorities 635 (78%), guiding clinical practice 572 (70%) and informing public health policy 575 (70%). Similar responses were received from researchers and public health professionals.

Conclusions:  The APSU fulfils its objectives and meets relevant CDC criteria for usefulness, simplicity, acceptability and representativeness, sensitivity and timeliness of data quality. However, stability is threatened by lack of continuing core funding. APSU is highly productive and valued by child health clinicians, researchers and public health professionals.
The learning environment of paediatric trainees in New Zealand
Authors: Pinnock Ralph , Reed Peter , Wright Matthew
Published: August 2009

Aims:  To assess the learning environment of New Zealand paediatric trainees, examine the factors influencing the trainee's perceptions of their learning environment and to assess the suitability of using the Postgraduate Hospital Education Environment Measure (PHEEM) in New Zealand.

Methods:  Paediatric trainees completed the PHEEM questionnaire and returned this anonymously by email.

Results:  Both basic and advanced trainees' perceptions of the environment were generally positive but significant concerns were identified. There were differences in perceptions of the learning environment between the basic and advanced trainees and between sites with more than six trainees compared with those with six or fewer trainees. The PHEEM is practical to use, showed good internal consistency and was acceptable to trainees.

Conclusions:  Both basic and advanced trainees perceived the learning environment positively but significant concerns must be addressed.

The advanced trainees perceived the overall learning environment and the teaching they receive more positively than basic trainees. Trainees at smaller hospitals perceived that their social supports were better than at larger hospitals.

The PHEEM can be used to assess the paediatric training environment in New Zealand.
Acute pancreatitis associated with varicella infection in an immunocompetent child
Authors: Franco João , Fernandes Ricardo , Oliveira Marta , Alves Ana Dias , Braga Manuela , Soares Isabel , Calhau Paulo
Published: August 2009

Acute pancreatitis associated with varicella‐zoster infection is a rare event, particularly in immunocompetent children. We report on a case of acute pancreatitis in a 6‐year old girl presenting with acute abdominal pain less than 72 hours after the onset of a typical vesicular rash. The diagnosis was confirmed through hyperamylasaemia, ultrasonographic findings of oedematous pancreatitis and acute seroconversion to varicella‐zoster virus, after excluding more common causes of acute pancreatitis. Conservative treatment was initiated, with complete resolution of symptoms and absence of local or systemic complications on follow up. A review of the literature revealed only three previously reported cases, with very different outcomes, highlighting the need to consider this potentially fatal complication in every child presenting with acute abdominal pain during the course of varicella disease.
Left ventricular mass in hypertensive patients with mild‐to‐moderate reduction of renal function
Authors: CERASOLA GIOVANNI , NARDI EMILIO , MULÈ GIUSEPPE , PALERMO ALESSANDRO , CUSIMANO PAOLA , GUARNERI MARCO , ARSENA ROSALIA , GIAMMARRESI GAIA , CAROLA FORACI ANNA , COTTONE SANTINA
Published: August 2009

Aim:  Left ventricular hypertrophy (LVH) is an independent predictor of cardiovascular (CV) morbidity and mortality. The aim of the present study was to evaluate the relationship between LV mass and mild‐to‐moderate renal dysfunction in a group of non‐diabetic hypertensives, free of CV diseases, participating in the Renal Dysfunction in Hypertension (REDHY) study.

Methods:  Patients with diabetes, a body mass index (BMI) of more than 35 kg/m2, secondary hypertension, CV diseases and a glomerular filtration rate (GFR) of less than 30 mL/min per 1.73 m2 were excluded. The final sample included 455 patients, who underwent echocardiographic examination and ambulatory blood pressure monitoring.

Results:  There was a significant trend for a stepwise increase in LV mass, indexed by both body surface area (LVMI) and height elevated to 2.7 (LVMH2.7), with the declining renal function, that remained statistically significant after correction for potential confounders. The prevalence of LVH, defined either as LVMI of 125 g/m2 or more or as LVMH2.7 of 51 g/m2.7 or more, was higher in subjects with lower values of GFR than in those with normal renal function (P < 0.001 in both cases). The multiple regression analysis confirmed that the inverse association between GFR and LVM was independent of confounding factors.

Conclusion:  The present study confirms the high prevalence of LVH in patients with mild or moderate renal dysfunction. In the patients studied (all with a GFR of 30 mL/min per 1.73 m2), the association between LVM and GFR was independent of potential confounders, including 24 h blood pressure load. Taking into account the negative prognostic impact of LVH, further studies focusing on a deeper comprehension of the mechanisms underlying the development of LVH in chronic kidney disease patients are needed.
Plant species loss decreases arthropod diversity and shifts trophic structure
Authors: Haddad Nick M. , Crutsinger Gregory M. , Gross Kevin , Haarstad John , Knops Johannes M.H. , Tilman David
Published: August 2009

Plant diversity is predicted to be positively linked to the diversity of herbivores and predators in a foodweb. Yet, the relationship between plant and animal diversity is explained by a variety of competing hypotheses, with mixed empirical results for each hypothesis. We sampled arthropods for over a decade in an experiment that manipulated the number of grassland plant species. We found that herbivore and predator species richness were strongly, positively related to plant species richness, and that these relationships were caused by different mechanisms at herbivore and predator trophic levels. Even more dramatic was the threefold increase, from low‐ to high‐plant species richness, in abundances of predatory and parasitoid arthropods relative to their herbivorous prey. Our results demonstrate that, over the long term, the loss of plant species propagates through food webs, greatly decreasing arthropod species richness, shifting a predator‐dominated trophic structure to being herbivore dominated, and likely impacting ecosystem functioning and services.
Reducing horizontal and vertical diversity in a foodweb triggers extinctions and impacts functions
Authors: Srivastava Diane S. , Bell Thomas
Published: August 2009

Species loss can result in secondary extinctions and changes in ecosystem functions at distant trophic levels. Such effects of species loss are predicted to be affected by both the number of species lost within a trophic level (horizontal diversity) and the number of trophic levels lost (vertical diversity). We experimentally manipulated horizontal and vertical diversity within an aquatic insect community, and examined responses throughout the food web. Horizontal and vertical diversity both impacted ciliates: reduction of detritivorous insect diversity resulted in secondary extinctions and decreased density of ciliates, but only when an insect predator was simultaneously absent. Horizontal and vertical diversity differed in their effect on other foodweb processes, including detrital processing, predator growth, and densities of rotifers, flagellates and flatworms. These results caution that foodweb effects of multitrophic species loss may not be reliably predicted from manipulations of just one dimension of diversity.
Behavioural interactions between ecosystem engineers control community species richness
Authors: Gribben Paul E. , Byers James E. , Clements Michael , McKenzie Louise A. , Steinberg Peter D. , Wright Jeffrey T.
Published: August 2009

Behavioural interactions between ecosystem engineers may strongly influence community structure. We tested whether an invasive ecosystem engineer, the alga Caulerpa taxifolia, indirectly facilitated community diversity by modifying the behaviour of a native ecosystem engineer, the clam Anadara trapezia, in southeastern Australia. In this study, clams in Caulerpa‐invaded sediments partially unburied themselves, extending >30% of their shell surface above the sediment, providing rare, hard substrata for colonization. Consequently, clams in Caulerpa had significantly higher diversity and abundance of epibiota compared with clams in unvegetated sediments. To isolate the role of clam burial depth from direct habitat influences or differential predation by habitat, we manipulated clam burial depth, predator exposure and habitat (Caulerpa or unvegetated) in an orthogonal experiment. Burial depth overwhelmingly influenced epibiont species richness and abundance, resulting in a behaviourally mediated facilitation cascade. That Caulerpa controls epibiont communities by altering Anadara burial depths illustrates that even subtle behavioural responses of one ecosystem engineer to another can drive extensive community‐wide facilitation.
A national survey of the current state of screening services for diabetic retinopathy: ABCD–Diabetes UK survey of specialist diabetes services 2006
Authors: Nagi D. K. , Gosden C. , Walton C. , Winocour P. H. , Turner B. , Williams R. , James J. , Holt R. I. G.
Published: August 2009

The main aims were to ascertain the progress made in the implementation of retinal screening services and to explore any barriers or difficulties faced by the programmes. The survey focused on all the essential elements for retinal screening, including assessment and treatment of screen‐positive cases. Eighty‐five per cent of screening programmes have a coordinated screening service and 73% of these felt that they have made significant progress. Eighty‐five per cent of screening units use ‘call and recall’ for appointments and 73.5% of programmes follow the National Screening Committee (NSC) guidance. Although many units worked closely with ophthalmology, further assessment and management of screen‐positive patients was a cause for concern. The fast‐track referral system, to ensure timely and appropriate care, has been difficult to engineer by several programmes. This is demonstrated by 48% of programmes having waiting lists for patients identified as needing further assessment and treatment for retinopathy. Ophthalmology service for people with diabetic retinopathy was provided by a dedicated ophthalmologist in 89.4% of the programmes. Sixty‐six per cent of the programmes reported inadequate resources to sustain a high‐quality service, while 26% highlighted the lack of infrastructure and 49% lacked information technology (IT) support. In conclusion, progress has been made towards establishing a national screening programme for diabetic retinopathy by individual screening units, with a number of programmes providing a structured retinal screening service. However, programmes face difficulties with resource allocation and compliance with Quality Assurance (QA) standards, especially those which apply to ophthalmology and IT support. Screening programmes need to be resourced adequately to ensure comprehensive coverage and compliance with QA.
Moderating effects of coping styles on anxiety and depressive symptoms caused by psychological stress in Chinese patients with Type 2 diabetes
Authors: Zhang C.‐X. , Tse L.‐A. , Ye X.‐Q. , Lin F.‐Y. , Chen Y.‐M. , Chen W.‐Q.
Published: August 2009

Aims  This study aimed to assess possible interactive effects of coping styles and psychological stress on depression and anxiety symptoms in Chinese patients with Type 2 diabetes.

Methods  Three hundred and four patients with Type 2 diabetes underwent a face‐to‐face interview by trained research staff according to a standardized questionnaire including information on socio‐demographic characteristics, psychological stress, coping styles and anxiety and depressive symptoms. The interactive effects of coping styles and psychological stress on depression and anxiety symptoms were assessed by hierarchical multiple regression analyses.

Results  There were significant associations of the four domains of psychological stress with anxiety and depressive symptoms, except for the relationship between ‘reduced economic condition’ and depressive symptoms. ‘Negative coping style’ significantly increased the level of both anxiety and depressive symptoms; whereas, ‘active coping style’ and ‘avoidant coping style’ decreased the risk of depressive symptoms. The interactions of ‘negative coping style’ with ‘worrying about decline in body/physical function’ and ‘reduced economic condition’ significantly increased the risk of anxiety and depressive symptoms, and the interaction of ‘social/family crisis caused by the disease’ with ‘avoidance coping style’ and ‘worrying about decline in body/physical function’ with ‘active coping style’ significantly decreased the risk of depressive symptoms.

Conclusions  The results of this study suggest that certain coping styles might moderate the association of psychological stress with anxiety and depressive symptoms in Chinese patients with Type 2 diabetes.
Evaluation of proposed oral disposition index measures in relation to the actual disposition index
Authors: Retnakaran R. , Qi Y. , Goran M. I. , Hamilton J. K.
Published: August 2009

Aims  While the disposition index provides a useful measure of B‐cell function, its calculation requires the performance of a frequently sampled intravenous glucose tolerance test (FSIVGTT). Recently, the demonstration of a hyperbolic relationship between indices of insulin secretion and insulin sensitivity derived from the oral glucose tolerance test (OGTT) has led to the introduction of two novel OGTT‐based measures of B‐cell function analogous to the disposition index: (i) the insulin secretion‐sensitivity index‐2 (ISSI‐2) (defined as the ratio of the area‐under‐the‐insulin‐curve to the area‐under‐the‐glucose curve, multiplied by the Matsuda index) and (ii) insulinogenic index (IGI)/fasting insulin. However, neither of these two measures has been directly compared with the disposition index.

Methods  Two hundred and thirteen non‐diabetic children (122 boys, 91 girls) underwent both OGTT and FSIVGTT, allowing for the calculation of ISSI‐2, IGI/fasting insulin and the disposition index.

Results  ISS1‐2 and IGI/fasting insulin were strongly correlated with each other (r = 0.82, P < 0.0001). Both measures correlated with the disposition index, with ISSI‐2 showing a modestly stronger association (ISSI‐2: r = 0.24, P = 0.0003; IGI/fasting insulin: r = 0.21, P = 0.0022). Standardized linear regression analyses confirmed that the relationship between log ISSI‐2 and the disposition index (standardized regression coefficient = 0.224, P = 0.001) was stronger than that between log IGI/fasting insulin and the disposition index (standardized regression coefficient = 0.166, P = 0.015).

Conclusions  The OGTT‐derived measures ISSI‐2 and IGI/fasting insulin exhibit modest correlations with the disposition index. These relationships require further assessment in other patient populations.
Seed‐specific expression of the wheat puroindoline genes improves maize wet milling yields
Authors: Zhang Jinrui , Martin John M. , Beecher Brian , Morris Craig F. , Curtis Hannah L. , Giroux Michael J.
Published: August 2009

The texture of maize (Zea mays L.) seeds is important to seed processing properties, and soft dent maize is preferred for both wet‐milling and livestock feed applications. The puroindoline genes (Pina and Pinb) are the functional components of the wheat (Triticum aestivum L.) Hardness locus and together function to create soft grain texture in wheat. The PINs (PINA and PINB) are believed to act by binding to lipids on the surface of starch granules, preventing tight adhesion between starch granules and the surrounding protein matrix during seed maturation. Here, maize kernel structure and wet milling properties were successfully modified by the endosperm‐specific expression of wheat Pins (Pina and Pinb). Pins were introduced into maize under the control of a maize γ‐Zein promoter. Three Pina/Pinb expression positive transgenic lines were evaluated over two growing seasons. Textural analysis of the maize seeds indicated that the expression of PINs decreased adhesion between starch and protein matrix and reduced maize grain hardness significantly. Reduction in pressure required to fracture kernels ranged from 15.65% to 36.86% compared with control seeds. Further, the PINs transgenic maize seeds had increased levels of extractable starch as characterized by a small scale wet milling method. Starch yield was increased by 4.86% on average without negatively impacting starch purity. The development of softer maize hybrids with higher starch extractability would be of value to maize processors.
Optimal Sensor Locations for Freeway Bottleneck Identification
Authors: Liu Henry X. , Danczyk Adam
Published: August 2009

Abstract:  In the field of traffic operations, accurate performance measures are crucial for many of the intelligent transportation systems applications. Achieving this accuracy and quality requires that network‐based roadway sensors are allocated in locations beneficial to traffic operations. However, with the budgetary restrictions most transportation agencies face, these roadway sensors cannot be placed as thoroughly as obligatory for ideal accuracy, requiring these agencies to select a limited number of installments that produce the most optimal results. In this article, a nonlinear integer program is proposed to optimally allocate point sensors along a one‐directional freeway corridor, given that any pair of adjacent sensors can produce a benefit for bottleneck identification. The objective of this model is to optimize the accuracy of bottleneck identification subject to resource and monetary constraints. This model is nonlinear and, due to a non‐differentiable function, genetic algorithm is applied to find a solution. We demonstrate that on a case study network with bottlenecks at unknown locations, the model successfully allocates sensors in a manner that optimizes bottleneck identification accuracy.
The Use of LiDAR in Digital Surface Modelling: Issues and Errors
Authors: Leigh Charlotte L , Kidner David B , Thomas Malcolm C
Published: August 2009

Modelling and extracting 3D geographical data presents numerous challenges that require continual research to attempt to evolve an efficient, reliable and accurate solution. LiDAR data capture and analysis has become a preferred acquisition choice for elevation data because the resulting quality and level of detail far exceeds traditional methods for large survey areas. As with any data collection system, LiDAR is prone to errors. Analysing these errors, ascertaining causes and producing error correction strategies is vital if accurate and confident results are to be obtained. Eight years of LiDAR datasets (from 1998 to 2005) have been closely analysed for a large coastal area of South Wales. This article provides a detailed and accurate summary of the identified LiDAR data issues and subsequent errors which affect the accuracy of end products such as Digital Surface Models (DSMs).
A GIS Approach to Estimation of Building Population for Micro‐spatial Analysis
Authors: Lwin KoKo , Murayama Yuji
Published: August 2009

Population data used in GIS analyses is generally assumed to be homogeneous and planar (i.e. census tracts, townships or prefectures) due to the public unavailability of building population data. However, information on building population is required for micro‐spatial analysis for improved disaster management and emergency preparedness, public facility management for urban planning, consumer and retail market analysis, environment and public health programs and other demographic studies. This article discusses a GIS approach using the Areametric and Volumetric methods for estimating building population based on census tracts and building footprint datasets. The estimated results were evaluated using actual building population data by visual, statistical and spatial means, and validated for use in micro‐spatial analysis. We have also implemented a standalone GIS tool (known as ‘PopShape GIS’) for generating new building footprint with population attribute information based on user‐defined criteria.
THEISTIC NATURALISM AND “SPECIAL” DIVINE PROVIDENCE
Authors: Knight Christopher C.
Published: August 2009

Although naturalistic perspectives are an important component of their accounts of divine action, most participants in the current dialogue between science and theology eschew a purely naturalistic model. They believe that certain events of divine providence require a special mode of divine action, over and above that inherent in naturalistic processes. The analogy of human providential action suggests, however, that a strong theistic naturalism can account for these events. This model does not depend on a particular notion of God's relationship to time and is not inherently implausible from a scientific perspective. Although it can be interpreted deistically, the model also is consonant with a nondeistic theology that may be described as involving a pansacramental or incarnational naturalism.
JOHN POLKINGHORNE AND BERNARD LONERGAN ON THE SCIENTIFIC STATUS OF THEOLOGY
Authors: Hogan Edward M.
Published: August 2009

On the basis of his acquaintance with theoretical elementary particle physics, and following the lead of Thomas Torrance, John Polkinghorne maintains that the data upon which a science is based, and the method by which it treats those data, must respect the idiosyncratic nature of the object with which the science is concerned. Polkinghorne calls this the “accommodation” (or “conformity”) of a discipline to its object. The question then arises: What should we expect religious experience and theological method to be like if they are accommodated to the idiosyncratic nature of God? Polkinghorne's methodological program is typical of postcritical positions in the theology‐science dialogue in holding that the fiduciary element in theological method is simply a species of the fiduciary element that is a de facto part of all knowing—in other words, theological method does not differ in fundamental kind from the methods of the natural sciences. But this program may contain the seeds of an alienation of theological method from the transcendence of God similar to the double self‐alienation of theology described by Michael Buckley in At the Origins of Modern Atheism. I contend that something like Bernard Lonergan's position on how the method of faith seeking understanding is related to the methods of the natural sciences is exactly the sort of thing that one should expect on the supposition of Polkinghorne's principle of accommodation, at least if the God who is the object of theological science is transcendent. The way in which the divine differs from all other objects ought to be disclosed or reflected in religious experience and theological method. Polkinghorne charts the course for an accommodated theology, but it seems to be Lonergan who is more intent on following it.
MINDSCAPES AND LANDSCAPES: EXPLORING THE EXTENDED MIND
Authors: Marsh Leslie
Published: August 2009

This brief article introduces a symposium discussing the extended mind thesis and its suggestive relation to religious thought. Essays by Mark Rowlands, Lynne Rudder Baker, Teed Rockwell, Joel Krueger, Leonard Angel, and Matthew Day present a variety of perspectives.
THE EXTENDED MIND
Authors: Rowlands Mark
Published: August 2009

The extended mind is the thesis that some mental—typically cognitive—processes are partly composed of operations performed by cognizing organisms on the world around them. The operations in question are ones of manipulation, transformation, or exploitation of environmental structures. And the structures in question are ones that carry information pertinent to the success or efficacy of the cognitive process in question. This essay examines the thesis of the extended mind and evaluates the arguments for and against it.
CONSTRUCTING RELIGION WITHOUTTHE SOCIAL: DURKHEIM, LATOUR, AND EXTENDED COGNITION
Authors: Day Matthew
Published: August 2009

I take up the question of how models of extended cognition might redirect the academic study of religion. Entering into a conversation of sorts with Emile Durkheim and Bruno Latour regarding the “overtakenness” of social agency, I argue that a robust portrait of extended cognition must redirect our interest in explaining religion in two key ways. First, religious studies should take up the methodological principle of symmetry that informs contemporary histories of science and begin theorizing the efficacy of gods as social actors. Second, theorists of religion should begin noting how the work required to construct spaces in which the gods appear depends on the construction of disciplined and capable subjects.
“Desperate Fighting at the Cape”: The Salvation Army's Arrival and Earliest Work in Late‐Victorian Cape Town
Authors: EASON ANDREW M.
Published: August 2009

Many scholars writing on colonial themes have associated the early Salvation Army with imperialism and related ideologies. Historians of Victorian Cape Town have been no exception. Their research has essentially identified the organisation with the imperial concerns of the city and its dominant middle‐class culture. While there is some truth to this assessment, especially after the Army adopted an extensive social scheme in 1890, the earliest efforts of Salvationists at the Cape were often defined by very different objectives. The military‐clad Salvationists arriving in Cape Town in 1883 owed something to a colonial age, but their sensational methods of evangelism quickly angered the local authorities. Despite sharing a bourgeois interest in temperance, the Army's working‐class followers also received little support from the middle classes. Animated by a revivalism that violated conventional notions of religion, gender, and race, its pioneers in South Africa possessed few ties to imperialism or middle‐class ideology.
Theological Innovation from Spiritual Experience: Henry Alline's Anti‐Calvinism in Late Eighteenth‐Century Nova Scotia and New England*
Authors: FLATT KEVIN
Published: August 2009

The strident anti‐Calvinism of Nova Scotian revivalist Henry Alline (1748–1784), who left a substantial mark on the religious landscape of Nova Scotia and parts of New England, has been noted but largely neglected by historians. This article investigates Alline's anti‐Calvinism and concludes that it is best explained as arising from his own interpretation of his vivid spiritual experiences, particularly his dramatic conversion. Rather than simply rejecting Calvinist theology in favour of an emotive, experiential religion, however, Alline drew on his experiences to formulate an alternative anti‐Calvinist theology. Alongside other examples from the period, Alline's case suggests that evangelical “democratization” of popular religion in the eighteenth‐century transatlantic revivals could result in theological innovation rather than the abandonment of theology.
Utopians at the Parliament: The World's Parliament of Religions and the Columbian Exposition of 1893
Authors: NORDSTROM JUSTIN
Published: August 2009

This article examines the Columbian Exposition and World's Parliament of Religions, both held in Chicago in 1893. While both events drew on nineteenth‐century beliefs in the superiority of Western Christianity, they reflect divergent views on technology, social inequality, and urban reform. The Exposition's “White City” offered visitors a temporary, otherwordly escape, whereas the World's Parliament emphasized the importance and possibility of concrete solutions to social problems. As such, these events express radically different forms of utopian speculation in Gilded‐Age America.
The application of the Kalman filter to nonstationary time series through time deformation
Authors: Wang Zhu , Woodward Wayne A. , Gray Henry L.
Published: August 2009

Abstract. An increasingly valuable tool for modelling a nonstationary time series,X(t), is time deformation. In this procedure time,t, is transformed to a ‘time’ scale,u = g(t), on which the processY(u) = X(g(t)) is stationary. However, since the time scale is transformed, equally spaced data on the original time scale data become unequally spaced data in transformed time. In practice interpolation in the original time scale is currently used to obtain equally spaced data in transformed time which can then be modelled using the classical autoregressive moving average modelling techniques. In this article, the need for interpolation is eliminated by employing the continuous time autoregressive model and estimating the parameters using the Kalman filter. The resulting improvements include more accurate estimation of the spectrum, and the separation of the data into its time‐varying latent components. The technique is applied to simulated and real data for illustrations.
Immunosuppression among HIV‐1‐positive patients attending for care: experience from two large HIV centres in the United Kingdom
Authors: Harte D , Dosekun O , Sethi G , Chadborn T , De Ruiter A , Copas A , Edwards SG , Miller RF
Published: August 2009

Objectives

The aim of the study was to describe the prevalence of and examine the factors associated with immunosuppression (CD4<200 cells/μL) among HIV‐infected patients attending two large inner London treatment centres.

Methods

Patients attending for care who had a CD4 count <200 cells/μL during a 6‐month period (1 January to 30 June 2007) were identified from the UK national CD4 surveillance database. Corresponding case notes were reviewed and factors associated with the most recent immunosuppressive episode examined. Patients either previously had a CD4 count >200 cells/μL at any time under follow‐up which had decreased (group A) or never had a CD4 count >200 cells/μL (group B; late presenters).

Results

Of 4589 patients, 10.2% (467) had at least one CD4 count <200 cells/μL. In group A (60.1% of patients), 70.4% were not receiving antiretroviral therapy (ART) at the time at which the CD4 count fell to <200 cells/μL. Reasons included: treatment interruption (TI; 32.6%), patient declined ART (20.2%), infrequent attendance (19.1%), physician delay in offer (23.1%) and transient CD4 cell count decrease (3.9%). Among those receiving ART, one in three had poor adherence. In group B, 92.3% had started ART after presentation: most had recently started and were responding virologically. AIDS‐defining diagnoses occurred in the year preceding the decrease in CD4 cell count in 12.6% of patients in group A and 33.3% of those in group B.

Conclusion

The majority of patients became immunosuppressed while under care. Our findings suggest that, in addition to strategies aimed at earlier diagnosis, there are further opportunities to reduce severe immunosuppression in patients already attending for HIV care.
Tests of Association for Quantitative Traits in Nuclear Families Using Principal Components to Correct for Population Stratification
Authors: Zhang Lei , Li Jian , Pei Yu‐Fang , Liu Yongjun , Deng Hong‐Wen
Published: August 2009

Traditional transmission disequilibrium test (TDT) based methods for genetic association analyses are robust to population stratification at the cost of a substantial loss of power. We here describe a novel method for family‐based association studies that corrects for population stratification with the use of an extension of principal component analysis (PCA). Specifically, we adopt PCA on unrelated parents in each family. We then infer principal components for children from those for their parents through a TDT‐like strategy. Two test statistics within the variance‐components model are proposed for association tests. Simulation results show that the proposed tests have correct type I error rates regardless of population stratification, and have greatly improved power over two popular TDT‐based methods: QTDT and FBAT. The application to the Genetic Analysis Workshop 16 (GAW16) data sets attests to the feasibility of the proposed method.