bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recommendations for best practice in deep-sea habitat classification: Bullimore et al. as a case study
Authors: Henry Lea-Anne , Roberts J. Murray 
Published: November 2013

Abstract
We assert that the reef framework-forming coral, Solenosmilia variabilis Duncan, 1873, is sometimes incorrectly recorded as another coral, Lophelia pertusa (Linnaeus, 1758) in surveys of deep-sea habitat (e.g. Bullimore, R., Foster, N., and Howell, K. 2013. Coral-characterized benthic assemblages of the deep Northeast Atlantic: defining “Coral Gardens” to support future habitat mapping efforts. ICES Journal of Marine Science, 70: 511–522). Accurate species lists are critical for developing robust deep-sea habitat classification schemes that allow us to map the distribution of different vulnerable marine ecosystems (VMEs) and predict their occurrences under future climate change scenarios, both of which help prioritize areas for marine protected areas. We recommend that the survey reported by Bullimore et al. (2013), as well as analogous surveys, consider the likelihood of Solenosmilia having been misidentified, and revise their data if necessary. We also make two further recommendations for best practice in deep-sea habitat classification using Bullimore et al. (2013) as a case study. Preferably, physical specimens should be obtained during deep-sea surveys. However, in the absence of identifications confirmed with specimens, image-based analyses of deep-sea communities can be achieved with high confidence when (i) independent validation is provided by senior taxonomic specialists in taxa that are indicators of VMEs, such as cold-water coral reefs, coral gardens, sponge grounds, cold seeps and xenophyophore fields; and (ii) stronger consideration is given to methods in classical taxonomy, the chemical oceanographic setting and community ecology.
Estimates of acoustic target strength for giant jellyfish Nemopilema nomurai Kishinouye in the coastal Northwest Pacific
Authors: Kang Donhyug , Park Jusam , Jung Seom-Kyu , Cho Sungho 
Published: November 2013

Abstract
Acoustic target strength (TS) measurements were made of ex situ giant jellyfish Nemopilema nomurai Kishinouye at 38 and 120 kHz. These TS data may be useful for developing acoustic scattering models, and surveying giant jellyfish distributions and biomasses. Each jellyfish was tethered in seawater using a monofilament line that vertically penetrated its bell's centre. During the acoustic measurements, an underwater video camera was used to continuously monitor the jellyfish's behaviour. Acoustic measurements were made using split-beam transducers. TS measurements were made of 27 individual jellyfish, but data were analysed for 23 specimens (bell diameter in air, Dair = 21–65 cm) at 38 kHz, and 19 specimens (Dair = 21–46 cm) at 120 kHz, respectively. Least-squares regression fits of TS vs. log(Dair) were TS38kHz = 20•log10Dair–82.7 (r = 0.76) and TS120kHz = 20•log10Dair–86.7 (r = 0.79). The mean TS values at 38 and 120 kHz, using the average Dair = 40.3 cm and 35.5 cm, respectively, were −50.6 and −55.7 dB. The reduced TS, a function of the ratio of Dair to wavelength (λ), was RTS(Dair/λ) = −6.1•log10(Dair/λ) –36.1 (r = 0.51). These RTS values decreased with increasing Dair/λ. Symbiotic medusa shrimp (Latreutes anoplonyx Kemp) contributed negligible bias to our TS measurements of giant jellyfish. These ex situ TS measurements may be used in acoustic surveys to estimate the distributions and biomasses of N. nomurai.
Radiative levitation of silicon in the atmospheres of two Hyades DA white dwarfs
Authors: Chayer P. 
Published: November 2013

Abstract
The presence of silicon at the surface of the two Hyades DA white dwarfs WD 0421+162 and WD 0431+126 requires mechanisms that counteract the effects of the downward diffusion. Radiative levitation calculations indicate that the silicon abundance observed in WD 0431+126 corresponds to the abundance supported by radiative levitation. Detailed time-dependent diffusion calculations that take into account radiative levitation and accretion indicate that accretion with rates of $\dot{M}_{\rm {Si}} \lesssim 10^4$ g s−1 could also be present without disrupting the abundance supported by radiative levitation. In the case of WD 0421+162, accretion with a rate of $\dot{M}_{\rm {Si}} = 10^{5.1}$ g s−1 must be invoked, because its observed silicon abundance is larger than the abundance supported by radiative levitation. This accretion rate is lower than the accretion rate given by the accretion–diffusion model, because the radiative levitation slows down the downward diffusion of silicon. The silicon abundances observed in the two Hyades white dwarfs cannot be interpreted solely in terms of accretion. The interpretation of the silicon abundances must take into account the interplay between radiative levitation and accretion.
Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination
Authors: Colloms Sean D. , Merrick Christine A. , Olorunniji Femi J. , Stark W. Marshall , Smith Margaret C. M. , Osbourn Anne , Keasling Jay D. , Rosser Susan J. 
Published: November 2013

Abstract
Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ϕC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ϕC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
“Last-Place Aversion”: Evidence and Redistributive Implications *
Authors: Kuziemko Ilyana , Buell Ryan W. , Reich Taly , Norton Michael I. 
Published: November 2013

AbstractWe present evidence from laboratory experiments showing that individuals are “last-place averse.” Participants choose gambles with the potential to move them out of last place that they reject when randomly placed in other parts of the distribution. In modified dictator games, participants randomly placed in second-to-last place are the most likely to give money to the person one rank above them instead of the person one rank below. Last-place aversion suggests that low-income individuals might oppose redistribution because it could differentially help the group just beneath them. Using survey data, we show that individuals making just above the minimum wage are the most likely to oppose its increase. Similarly, in the General Social Survey, those above poverty but below median income support redistribution significantly less than their background characteristics would predict.
Higher Protein Intake Improves Length, Not Weight, z Scores in Preterm Infants
Authors: Olsen Irene E. , Harris Cheryl L. , Lawson M. Louise , Berseth Carol L. 
Published: November 2013

ABSTRACTObjective:The aim of the study was to evaluate the relation between nutritional intake (kilocalories, protein) and weight and length growth in preterm infants, and to describe their metabolic tolerance with a focus on those with high protein intake (≥4.6 g · kg−1 · day−1).Methods:Secondary analysis of data from appropriate‐for‐gestational age preterm infants in a 28‐day randomized clinical trial that evaluated growth, tolerance, and safety of a new ultraconcentrated liquid human milk fortifier (original study n = 150). This subset of 56 infants had complete growth and nutrition data and met criteria for the original study's “efficacy analysis” (eg, >80% of kilocalorie intake from study diet). Nutritional intake was estimated, not actual. Regressions were used to test cumulative kilocalories and protein as the predictors of 28‐day change in weight and length z scores (growth status), and to evaluate protein tolerance.Results:Average intake was 118 ± 8 kcal · kg−1 · day−1 and 4.3 ± 0.4 g protein · kg−1 · day−1, with 16 ± 3 g · kg−1 · day−1 and 1.1 ± 0.2 cm/week growth for 28 days. Cumulative total kilocalories and protein were significant predictors of improved length z score (P = 0.0054, 0.0005) but not weight z score change. Regression models indicated that protein not kilocalories explained the improvement in length z score, with protein explaining 19% of the variability. The high protein group averaged 4.6 to 5.5 g · kg−1 · day−1 (n = 16). Protein tolerance was adequate for all of the study infants based on metabolic measures (blood urea nitrogen, serum carbon dioxide, pH).Conclusions:Higher cumulative protein intake was tolerated and overall lessened the commonly occurring decline in the length but not weight growth status in a 28‐day study of preterm infants.
ESPGHAN Revised Porto Criteria for the Diagnosis of Inflammatory Bowel Disease in Children and Adolescents
Authors: Levine Arie , Koletzko Sibylle , Turner Dan , Escher Johanna C. , Cucchiara Salvatore , de Ridder Lissy , Kolho Kaija‐Leena , Veres Gabor , Russell Richard K. , Paerregaard Anders , Buderus Stephan , Greer Mary‐Louise C. , Dias Jorge A. , Veereman‐Wauters Gigi , Lionetti Paolo , Sladek Malgorzata , Martin de Carpi Javier , Staiano Annamaria , Ruemmele Frank M. , Wilson David C. 
Published: November 2013

ABSTRACTBackground:The diagnosis of pediatric‐onset inflammatory bowel disease (PIBD) can be challenging in choosing the most informative diagnostic tests and correctly classifying PIBD into its different subtypes. Recent advances in our understanding of the natural history and phenotype of PIBD, increasing availability of serological and fecal biomarkers, and the emergence of novel endoscopic and imaging technologies taken together have made the previous Porto criteria for the diagnosis of PIBD obsolete.Methods:We aimed to revise the original Porto criteria using an evidence‐based approach and consensus process to yield specific practice recommendations for the diagnosis of PIBD. These revised criteria are based on the Paris classification of PIBD and the original Porto criteria while incorporating novel data, such as for serum and fecal biomarkers. A consensus of at least 80% of participants was achieved for all recommendations and the summary algorithm.Results:The revised criteria depart from existing criteria by defining 2 categories of ulcerative colitis (UC, typical and atypical); atypical phenotypes of UC should be treated as UC. A novel approach based on multiple criteria for diagnosing IBD‐unclassified (IBD‐U) is proposed. Specifically, these revised criteria recommend upper gastrointestinal endoscopy and ileocolonscopy for all suspected patients with PIBD, with small bowel imaging (unless typical UC after endoscopy and histology) by magnetic resonance enterography or wireless capsule endoscopy.Conclusions:These revised Porto criteria for the diagnosis of PIBD have been developed to meet present challenges and developments in PIBD and provide up‐to‐date guidelines for the definition and diagnosis of the IBD spectrum.
Long‐Term Outcome of Home Parenteral Nutrition in Patients With Ultra‐Short Bowel Syndrome
Authors: Diamanti Antonella , Conforti Andrea , Panetta Fabio , Torre Giuliano , Candusso Manila , Bagolan Pietro , Papa Raffaele Edo , Grimaldi Chiara , Fusaro Fabio , Capriati Teresa , Elia Domenica , de Goyet Jean De Ville 
Published: November 2013

ABSTRACTObjective:The patients with ultra‐short bowel syndrome (U‐SBS) have been considered potential candidates for a preemptive/rehabilitative intestinal transplantation owing to the high risk of death from the underlying disease. We hypothesized that children with U‐SBS, in the absence of intestinal failure‐associated liver disease (IFALD), could also have a good rate of survival on home parenteral nutrition (HPN).Methods:A prospective database from the “Bambino Gesù” Artificial Nutrition and Intestinal Failure Program was used to evaluate outcomes and morbidities of consecutive patients with ≤10 cm of small bowel enrolled since 2000.Results:Eleven patients were identified with a median bowel length of 7.5 (3–9) cm. Eight patients developed IFALD, which reversed in 7 of them; the IFALD progressively worsened in 1 patient until death. One patient underwent isolated intestinal transplantation and 1 patient is no longer receiving parenteral nutrition (PN) and both are fully enterally fed. The other patients remained at least partially dependent on HPN. The number of days of inpatient care decreased in all of the patients except for the 1 who had repeated episodes of central line infections.Conclusions:The survival of patients with U‐SBS receiving HPN was good. Although IFALD was frequent, it had been manageable in most of the patients, but in a single complex case, it led to death. The multidisciplinary management warranted to these patients to approach the school age, to grow, and to maintain the oral intake. Patients with U‐SBS are rare, and to better understand their long‐term survival, further studies, including more large patient populations, are required.
Recognition of the Protein Kinase AVRPPHB SUSCEPTIBLE1 by the Disease Resistance Protein RESISTANCE TO PSEUDOMONAS SYRINGAE5 Is Dependent onS-Acylation and an Exposed Loop in AVRPPHB SUSCEPTIBLE1
Authors: Qi Dong , Dubiella Ullrich , Kim Sang Hee , Sloss D. Isaiah , Dowen Robert H. , Dixon Jack E. , Innes Roger W. 
Published: November 2013

AbstractThe recognition of pathogen effector proteins by plants is typically mediated by intracellular receptors belonging to the nucleotide-binding leucine-rich repeat (NLR) family. NLR proteins often detect pathogen effector proteins indirectly by detecting modification of their targets. How NLR proteins detect such modifications is poorly understood. To address these questions, we have been investigating the Arabidopsis (Arabidopsis thaliana) NLR protein RESISTANCE TO PSEUDOMONAS SYRINGAE5 (RPS5), which detects the Pseudomonas syringae effector protein Avirulence protein Pseudomonas phaseolicolaB (AvrPphB). AvrPphB is a cysteine protease that specifically targets a subfamily of receptor-like cytoplasmic kinases, including the Arabidopsis protein kinase AVRPPHB Susceptible1 (PBS1). RPS5 is activated by the cleavage of PBS1 at the apex of its activation loop. Here, we show that RPS5 activation requires that PBS1 be localized to the plasma membrane and that plasma membrane localization of PBS1 is mediated by amino-terminal S-acylation. We also describe the development of a high-throughput screen for mutations in PBS1 that block RPS5 activation, which uncovered four new pbs1 alleles, two of which blocked cleavage by AvrPphB. Lastly, we show that RPS5 distinguishes among closely related kinases by the amino acid sequence (SEMPH) within an exposed loop in the C-terminal one-third of PBS1. The SEMPH loop is located on the opposite side of PBS1 from the AvrPphB cleavage site, suggesting that RPS5 associates with the SEMPH loop while leaving the AvrPphB cleavage site exposed. These findings provide support for a model of NLR activation in which NLR proteins form a preactivation complex with effector targets and then sense a conformational change in the target induced by effector modification.
Cohort profile: Risk evaluation of cancers in Chinese diabetic individuals: a longitudinal (REACTION) study (队列简介：中国糖尿病患者肿瘤发生风险的纵向研究（REACTION研究）)
Authors: Bi Yufang , Lu Jieli , Wang Weiqing , Mu Yiming , Zhao Jiajun , Liu Chao , Chen Lulu , Shi Lixin , Li Qiang , Wan Qin , Wu Shengli , Yang Tao , Yan Li , Liu Yan , Wang Guixia , Luo Zuojie , Tang Xulei , Chen Gang , Huo Yanan , Gao Zhengnan , Su Qing , Ye Zhen , Wang Youming , Qin Guijun , Deng Huacong , Yu Xuefeng , Shen Feixia , Chen Li , Zhao Liebin , Zhang Jie , Sun Jichao , Dai Meng , Xu Min , Xu Yu , Chen Yuhong , Lai Shenghan , Bloomgarden Zachary T. , Li Donghui , Ning Guang 
Published: November 2013

AbstractObjectiveTo demonstrate whether abnormal glucose metabolism (diabetes and prediabetes) is associated with increased risk for cancer in the Chinese population and to identify factors that modify the risk of cancer among individuals with abnormal glucose metabolism.MethodsBetween 2011 and 2012, 259 657 community‐dwelling adults, aged 40 years and older, were recruited from 25 centers across mainland China to participant in the baseline survey of the REACTION study, with follow‐up investigations performed 3, 5, and 10 years later. Detailed questionnaires about lifestyles, physical and biochemical measurement, bio‐samples including serum, urine, and whole blood for DNA extraction were collected for all the participants.ResultsThe mean ± standard deviation (SD) age of this cohort was 57 ± 10 years. And the prevalence of pre‐existing and newly diagnosed diabetes was 10.32% and 10.57%, respectively. A total of 4511 prevalent cancer cases (988 men and 3523 women) were identified, the prevalence was 1.79. Compared to those with normal glucose metabolism, men with diabetes had a significantly lower adjusted prevalence ratio (PR) of stomach cancer (PR: 0.38, 95% CI: 0.16–0.89), and women with diabetes had significantly higher adjusted PRs of cancer of all sites (PR: 1.36, 95% CI: 1.20–1.56), and cancer of the breast (PR: 1.56, 95% CI: 1.21–2.00), the endometrium (PR: 1.58, 95% CI: 1.16–2.15), and the thyroid (PR: 1.53, 95% CI: 1.03–2.27).ConclusionThe multi‐center REACTION study has captured a broad range of data on physical, psychological and metabolic function as well as health status, biochemical and lifestyle information in 259 657 adults from the general population across the China.
Early interaction between infants and their parents predicts social competence at the age of four
Authors: Hedenbro Monica , Rydelius Per‐Anders 
Published: November 2013

AbstractAimTo investigate the impact that the interaction between first‐born children and their parents, from the age of 3 months, has on peer and social competence when the children are 4 years of age.MethodsFifteen families were videotaped in Lausanne Trilogue Play situations (child–mother–father interactions), when the children were three, nine, 18 and 48 months of age. The findings were then related to peer and social competence assessments carried out by preschool teachers when the children were four.ResultsThere was a correlation between the parents' responsiveness and the child's capacity to initiate (make contributions to) turn‐taking sequences in the family triad early in life. This, in turn, was associated with the child's later peer and social competence. At the age of 3 months, the child's contributions to the triadic interaction were interpreted by the parents as intentional communication. According to the preschool teachers' assessments, children who initiated turn‐taking sequences at 9 months of age had better peer competence (p = 0.008) and social competence (p = 0.028) at 48 months.ConclusionThe results highlight the opportunities that parents have to stimulate their child's later social competence. They also show that a Lausanne Trilogue Play situation can be used to identify competent children and children/families with communication deficits.
Maternal western diet primes non‐alcoholic fatty liver disease in adult mouse offspring
Authors: Pruis M. G. M. , Lendvai Á. , Bloks V. W. , Zwier M. V. , Baller J. F. W. , de Bruin A. , Groen A. K. , Plösch T. 
Published: November 2013

AbstractAimMetabolic programming via components of the maternal diet during gestation may play a role in the development of different aspects of the metabolic syndrome. Using a mouse model, we aimed to characterize the role of maternal western‐type diet in the development of non‐alcoholic fatty liver disease (NAFLD) in the offspring.MethodsFemale mice were fed either a western (W) or low‐fat control (L) semisynthetic diet before and during gestation and lactation. At weaning, male offspring were assigned either the W or the L diet, generating four experimental groups: WW, WL, LW and LL offspring. Biochemical, histological and epigenetic indicators were investigated at 29 weeks of age.ResultsMale offspring exposed to prenatal and post‐weaning western‐style diet (WW) showed hepatomegaly combined with accumulation of hepatic cholesterol and triglycerides. This accumulation was associated with up‐regulation of de novo lipid synthesis, inflammation and dysregulation of lipid storage. Elevated hepatic transaminases and increased expression of Tnfa, Cd11, Mcp1 and Tgfb underpin the severity of liver injury. Histopathological analysis revealed the presence of advanced steatohepatitis in WW offspring. In addition, alterations in DNA methylation in key metabolic genes (Ppara, Insig, and Fasn) were detected.ConclusionMaternal dietary fat intake during early development programmes susceptibility to liver disease in male offspring, mediated by disturbances in lipid metabolism and inflammatory response. Long‐lasting epigenetic changes may underlie this dysregulation.
Trade policy and industrial development: iron and steel in a small open economy, 1870−1913
Authors: Inwood Kris , Keay Ian 
Published: November 2013

AbstractIn this paper we argue that effective tariff protection associated with the 1879 National Policy and the 1887 Tupper tariffs triggered investment in new, technologically advanced blast furnaces that were capable of accommodating rapid output expansion. This conclusion is based on an appreciation of the timing of late nineteenth‐century investments in Canada and their connection to changes in government policy and other demand determinants. In our empirical investigation we use new information on westbound transatlantic freight rates, intra‐continental transport costs, and furnace‐specific micro‐data, and we acknowledge the endogenous relationships linking investment to domestic demand, labour costs, and tariffs.
Imputing rent in consumption measures, with an application to consumption poverty in Canada, 1997–2009
Authors: Norris Sam , Pendakur Krishna 
Published: November 2013

AbstractWe consider two econometric problems in the measurement of poverty, both relating to rent imputation. First, we account for quality differences correlated with selection into owner‐occupied versus rental tenure. This correction increases estimated household consumption by 5% over uncorrected estimates and decreases estimated poverty rates quite dramatically. Second, we propose that measurement error induced by the imputation be corrected by imputing a consumption distribution, rather than a consumption level, for each household. This correction increases estimated poverty rates slightly. We use our methods to measure consumption poverty in Canada, and find that the imputation strategy used influences the patterns observed. For example, measured poverty among the elderly barely declines when one uses our methods, in contrast to the almost 6 percentage point reduction we find using traditional methods. In our assessment of the over‐time evolution of consumption poverty, we find that substantial progress has been made on overall poverty and on child poverty, but that poverty among the elderly hardly changed.