bluuebunny/crossref_metadata_2025 huggingface dataset:
ChemInform Abstract: Synthesis and Properties of Functional π‐Expanded Compounds Prepared by Thermal or Photochemical Conversion of the Precursors
Authors: Yamada Hiroko , Kuzuhara Daiki , Katsuta Shuhei , Okujima Tetsuo
Published: January 2012

Review: about 60 refs.
ChemInform Abstract: MiR‐210: More than a Silent Player in Hypoxia
Authors: Devlin Cecilia , Greco Simona , Martelli Fabio , Ivan Mircea
Published: January 2012

Review: 61 refs.
ChemInform Abstract: Polysaccharides and Phytochemicals: A Natural Reservoir for the Green Synthesis of Gold and Silver Nanoparticles
Authors: Park Y. , Hong Y. N. , Weyers A. , Kim Y. S. , Linhardt R. J.
Published: January 2012

Review: 73 refs.
ChemInform Abstract: Membrane Biological Reactors
Authors: Hai F. I. , Yamamoto K.
Published: January 2012

Review: 360 refs.
ChemInform Abstract: Chemical Synthesis of Integral Membrane Proteins: Methods and Applications
Authors: Shen Fei , Huang Yi‐Chao , Tang Shan , Chen Yong‐Xiang , Liu Lei
Published: January 2012

Review: 83 refs.
ChemInform Abstract: Theoretical Aspects of Spin—Spin Couplings
Authors: Jazwinski Jaroslaw
Published: January 2012

Review: 136 refs.
Retracted: A Facile Synthetic Route to New Fluorinated Building‐Blocks of 1‐Fluoroalkynes and 1‐Fluorodiynes
Authors: Liu Cuibo , Ma Hai , Nie Jing , Ma Junan
Published: January 2012

A facile and direct fluorination process of alkynes and diynes was developed. In the presence of n‐butyllithium, the reaction of a series of terminal alkynes and diynes with the electrophilic fluorinating reagent (NFSI) proceeded to afford various 1‐fluoroalkynes and 1‐fluoro‐1,3‐diynes in moderate to high yields.
Photocatalytic Degradation of Imidacloprid by Phosphotungstic Acid Supported on a Mesoporous Sieve MCM‐41
Authors: Feng Changgen , Li Yanzhou , Liu Xia
Published: January 2012

Solid catalysts consisting of polyoxometalates (POM) namely phosphotungstic acid H3PW12O40 (HPW) supported on a mesoporous sieve MCM‐41 have been prepared and characterized by FT‐IR, X‐ray diffraction, nitrogen adsorption and high resolution transmission electron microscope (HRTEM). The HPW/MCM‐41 with different HPW loadings from 10 to 60 wt% possess large specific surface area and rather uniform mesopores. Keggin structure of HPW retains on the prepared composite catalysts. The photocatalytic performance of HPW/MCM‐41 was examined by degradation of a durable pesticide imidacloprid. It is found that the prepared photocatalysts exhibit high activity under irradiation of 365 nm monochromatic light. For 50 mL of imidacloprid (10 mg/L), conversion of imidacloprid using 20 mg of HPW/MCM‐41 with 50 wt% loading level and calcined at 300°C reaches 58.0% after 5 h irradiation.
Climate change and the decline of a once common bird
Authors: McClure Christopher J. W. , Rolek Brian W. , McDonald Kenneth , Hill Geoffrey E.
Published: January 2012

Climate change is predicted to negatively impact wildlife through a variety of mechanisms including retraction of range. We used data from the North American Breeding Bird Survey and regional and global climate indices to examine the effects of climate change on the breeding distribution of the Rusty Blackbird (Euphagus carolinus), a formerly common species that is rapidly declining. We found that the range of the Rusty Blackbird retracted northward by 143 km since the 1960s and that the probability of local extinction was highest at the southern range margin. Furthermore, we found that the mean breeding latitude of the Rusty Blackbird was significant and positively correlated with the Pacific Decadal Oscillation with a lag of six years. Because the annual distribution of the Rusty Blackbird is affected by annual weather patterns produced by the Pacific Decadal Oscillation, our results support the hypothesis that directional climate change over the past 40 years is contributing to the decline of the Rusty Blackbird. Our study is the first to implicate climate change, acting through range retraction, in a major decline of a formerly common bird species.
Multidimensional Latent Classification of ‘Street Robbery’ Offences
Authors: Goodwill Alasdair M. , Stephens Skye , Oziel Sandra , Yapp Jamie , Bowes Nicola
Published: January 2012

In a recent study of personal robbery, commissioned by the Home Office in the UK, a qualitative typology of robbery offences was proposed based on the approach used by the offender to commit the crime, consisting of four approach types: Blitz, Confrontation, Con, and Snatch. Conceptual inspection of the typology reveals that these proposed types may be hypothetically demarcated as the product of two latent dimensions: interaction (between the offender and the victim) and violence (used to threaten/harm the victim). The current paper utilises crime scene information from 72 incarcerated male offenders convicted of ‘street’ robbery to test this hypothesis. Convergent statistical analysis was utilised to test the structure of Smith's typology first using multidimensional scaling (MDS) and then principal component analysis (PCA). MDS and PCA analyses provided convergent support for the existence of the four robbery styles and the latent dimensions of interaction and violence. Implications of Smith's typological structure and latent behavioural dimensions on the conceptualisation and classification of robbery offences are discussed within the existing literature on ‘street’ robbery. Copyright © 2012 John Wiley & Sons, Ltd.
7 tesla imaging of cerebral radiation necrosis after arteriovenous malformations treatment using amide proton transfer (APT) imaging
Authors: Gerigk Lars , Schmitt Benjamin , Stieltjes Bram , Röder Falk , Essig Marco , Bock Michael , Schlemmer Heinz‐Peter , Röthke Matthias
Published: January 2012

Arteriovenous malformations (AVM) can be treated with stereotactic radiosurgery. An infrequent, but important complication of this treatment is radionecrosis, which can be detected by MRI. However, the imaging characteristics of necrosis are unspecific in conventional MRI. Here, we report a case of necrosis after radiotherapy of an AVM to illustrate the potential of 7 Tesla MRI including amide proton transfer (APT) for necrosis imaging. J. Magn. Reson. Imaging 2012;35:1207‐1209. © 2012 Wiley Periodicals, Inc.
The Influence of Silkworm Species on Cellular Interactions with Novel PVA/Silk Sericin Hydrogels
Authors: Lim Khoon S. , Kundu Joydip , Reeves April , Poole‐Warren Laura A. , Kundu Subhas C. , Martens Penny J.
Published: January 2012

Sericin peptides and PVA are chemically modified with methacrylate groups to produce a covalent PVA/sericin hydrogel. Preservation of the sericin bioactivity following methacrylation is confirmed, and PVA/sericin hydrogels are fabricated for both B. mori and A. mylitta sericin. Cell adhesion studies confirm the preservation of sericin bioactivity post incorporation in PVA gels. PVA/A. mylitta gels are observed to facilitate cell adhesion to a significantly greater degree than PVA/B. mori gels. Overall, the incorporation of sericin does not alter the physical properties of the PVA hydrogels but does result in significantly improved cellular interaction, particularly from A. mylitta gels.

magnified image
Preparation and Characterization of Anisotropic Submicron Particles From Semicrystalline Polymers
Authors: Staff Roland H. , Lieberwirth Ingo , Landfester Katharina , Crespy Daniel
Published: January 2012

The synthesis of colloidally stable submicron particles of syndiotactic polystyrene (sPS) and isotactic polystyrene (iPS) is reported. Model particles based on poly‐L‐lactic acid (PLLA), atactic polystyrene (aPS), sPS, and iPS are prepared by the evaporation of a solvent present in miniemulsion droplets. The degree of crystallinity of the particles is found to decrease with their size, as shown by DSC and WAXS measurements. Remarkably, nonspherical particles can be formed in the dispersed state with sPS and iPS, whereas PLLA and aPS particles always display spherical morphologies.
Spatially resolved extended phase graphs: Modeling and design of multipulse sequences with parallel transmission
Authors: Malik Shaihan J. , Padormo Francesco , Price Anthony N. , Hajnal Joseph V.
Published: January 2012

A spatially resolved extended phase graph (SR‐EPG) framework is proposed for prediction of echo amplitudes in the presence of spatially variable radio frequency (RF) fields. The method may be used to examine any regularly repeating pulse sequence and provides a design framework for parallel transmission (PTx) systems; in this work signal homogeneity in static pseudo‐steady state (SPSS) turbo spin echo (TSE) imaging was investigated. Building on SR‐EPG calculations with PTx, a dynamic RF‐shimming approach is proposed in which, RF pulse amplitudes and phases are optimized on a per channel and per pulse basis to yield the desired signal response for all echoes. Results show significant improvements over “static” RF shimming (in which the relative amplitude/phase of the PTx channels are fixed for all pulses). SPSS‐TSE imaging using dynamic RF shimming resulted in excellent image quality, both in phantoms and in vivo, and confirmed SR‐EPG predictions. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
How advancement in biological network analysis methods empowers proteomics
Authors: Goh Wilson W. B. , Lee Yie H. , Chung Maxey , Wong Limsoon
Published: January 2012

Proteomics provides important information ‐ that may not be inferable from indirect sources such as RNA or DNA ‐ on key players in biological systems or disease states. However, it suffers from coverage and consistency problems. The advent of network‐based analysis methods can help in overcoming these problems but requires careful application and interpretation. This review considers briefly current trends in proteomics technologies and understanding the causes of critical issues that need to be addressed ‐ i.e., incomplete data coverage and inter‐sample inconsistency. On the coverage issue, we argue that holistic analysis based on biological networks provides a suitable background on which more robust models and interpretations can be built upon; and we introduce some recently developed approaches. On consistency, group‐based approaches based on identified clusters, as well as on properly integrated pathway databases, are particularly useful. Despite that protein interactions and pathway networks are still largely incomplete, given proper quality checks, applications and reasonably sized data sets, they yield valuable insights that greatly complement data generated from quantitative proteomics.
Cloning and characterization of two new thermostable and alkalitolerant α-amylases from the Anoxybacillus species that produce high levels of maltose
Authors: Chai Yen Yen , Rahman Raja Noor Zaliha Raja Abd , Illias Rosli Md , Goh Kian Mau
Published: January 2012

Two genes that encode α-amylases from two Anoxybacillus species were cloned and expressed in Escherichia coli. The genes are 1,518 bp long and encode 506 amino acids. Both sequences are 98% similar but are distinct from other well-known α-amylases. Both of the recombinant enzymes, ASKA and ADTA, were purified using an α-CD–Sepharose column. They exhibited an optimum activity at 60°C and pH 8. Both amylases were stable at pH 6–10. At 60°C in the absence of Ca2+, negligible reduction in activity for up to 48 h was observed. The activity half-life at 65°C was 48 and 3 h for ASKA and ADTA, respectively. In the presence of Ca2+ ions, both amylases were highly stable for at least 48 h and had less than a 10% decrease in activity at 70°C. Both enzymes exhibited similar end-product profiles, and the predominant yield was maltose (69%) from starch hydrolysis. To the best of our knowledge, most α-amylases that produce high levels of maltose are active at an acidic to neutral pH. This is the first report of two thermostable, alkalitolerant recombinant α-amylases from Anoxybacillus that produce high levels of maltose and have an atypical protein sequence compared with known α-amylases.
Determinants and Consequences of Child Culture Brokering in Families from the Former Soviet Union
Authors: Jones Curtis J. , Trickett Edison J. , Birman Dina
Published: January 2012

Child culture brokering occurs when immigrant children help their families navigate the new culture and language. The present study develops a model of the child culture broker role that situates it within the family and community economic and acculturative contexts of 328 families from the former Soviet Union. Path analysis was utilized to explore the relationships of community and family economic and cultural contexts with child culture brokering, child emotional distress, and family disagreements. All children reported some culture brokering for their parents. Less English proficient parents with lower status jobs, and living in areas with more Russian speaking families tended to utilize their children as brokers more often. Further, community economic conditions also predicted brokering indirectly, mediated by parent job social status. Brokering was related to child emotional distress and family disagreements. Further, culture brokering was a mediator of the impact of parent job social status on both child emotional distress and family disagreements. These results add to our understanding of the culture broker role and emphasize the utility of approaching research on it from an ecological perspective.
Northeast Asian Linguistic Ecology and the Advent of Rice Agriculture in Korea and Japan
Authors: Whitman John
Published: January 2012

The languages of Northeast Asia show evidence of dispersal from south to north, consistent with the hypothesis that agriculture spread north and east from the vicinity of Liaoning, beginning with the millets approximately 5500 BP. Wet rice agriculture in Korea and Japan results from a later spread, also beginning in Shandong, crossing via the Liaodong peninsula and reaching the Korean peninsula around 1500 BCE. This dispersal is associated with the Mumun archaeological culture after 1500 BCE in the Korean peninsula and the Yayoi culture after 950 BCE in the Japanese archipelago. From a linguistic standpoint, it is associated with the entry of the Japonic language family, first into the Korean peninsula, subsequently into the Japanese archipelago. The arrival of Koreanic is associated with the advent of the Korean-style bronze dagger culture and a temporary hiatus in wet rice agriculture sites around 300 BCE. Both Koreanic and Japonic are relatively shallow language families, with Koreanic the shallower of the two, consistent with the chronology above. The gap between the earliest linguistically motivated dates for these language families and the archaeological events is the result of a linguistic founders effect, providing further evidence for demic diffusion as a source for their distribution.
MicroRNA‐195‐5p suppresses glucose uptake and proliferation of human bladder cancer T24 cells by regulating GLUT3 expression
Authors: Fei Xiang , Qi Manlong , Wu Bin , Song Yongsheng , Wang Yueping , Li Tingting
Published: January 2012

It has been reported that expression of glucose transporter member 3 (GLUT3) is up‐regulated in bladder cancers. However, the regulating mechanism remains unknown. Here, we assessed whether microRNAs (miRNAs) regulate GLUT3 expression in bladder cancers. In our study, miR‐195‐5p was identified to directly targeted GLUT3 3′‐untranslated region (UTR) in bladder cancer T24 cells. Small interfering RNA (siRNA)‐ and miR‐195‐5p‐mediated GLUT3 knockdown experiments revealed that miR‐195‐5p decreased T24 cells glucose uptake, inhibited cell growth and promoted cell apoptosis through suppression of GLUT3 expression. Therefore, miR‐195‐5p is a novel and also the first identified miRNA that targets GLUT3, and the aberrant decreased expression of miR‐195‐5p and consequent GLUT3 up‐regulation may contribute to bladder carcinogenesis.
Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1
Authors: Ruan Jianbin , Xu Chao , Bian Chuanbing , Lam Robert , Wang Jia-Pey , Kania Joanna , Min Jinrong , Zang Jianye
Published: January 2012

Lamin‐B and Lamin‐B bind by x‐ray crystallography (View interaction)
Homocysteine-lowering therapy does not lead to reduction in cardiovascular outcomes in chronic kidney disease patients: a meta-analysis of randomised, controlled trials
Authors: Pan Yu , Guo Li Li , Cai Ling Ling , Zhu Xiao Juan , Shu Jin Lian , Liu Xiao Li , Jin Hui Min
Published: January 2012

The efficacy of homocysteine (Hcy)-lowering therapy in reducing the risk of CVD among patients with chronic kidney disease (CKD) remains controversial. We performed a meta-analysis to determine whether pooling the data from the few small randomised, controlled trials that address this topic would improve the statistical power of the analysis and resolve some of the inconsistencies in the results. Randomised, controlled clinical trials (RCT) were identified from MEDLINE, EMBASE, www.clinicaltrials.gov, the Cochrane Controlled Clinical Trials Register Database and Nephrology Filters. Independent extraction of articles was performed using predefined data fields. The primary outcome was relative risk (RR) of CVD, CHD, stroke and all-cause mortality for the pooled trials. A stratified analysis was planned, assessing the RR for cardiovascular events between the patients on and not on dialysis. Overall, ten studies met the inclusion criteria. The estimated RR were not significantly different for any outcomes, including CHD (RR 1·00, 95 % CI 0·75, 1·31, P = 0·97), CVD (RR 0·94, 95 % CI 0·84, 1·05, P = 0·30), stroke (RR 0·83, 95 % CI 0·57, 1·19, P = 0·31) and all-cause mortality (RR 1·00, 95 % CI 0·92, 1·09, P = 0·98). In the stratified analysis, the estimated RR were not significantly different for cardiovascular events regardless of dialysis or in combination with vitamin B therapy or the degree of reduction in Hcy levels. Our meta-analysis of RCT supports the conclusion that Hcy-lowering therapy was not associated with a significant decrease in the risk for CVD events, stroke and all-cause mortality among patients with CKD.
SATgenɛ dietary model to implement diets of differing fat composition in prospectively genotyped groups (apoE) using commercially available foods
Authors: Lockyer Stacey , Tzanetou Maria , Carvalho-Wells Andrew L. , Jackson Kim G. , Minihane Anne M. , Lovegrove Julie A.
Published: January 2012

Response to dietary fat manipulation is highly heterogeneous, yet generic population-based recommendations aimed at reducing the burden of CVD are given. The APOE epsilon genotype has been proposed to be an important determinant of this response. The present study reports on the dietary strategy employed in the SATgenɛ (SATurated fat and gene APOE) study, to assess the impact of altered fat content and composition on the blood lipid profile according to the APOE genotype. A flexible dietary exchange model was developed to implement three isoenergetic diets: a low-fat (LF) diet (target composition: 24 % of energy (%E) as fat, 8 %E SFA and 59 %E carbohydrate), a high-saturated fat (HSF) diet (38 %E fat, 18 %E SFA and 45 %E carbohydrate) and a HSF-DHA diet (HSF diet with 3 g DHA/d). Free-living participants (n 88; n 44 E3/E3 and n 44 E3/E4) followed the diets in a sequential design for 8 weeks, each using commercially available spreads, oils and snacks with specific fatty acid profiles. Dietary compositional targets were broadly met with significantly higher total fat (42·8 %E and 41·0 %E v. 25·1 %E, P ≤ 0·0011) and SFA (19·3 %E and 18·6 %E v. 8·33 %E, P ≤ 0·0011) intakes during the HSF and HSF-DHA diets compared with the LF diet, in addition to significantly higher DHA intake during the HSF-DHA diet (P ≤ 0·0011). Plasma phospholipid fatty acid analysis revealed a 2-fold increase in the proportion of DHA after consumption of the HSF-DHA diet for 8 weeks, which was independent of the APOE genotype. In summary, the dietary strategy was successfully implemented in a free-living population resulting in well-tolerated diets which broadly met the dietary targets set.
Effect of the protein:carbohydrate ratio in hypoenergetic diets on metabolic syndrome risk factors in exercising overweight and obese women
Authors: Campbell Dawn D. , Meckling Kelly A.
Published: January 2012

Overweight and obesity are growing problems both in Canada and around the world. Obesity is associated with a number of chronic diseases including type 2 diabetes and CVD, which puts a tremendous burden on the health care systems in place. The present study sought to investigate whether there were differences in the effectiveness of three low-fat, hypo- and isoenergetic diets differing in protein:carbohydrate ratio, low protein (LP, 1 g protein:4 g carbohydrate), normal protein (NP, 1 g protein:2 g carbohydrate) or high protein (HP, 1 g protein:1 g carbohydrate), on weight loss and markers of the metabolic syndrome (MetS) in overweight women. Subjects were randomly assigned to receive one of three intervention diets, all of which included a 60 min exercise programme three times/week for 12 weeks. Of the total subjects, fifty-four overweight and obese local women with MetS risk factors completed the study. All groups had similar improvements in body weight, insulin sensitivity, lipid profile, blood pressure and fitness. Subjects reported that the NP diet was easier to comply with and achieved better improvements in body fat, waist circumference and waist:hip ratio, and preservation of lean mass compared with the other two diets. In conclusion, energy restriction and exercise both facilitate weight loss in overweight and obese subjects and reduce symptoms of the MetS. A diet with a 1:2 protein:carbohydrate ratio promoted better improvements than either the LP or HP diets, and may be superior in reducing long-term chronic disease risk in this population.
A high-fat diet containing whole walnuts (Juglans regia) reduces tumour size and growth along with plasma insulin-like growth factor 1 in the transgenic adenocarcinoma of the mouse prostate model
Authors: Davis Paul A. , Vasu Vihas T. , Gohil Kishorchandra , Kim Hyunsook , Khan Imran H. , Cross Carroll E. , Yokoyama Wallace
Published: January 2012

Prostate cancer (PCa) has been linked to fat intake, but the effects of both different dietary fat levels and types remain inconsistent and incompletely characterised. The effects on PCa in the transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model of an elevated fat (20 % of energy as fat) diet containing 155 g of whole walnuts were compared to those of an elevated fat (20 % of energy as soyabean oil) diet with matched macronutrients, tocopherols as well as a low-fat (8 % of energy as soyabean oil) diet. Mice, starting at 8 weeks of age, consumed one of the three different dietsad libitum; and prostates, livers and blood were obtained after 9, 18 or 24 weeks of feeding. No differences were observed in whole animal growth rates in either high-fat (HF) diet group, but prostate tumour weight and growth rate were reduced in the walnut diet group. Walnut diet group prostate weight, plasma insulin-like growth factor 1, resistin and LDL were lower at 18 weeks, while no statistically significant prostate weight differences by diet were seen at 9 or 24 weeks. Multiple metabolites in the livers differed by diet at 9 and 18 weeks. The walnut diet's beneficial effects probably represent the effects of whole walnuts' multiple constituents and not via a specific fatty acid or tocopherols. Moreover, as the two HF diets had dissimilar effects on prostate tumour growth rate and size, and yet had the same total fat and tocopherol composition and content, this suggests that these are not strongly linked to PCa growth.
Dietary silk protein, sericin, improves epidermal hydration with increased levels of filaggrins and free amino acids in NC/Nga mice
Authors: Kim Hyunae , Lim Yu-ji , Park Ji-Ho , Cho Yunhi
Published: January 2012

Epidermal hydration is maintained primarily by natural moisturising factors (NMF), of which free amino acids (AA) are major constituents that are generated by filaggrin degradation. To identify dietary sources that may improve skin dryness of atopic dermatitis (AD), we investigated dietary effects of silk proteins, sericin and fibroin, on epidermal levels of hydration, filaggrins and free AA, as well as PPARγ, peptidylarginine deiminase-3 (PAD3) and caspase-14 proteins involved in filaggrin expression and degradation processes. NC/Nga mice, an animal model of AD, were fed a control diet (group CA: atopic control) or diets with 1 % sericin (group S) or fibroin (group F) for 10 weeks. In group S, epidermal levels of hydration, total filaggrins and total free AA, as well as PPARγ, PAD3 and caspase-14, which were reduced in group CA, were increased to higher or similar levels of a normal control group of BALB/c mice (group C). Furthermore, profilaggrin, a precursor with multiple filaggrin repeats, and three repeat intermediates were increased, while two repeat intermediates and filaggrin were decreased in parallel with increased levels of glutamate and serine, major AA of NMF in group S. Despite increased levels of total filaggrins, total free AA, PPARγ and PAD3, epidermal levels of hydration, glutamate, serine and caspase-14 were not increased, but other minor AA of NMF were highly detected in group F. Dietary sericin improves epidermal hydration in parallel with enhancing profilaggrin expression and degradation into free AA that is coupled with elevated levels of PPARγ, PAD3 and caspase-14 proteins.
Maximizing points and coboundaries for an irrational rotation on a circle
Authors: BRÉMONT JULIEN , BUCZOLICH ZOLTÁN
Published: January 2012

Consider an irrational rotation of a unit circle and a real continuous function. A point is declared ‘maximizing’ if the growth of the ergodic sums at this point is maximal up to an additive constant. In the case of two-sided ergodic sums, the existence of a maximizing point for a continuous function implies that it is the coboundary of a continuous function. In contrast, we build, for the ‘usual’ one-sided ergodic sums, examples in Hölder or smooth classes, indicating that all kinds of behaviour of the function with respect to the dynamical system are possible. We also show that generic continuous functions are without maximizing points, not only for rotations, but also for the transformation 2x mod 1. For this latter transformation, it is known that any Hölder continuous function has a maximizing point.
WRF simulation over complex terrain during a southern California wildfire event
Authors: Lu W. , Zhong S. , Charney J. J. , Bian X. , Liu S.
Published: January 2012

In October 2007, the largest wildfire‐related evacuation in California's history occurred as severe wildfires broke out across southern California. Smoke from these wildfires contributed to elevated pollutant concentrations in the atmosphere, affecting air quality in a vast region of the western United States. High‐resolution numerical simulations were performed using the Weather Research and Forecast (WRF) model to understand the atmospheric conditions during the wildfire episode and how the complex circulation patterns might affect smoke transport and dispersion. The simulated meteorological fields were validated using surface and upper air observations in California and Nevada. To distinguish the performance of the WRF in different geographic regions, the surface stations were grouped into coastal sites, valley and basin sites, and mountain sites, and the results for the three categories were analyzed and intercompared. For temperature and moisture, the mountain category has the best agreement with the observations, while the coastal category was the worst. For wind, the model performance for the three categories was very similar. The flow patterns over complex terrain were also analyzed under different synoptic conditions and the possible impact of the terrain on smoke and pollutant pathways is analyzed by employing a Lagrangian Particle Dispersion Model. When high mountains prevent the smoke from moving inland, the mountain passes act as active pathways for smoke transport; meanwhile, chimney effect helps inject the pollutants to higher levels, where they are transported regionally. The results highlight the role of complex topography in the assessment of the possible smoke transport patterns in the region.
The multifunctional poly(A)-binding protein (PABP) 1 is subject to extensive dynamic post-translational modification, which molecular modelling suggests plays an important role in co-ordinating its activities
Authors: Brook Matthew , McCracken Lora , Reddington James P. , Lu Zhi-Liang , Morrice Nicholas A. , Gray Nicola K.
Published: January 2012

PABP1 [poly(A)-binding protein 1] is a central regulator of mRNA translation and stability and is required for miRNA (microRNA)-mediated regulation and nonsense-mediated decay. Numerous protein, as well as RNA, interactions underlie its multi-functional nature; however, it is unclear how its different activities are co-ordinated, since many partners interact via overlapping binding sites. In the present study, we show that human PABP1 is subject to elaborate post-translational modification, identifying 14 modifications located throughout the functional domains, all but one of which are conserved in mouse. Intriguingly, PABP1 contains glutamate and aspartate methylations, modifications of unknown function in eukaryotes, as well as lysine and arginine methylations, and lysine acetylations. The latter dramatically alter the pI of PABP1, an effect also observed during the cell cycle, suggesting that different biological processes/stimuli can regulate its modification status, although PABP1 also probably exists in differentially modified subpopulations within cells. Two lysine residues were differentially acetylated or methylated, revealing that PABP1 may be the first example of a cytoplasmic protein utilizing a ‘methylation/acetylation switch’. Modelling using available structures implicates these modifications in regulating interactions with individual PAM2 (PABP-interacting motif 2)-containing proteins, suggesting a direct link between PABP1 modification status and the formation of distinct mRNP (messenger ribonucleoprotein) complexes that regulate mRNA fate in the cytoplasm.
A spin-adapted size-extensive state-specific multi-reference perturbation theory. I. Formal developments
Authors: Mao Shuneng , Cheng Lan , Liu Wenjian , Mukherjee Debashis
Published: January 2012

We present in this paper a comprehensive formulation of a spin-adapted size-extensive state-specific multi-reference second-order perturbation theory (SA-SSMRPT2) as a tool for applications to molecular states of arbitrary complexity and generality. The perturbative theory emerges in the development as a result of a physically appealing quasi-linearization of a rigorously size-extensive state-specific multi-reference coupled cluster (SSMRCC) formalism [U. S. Mahapatra, B. Datta, and D. Mukherjee, J. Chem. Phys. 110, 6171 (1999)10.1063/1.478523]. The formulation is intruder-free as long as the state-energy is energetically well-separated from the virtual functions. SA-SSMRPT2 works with a complete active space (CAS), and treats each of the model space functions on the same footing. This thus has the twin advantages of being capable of handling varying degrees of quasi-degeneracy and of ensuring size-extensivity. This strategy is attractive in terms of the applicability to bigger systems. A very desirable property of the parent SSMRCC theory is the explicit maintenance of size-extensivity under a variety of approximations of the working equations. We show how to generate both the Rayleigh-Schrödinger (RS) and the Brillouin-Wigner (BW) versions of SA-SSMRPT2. Unlike the traditional naive formulations, both the RS and the BW variants are manifestly size-extensive and both share the avoidance of intruders in the same manner as the parent SSMRCC. We discuss the various features of the RS as well as the BW version using several partitioning strategies of the hamiltonian. Unlike the other CAS based MRPTs, the SA-SSMRPT2 is intrinsically flexible in the sense that it is constructed in a manner that it can relax the coefficients of the reference function, or keep the coefficients frozen if we so desire. We delineate the issues pertaining to the spin-adaptation of the working equations of the SA-SSMRPT2, starting from SSMRCC, which would allow us to incorporate essentially any type open-shell configuration-state functions (CSF) within the CAS. The formalisms presented here will be applied extensively in a companion paper to assess their efficacy.
Observation of a snap-through instability in graphene
Authors: Scharfenberg Scott , Mansukhani Nikhita , Chialvo Cesar , Weaver Richard L. , Mason Nadya
Published: January 2012

We examine the competition between adhesive and bending energies for few-layer graphene (FLG) samples placed on microscale-corrugated metallic substrates. Using atomic force microscopy, we show that the graphene undergoes a sharp “snap-through” transition as a function of layer thickness, where the material transitions between conforming to the substrate and lying flat on top of the substrate. By utilizing the critical snap-through thickness in an elasticity model for the FLG’s bending, we extract a value for graphene-surface adhesion energy of 1.1 eV/nm2.
The Italian transition that never was
Authors: Bull Martin J.
Published: January 2012

The recent argument that the notion of ‘transition’ should be set aside in attempting to explain the trajectory of Italian politics in the past two decades is to be welcomed, but does not go far enough in explaining why we, as Italianists, got our case wrong and how exactly we might get our case right today. The transitional ‘myth’ was born and maintained despite growing evidence of its inherently problematic nature, in both conceptual and empirical terms. The concept of ‘transition’ needs more serious conceptual treatment and empirical application, but even with this work it is unlikely to be concluded that Italy is in transition. Freeing Italy and Italianists from this conventional wisdom, while, at the same time, not abandoning the idea that something exceptional happened to Italian politics in the early 1990s will help enrich the debate on the nature of the political change that Italy has experienced in the past 17 years.
Kink instabilities in high-beta JET advanced scenarios
Authors: Buratti P. , Baruzzo M. , Buttery R.J. , Challis C.D. , Chapman I.T. , Crisanti F. , Figini L. , Gryaznevich M. , Hender T.C. , Howell D.F. , Han H. , Imbeaux F. , Joffrin E. , Hobirk J. , Kwon O.J. , Litaudon X. , Mailloux J.
Published: January 2012

Stability of high-beta plasmas is studied on discharges from a series of JET experiments on steady-state and hybrid advanced scenarios, with a wide range of safety factor (q) profiles and normalized beta values extending to βN = 4. Bursting and continuous forms of global n = 1 instabilities are encountered that degrade confinement or, in some cases, give rise to disruptions. Mode frequencies are well above the inverse wall time and correspond to plasma rotation at around mid-radius. Stability boundaries in terms of q
min and pressure peaking are examined. For relatively broad pressure profiles the stability limit decreases from βN = 4 at q
min = 1 to βN = 2 at q
min = 3, while at fixed q
min it decreases with increasing pressure peaking. Metastable and unstable regions are identified in the βN–q
min diagram by mode-trigger analysis. Tearing and kink mode structures are found from phase analysis of temperature profile oscillations; for a selection of kink cases, instability conditions and mode structure are compared with ideal stability calculations.
Serum proteomic profiling in patients with drug‐induced liver injury
Authors: Bell L. N. , Vuppalanchi R. , Watkins P. B. , Bonkovsky H. L. , Serrano J. , Fontana R. J. , Wang M. , Rochon J. , Chalasani N.
Published: January 2012

Background

Idiosyncratic drug‐induced liver injury (DILI) is a complex disorder that is difficult to predict, diagnose and treat.

Aim

To describe the global serum proteome of patients with DILI and controls.

Methods

A label‐free, mass spectrometry‐based quantitative proteomic approach was used to explore protein expression in serum samples from 74 DILI patients (collected within 14 days of DILI onset) and 40 controls. A longitudinal analysis was conducted in a subset of 21 DILI patients with available 6‐month follow‐up serum samples.

Results

Comparison of DILI patients based on pattern, severity and causality assessment of liver injury revealed many differentially expressed priority 1 proteins among groups. Expression of fumarylacetoacetase was correlated with alanine aminotransferase (ALT; r = 0.237; P = 0.047), aspartate aminotransferase (AST; r = 0.389; P = 0.001) and alkaline phosphatase (r = −0.240; P = 0.043), and this was the only protein with significant differential expression when comparing patients with hepatocellular vs. cholestatic or mixed injury. In the longitudinal analysis, expression of 53 priority 1 proteins changed significantly from onset of DILI to 6‐month follow‐up, and nearly all proteins returned to expression levels comparable to control subjects. Ninety‐two serum priority 1 proteins with significant differential expression were identified when comparing the DILI and control groups. Pattern analysis revealed proteins that are components of inflammation, immune system activation and several hepatotoxicity‐specific pathways. Apolipoprotein E expression had the greatest power to differentiate DILI patients from controls (89% correct classification; AUROC = 0.97).

Conclusion

This proteomic analysis identified differentially expressed proteins that are components of pathways previously implicated in the pathogenesis of idiosyncratic drug‐induced liver injury.
Outcomes after escalation of infliximab therapy in ambulatory patients with moderately active ulcerative colitis
Authors: Rostholder E. , Ahmed A. , Cheifetz A. S. , Moss A. C
Published: January 2012

Background

Infliximab (IFX) therapy escalation during maintenance treatment occurs frequently in clinical practice in patients with ulcerative colitis (UC). Outcomes for these patients have not been described.

Aim

To describe the prevalence of, and outcomes after, IFX escalation during maintenance therapy in patients with moderate–severe UC.

Methods

Retrospective observational study of clinical outcomes in ambulatory patients with moderate–severe UC treated with maintenance IFX.

Results

Fifty‐six ambulatory patients received IFX for moderate–severe UC; fifty (89%) responded and proceeded to maintenance therapy. Mean duration of maintenance therapy was 14 months, with mean follow‐up of 38 months. Twenty‐seven patients (54%) required IFX therapy escalation after a mean of six maintenance infusions. Clinical remission was noted in 36% of the entire cohort (18/50) at 12 months; 19% in the escalation group and 56% in the non‐escalation group. Patients who required IFX escalation were less likely to be in clinical remission at 12 months (OR 0.2, 95% CI 0.1–0.6, P = 0.01) when compared with those who did not. During the follow‐up period, 27% of patients required a colectomy, and the mean time to colectomy was 17 months. Patients in the escalation group required a colectomy in 33% of cases, compared with 21% of non‐escalation patients.

Conclusions

A significant proportion of ambulatory patients with UC treated with maintenance infliximab required therapy escalation over time. This was associated with lower remission, and higher colectomy, rates.
Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project
Authors: Oudot‐Mellakh Tiphaine , Cohen William , Germain Marine , Saut Noémie , Kallel Choumous , Zelenika Diana , Lathrop Mark , Trégouët David‐Alexandre , Morange Pierre‐Emmanuel
Published: January 2012

Deficiencies of antithrombin (AT), protein C (PC) and protein S (PS) or an impaired PC anticoagulant pathway increase the risk of venous thrombosis (VT). By conducting a genome‐wide association study (GWAS) on two independent samples of VT patients totalling 951 subjects typed for 472 173 single nucleotide polymorphisms (SNPs), we observed that common SNPs explain 21% and 27% of the genetic variance of plasma AT and PS levels, even though no SNP reached genome‐wide significance. For PC, we showed that two PROCR SNPs, rs867186 (Ser219Gly) and rs6060278, additionally explained c. 20% (P = 1·19 × 10−31) of the variance of plasma PC levels. We also observed that c. 40% of the remaining genetic variance of PC levels could be due to yet unidentified common SNPs. The PROCR locus was also found to explain c. 8% (P < 10−10) of agkistrodon contortrix venom (ACV) (exploring the PC pathway) variability which was under the main control of the F5 and F2 loci that further explained about 40% and 10%, respectively. We presented here the first GWAS for plasma AT and free‐PS levels and ACV in Caucasian samples. We identified three independent loci associated with ACV (F2, F5 and PROCR) and replicated two independent effects on plasma PC levels at the PROCR locus.
Multi‐agency information practices in children's services: the metaphorical ‘jigsaw’ and professionals quest for a ‘full’ picture
Authors: Thompson Kellie
Published: January 2012

As there are a number of high‐profile public inquiries into child death tragedies, ‘information sharing’ has now become a moral and political imperative across England and Wales for improving the welfare and protection of children. This paper discusses multi‐agency information practices, at the stage of referral, which were observed and documented in the day‐to‐day practice of child protection work. Drawing on transcribed, professional narrative accounts, a ‘jigsaw’ metaphor is used to describe the process of piecing information together to ascertain a ‘full’ picture of children and families lives. However, these accounts highlight that there is something of a mismatch between the jigsaw, as articulated in the conceptual abstract accounts, and jigsaw practices operating on the ground. It is argued that abstracting professional information practices from situated contexts creates impoverished understandings of these practices. Thus, reported findings in this paper highlight the inherent complexities of jigsaw practices in the ‘everyday’ of child protection work, which challenges objectivist assumptions about a stability of meaning, and further highlight that the ‘endpoint’ of reaching a ‘full’ picture of a child's life is not fixed, nor does it have the same meaning for all professionals, but rather it is a complex process involving sense‐making, translation in context and organizational relevance.
Correlation and process in species distribution models: bridging a dichotomy
Authors: Dormann Carsten F. , Schymanski Stanislaus J. , Cabral Juliano , Chuine Isabelle , Graham Catherine , Hartig Florian , Kearney Michael , Morin Xavier , Römermann Christine , Schröder Boris , Singer Alexander
Published: January 2012

Within the field of species distribution modelling an apparent dichotomy exists between process‐based and correlative approaches, where the processes are explicit in the former and implicit in the latter. However, these intuitive distinctions can become blurred when comparing species distribution modelling approaches in more detail. In this review article, we contrast the extremes of the correlative–process spectrum of species distribution models with respect to core assumptions, model building and selection strategies, validation, uncertainties, common errors and the questions they are most suited to answer. The extremes of such approaches differ clearly in many aspects, such as model building approaches, parameter estimation strategies and transferability. However, they also share strengths and weaknesses. We show that claims of one approach being intrinsically superior to the other are misguided and that they ignore the process–correlation continuum as well as the domains of questions that each approach is addressing. Nonetheless, the application of process‐based approaches to species distribution modelling lags far behind more correlative (process‐implicit) methods and more research is required to explore their potential benefits. Critical issues for the employment of species distribution modelling approaches are given, together with a guideline for appropriate usage. We close with challenges for future development of process‐explicit species distribution models and how they may complement current approaches to study species distributions.
The role of syringic acid in the interaction between oil palm and Ganoderma boninense, the causal agent of basal stem rot
Authors: Chong K. P. , Atong M. , Rossall S.
Published: January 2012

Novel inoculation and assessment methods for Ganoderma boninense infection of oil palm are reported. The involvement of phenolic acids in the interaction was examined. HPLC was used to monitor changes in the concentrations of three specific phenolics: syringic acid (SA), caffeic acid and 4‐hydroxybenzoic acid, identified as the main compounds that accumulated. The work reported here focuses on SA, the most antifungal of the molecules detected. The oil palm cv. AVROS, reported by local planters to be less susceptible than others, showed higher accumulation of SA than cvs Ekona and Calabar. Accumulation was promoted by addition of chitosan to the plant growing medium. By the end of the time‐course, the concentration of SA decreased in the oil palm tissues inoculated with G. boninense, suggesting possible metabolism by the pathogen. This loss was, however, not detected in tissues treated with chitosan alone and was greatly reduced when G. boninense was combined with this polymer. In vitro studies on antifungal activity of SA were done using concentrations ranging from 50 to 110 μg mL−1, those typically recorded in oil palm roots. SA was found to be antifungal (EC50 90–100 μg mL−1). The concentration of SA detected in root tissues, especially in the presence of chitosan, could inhibit growth of G. boninense. The pathogen was shown to degrade SA in vitro. However, at the highest concentration tested, metabolism was greatly delayed, only occurring after a lag phase in pathogen growth. Accumulation of phenolic acids, especially SA, may prove a useful trait in breeding resistant oil palm cultivars.
A new scab‐like disease on apple caused by the formerly saprotrophic fungus Venturia asperata
Authors: Caffier V. , Le Cam B. , Expert P. , Tellier M. , Devaux M. , Giraud M. , Chevalier M.
Published: January 2012

Atypical scab‐like symptoms were reported for the first time in 2007 in the south of France on fruits of apple cultivars carrying the Rvi6 (=Vf) major resistance gene to Venturia inaequalis. With microscopic observations, nucleotide sequence data and pathological tests, it was shown that the causal agent was Venturia asperata. Scanning electron microscopy was used to compare its infection process and conidiogenesis to those of Venturia inaequalis on apple and Venturia pirina on pear. Venturia asperata produced fewer hyphae and fewer spores than the two other Venturia species, and resulted in weaker symptoms. This fungal species was previously described as a saprotroph on apple leaf litter. This is the first report of damage on apple fruits caused by V. asperata. Changes in host and cultural practices may have created a new context favourable for the emergence of this pathogen. It was also detected on symptomless leaves and on overwintered leaves on the ground. Pseudothecia developed on overwintered leaves and released ascospores over a 2‐month period from the end of March until the end of May, suggesting that the fungus is able to survive from season to season. However, it is not yet known if this new disease will establish over coming years and become an emergent disease.