bluuebunny/crossref_metadata_2025_split huggingface dataset:
Racial/ethnic and sociodemographic factors associated with micronutrient intakes and inadequacies among pregnant women in an urban US population
Authors: Brunst Kelly J , Wright Robert O , DiGioia Kimberly , Enlow Michelle Bosquet , Fernandez Harriet , Wright Rosalind J , Kannan Srimathi 
Published: December 2013

AbstractObjectiveTo assess sociodemographic correlates of micronutrient intakes from food and dietary supplements in an urban, ethnically diverse sample of pregnant women in the USA.DesignCross-sectional analyses of data collected using a validated semi-quantitative FFQ. Associations between racial, ethnic and sociodemographic factors and micronutrient intakes were examined using logistic regression controlling for pre-pregnancy BMI, maternal age and smoking status.SettingPrenatal clinics, Boston, MA, USA.SubjectsAnalyses included pregnant women (n 274) in the PRogramming of Intergenerational Stress Mechanisms (PRISM) study, an urban longitudinal cohort designed to examine how stress influences respiratory health in children when controlling for other environmental exposures (chemical stressors, nutrition).ResultsHigh frequencies of vitamin E (52 %), Mg (38 %), Fe (57 %) and vitamin D (77 %) inadequacies as well as suboptimal intakes of choline (95 %) and K (99 %) were observed. Factors associated with multiple antioxidant inadequacies included being Hispanic or African American, lower education and self-reported economic-related food insecurity. Hispanics had a higher prevalence of multiple methyl-nutrient inadequacies compared with African Americans; both had suboptimal betaine intakes and higher odds for vitamin B6 and Fe inadequacies compared with Caucasians. Nearly all women (98 %) reported Na intakes above the tolerable upper limit; excessive intakes of Mg (35 %), folate (37 %) and niacin (38 %) were also observed. Women reporting excessive intakes of these nutrients were more likely Caucasian or Hispanic, more highly educated, US-born and did not report food insecurity.ConclusionsRacial/ethnic and other sociodemographic factors should be considered when tailoring periconceptional dietary interventions for urban ethnic women in the USA.
Welfare implications of product choice regulation during the payout phase of funded pensions
Authors: HORNEFF VANYA , KASCHÜTZKE BARBARA , MAURER RAIMOND , ROGALLA RALPH 
Published: December 2013

AbstractIn many countries, governmental support for funded old-age programmes comes at the cost of at least partial mandatory annuitisation of accumulated assets in retirement. We survey regulatory frameworks for the payout phase of funded pension systems in seven European countries and the US and study the influence of mandatory annuitisation on the welfare of both rational and behaviourally influenced individuals using a dynamic life-cycle model. We show that mandatory immediate full annuitisation of retirement assets will reduce rational individuals’ certainty equivalent pension wealth by up to 54%. Softening the strict immediate annuitisation requirements along the line of regulatory realities in some of the surveyed countries reduces utility losses considerably. Behaviourally restricted individuals can benefit from full annuitisation at retirement, but generally they will also prefer more flexible regulation.
Crop physiological response across the Chicago metropolitan region: Developing recommendations for urban and peri-urban farmers in the North Central US
Authors: Wagstaff Ross K. , Wortman Sam E. 
Published: December 2013

AbstractDespite the surge of interest in urban agriculture, there have been few studies that address the biophysical challenges and opportunities of food production in urban environments. This study aims to determine the relative influence of atmospheric pollutants and microclimatic factors on the physiological response and productivity of vegetable crops across an urban-to-rural latitudinal transect in the greater Chicago metropolitan region. Data collected at each of six sites include continuous measures of atmospheric pollutants and microclimatic factors, and biweekly measures of physiological response and yield of various vegetable crops and cultivars. Preliminary data collected in early 2013 suggest that there is substantial variability in environmental factors and crop yield across this urban-to-rural transect. Results of this study will provide a scientific basis for crop adaptation to the urban environment and establish practical crop and cultivar recommendations for urban and peri-urban farmers in the North Central US.
Human herpesvirus 6 (HHV-6) alters E2F1/Rb pathways and utilizes the E2F1 transcription factor to express viral genes
Authors: Sharon Eyal , Volchek Ludmila , Frenkel Niza 
Published: December 2013

Significance
Human herpesvirus 6A (HHV-6A) and HHV-6B are prevalent viruses causing mild up to grave lethal diseases. Viruses modulate cell-cycle progression so as to use cellular replication machinery. The retinoblastoma (Rb) tumor suppressor protein represses the E2F1 transcription factor. This induces entry to the S phase, enabling efficient replication. Viruses employ different mechanisms modulating the Rb–E2F1 pathway. However, the mechanism(s) used by HHV-6 are unknown. We have found that HHV-6A infection induced Rb degradation while producing elevated levels of active E2F1 and DP1. Surprisingly, several cellular E2F target genes were not up-regulated, whereas active E2F1 was used to transcribe selected viral genes containing the E2F binding site in their promoters. These viral genes play significant roles in viral DNA synthesis.
Identifying the location and importance of spawning sites of Western Baltic herring using a particle backtracking model
Authors: Bauer R. K. , Gräwe U. , Stepputtis D. , Zimmermann C. , Hammer C. 
Published: December 2013

Abstract
The recruitment success of some herring stocks fluctuates strongly, and apparently, success is often already determined during the early life stages, i.e. before metamorphosis. In studying the survival of early life stages and its affecting factors, particularly those during the egg stage, it is crucial to examine the processes at the spawning sites, which often cannot be explored directly. A recent decline in the recruitment of Western Baltic spring-spawning herring (WBSSH) increases the urgency of filling the knowledge gap for this stock, especially because one bottleneck in the recruitment seems to occur before hatching. We examined the successful 2003–2009 spawning sites of WBSSH in the main spawning ground, the Greifswalder Bodden lagoon. Instead of using common techniques such as diving or underwater videography, which are usually unsuitable for mapping large areas, we applied a model approach. We tracked herring larvae at length 6–10 mm, recorded by larval surveys during March–June of the respective years, back to their hatching sites using a Lagrangian particle backtracking model. We compared the spawning areas identified by the model with the results of earlier field studies; however, we also analysed variations between years, larval length groups, and different applied growth models, which are needed to define hatch-dates. Although spawning sites could not be identified with high precision because of the strong diffusion in the area studied, results indicate that larvae up to 10 mm length are caught near their hatching sites. However, the location of successful spawning sites varied largely between years, with the main hatching sites situated in the Strelasund and the eastern entrance of the lagoon. This may reflect variations in spawning-site selection or quality. A better knowledge of the locations and relative importance of, and the processes occurring on, the different spawning sites will provide an important contribution to the sustainable management of this commercially valuable herring stock.
Bioinformatic analysis of the protein/DNA interface
Authors: Schneider Bohdan , Černý Jiří , Svozil Daniel , Čech Petr , Gelly Jean-Christophe , de Brevern Alexandre G. 
Published: December 2013

AbstractTo investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271–287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690–3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into ‘interaction matrices’ revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.
Piezotronics and piezo-phototronics: fundamentals and applications
Authors: Wang Zhong Lin , Wu Wenzhuo 
Published: December 2013

Abstract
Technology advancement that can provide new solutions and enable augmented capabilities to complementary metal–oxide–semiconductor (CMOS)-based technology, such as active and adaptive interaction between machine and human/ambient, is highly desired. Piezotronic nanodevices and integrated systems exhibit potential in achieving these application goals. Utilizing the gating effect of piezopotential over carrier behaviors in piezoelectric semiconductor materials under externally applied deformation, the piezoelectric and semiconducting properties together with optoelectronic excitation processes can be coupled in these materials for the investigation of novel fundamental physics and the implementation of unprecedented applications. Piezopotential is created by the strain-induced ionic polarization in the piezoelectric semiconducting crystal. Piezotronics deal with the devices fabricated using the piezopotential as a ‘gate’ voltage to tune/control charge-carrier transport across the metal–semiconductor contact or the p–n junction. Piezo-phototronics is to use the piezopotential for controlling the carrier generation, transport, separation and/or recombination for improving the performance of optoelectronic devices. This review intends to provide an overview of the rapid progress in the emerging fields of piezotronics and piezo-phototronics. The concepts and results presented in this review show promises for implementing novel nano-electromechanical devices and integrating with micro/nano-electromechanical system technology to achieve augmented functionalities to the state-of-the-art CMOS technology that may find applications in the human–machine interfacing, active flexible/stretchable electronics, sensing, energy harvesting, biomedical diagnosis/therapy, and prosthetics.
New insights in the formation of polyhydroxyalkanoate granules (carbonosomes) and novel functions of poly(3‐hydroxybutyrate)
Authors: Jendrossek Dieter , Pfeiffer Daniel 
Published: December 2013

SummaryThe metabolism of polyhydroxybutyrate (PHB) and related polyhydroxyalkanoates (PHAs) has been investigated by many groups for about three decades, and good progress was obtained in understanding the mechanisms of biosynthesis and biodegradation of this class of storage molecules. However, the molecular events that happen at the onset of PHB synthesis and the details of the initiation of PHB/PHA granule formation, as well as the complex composition of the proteinaceous surface layer of PHB/PHA granules, have only recently come into the focus of research and were not reviewed yet. In this contribution, we summarize the progress in understanding the initiation and formation of the PHA granule complex at the example of Ralstonia eutropha H16 (model organism of PHB‐accumulating bacteria). Where appropriate, we include information on PHA granules of Pseudomonas putida as a representative species for medium‐chain‐length PHA‐accumulating bacteria. We suggest to replace the previous micelle mode of PHB granule formation by the Scaffold Model in which the PHB synthase initiation complex is bound to the bacterial nucleoid. In the second part, we highlight data on other forms of PHB: oligo‐PHB with ≈100 to 200 3‐hydroxybutyrate (3HB) units and covalently bound PHB (cPHB) are unrelated in function to storage PHB but are presumably present in all living organisms, and therefore must be of fundamental importance.
Isolation and characterization of lipid rafts in Emiliania huxleyi: a role for membrane microdomains in host–virus interactions
Authors: Rose Suzanne L. , Fulton James M. , Brown Christopher M. , Natale Frank , Van Mooy Benjamin A. S. , Bidle Kay D. 
Published: December 2013

SummaryCoccolithoviruses employ a suite of glycosphingolipids (GSLs) to successfully infect the globally important coccolithophore Emiliania huxleyi. Lipid rafts, chemically distinct membrane lipid microdomains that are enriched in GSLs and are involved in sensing extracellular stimuli and activating signalling cascades through protein–protein interactions, likely play a fundamental role in host–virus interactions. Using combined lipidomics, proteomics and bioinformatics, we isolated and characterized the lipid and protein content of lipid rafts from control E. huxleyi cells and those infected with EhV86, the type strain for Coccolithovirus. Lipid raft‐enriched fractions were isolated and purified as buoyant, detergent‐resistant membranes (DRMs) in OptiPrep density gradients. Transmission electron microscopy of vesicle morphology, polymerase chain reaction amplification of the EhV major capsid protein gene and immunoreactivity to flotillin antisera served as respective physical, molecular and biochemical markers. Subsequent lipid characterization of DRMs via high performance liquid chromatography‐triple quadrapole mass spectrometry revealed four distinct GSL classes. Parallel proteomic analysis confirmed flotillin as a major lipid raft protein, along with a variety of proteins affiliated with host defence, programmed cell death and innate immunity pathways. The detection of an EhV86‐encoded C‐type lectin‐containing protein confirmed that infection occurs at the interface between lipid rafts and cellular stress/death pathways via specific GSLs and raft‐associated proteins.
Evaluation of a Headspace Solid‐Phase Microextraction Method for the Analysis of Ignitable Liquids in Fire Debris
Authors: Fettig Ina , Krüger Simone , Deubel Jan H. , Werrel Martin , Raspe Tina , Piechotta Christian 
Published: December 2013

AbstractThe chemical analysis of fire debris represents a crucial part in fire investigations to determine the cause of a fire. A headspace solid‐phase microextraction (HS‐SPME) procedure for the detection of ignitable liquids in fire debris using a fiber coated with a mixture of three different sorbent materials (Divinylbenzene/Carboxen/Polydimethylsiloxane, DVB/CAR/PDMS) is described. Gasoline and diesel fuel were spiked upon a preburnt matrix (wood charcoal), extracted and concentrated with HS‐SPME and then analyzed with gas chromatography/mass spectrometry (GC/MS). The experimental conditions—extraction temperature, incubation and exposure time—were optimized. To assess the applicability of the method, fire debris samples were prepared in the smoke density chamber (SDC) and a controlled‐atmosphere cone calorimeter. The developed methods were successfully applied to burnt particleboard and carpet samples. The results demonstrate that the procedure that has been developed here is suitable for detecting these ignitable liquids in highly burnt debris.
Engineering of a green‐light inducible gene expression system in Synechocystis sp. PCC6803
Authors: Abe Koichi , Miyake Kotone , Nakamura Mayumi , Kojima Katsuhiro , Ferri Stefano , Ikebukuro Kazunori , Sode Koji 
Published: December 2013

SummaryIn order to construct a green‐light‐regulated gene expression system for cyanobacteria, we characterized a green‐light sensing system derived from Synechocystis sp. PCC6803, consisting of the green‐light sensing histidine kinase CcaS, the cognate response regulator CcaR, and the promoter of cpcG2 (PcpcG2). CcaS and CcaR act as a genetic controller and activate gene expression from PcpcG2 with green‐light illumination. The green‐light induction level of the native PcpcG2 was investigated using GFPuv as a reporter gene inserted in a broad‐host‐range vector. A clear induction of protein expression from native PcpcG2 under green‐light illumination was observed; however, the expression level was very low compared with Ptrc, which was reported to act as a constitutive promoter in cyanobacteria. Therefore, a Shine‐Dalgarno‐like sequence derived from the cpcB gene was inserted in the 5′ untranslated region of the cpcG2 gene, and the expression level of CcaR was increased. Thus, constructed engineered green‐light sensing system resulted in about 40‐fold higher protein expression than with the wild‐type promoter with a high ON/OFF ratio under green‐light illumination. The engineered green‐light gene expression system would be a useful genetic tool for controlling gene expression in the emergent cyanobacterial bioprocesses.
Achieving consensus in ultrasonography synovitis scoring in rheumatoid arthritis
Authors: Cheung Peter P. , Kong Kok Ooi , Chew Li‐Ching , Chia Faith L. , Law Weng Giap , Lian Tsui Yee , Tan York Kiat , Cheng Yew Kuang 
Published: December 2013

AbstractObjectiveUltrasonography is sensitive for synovitis detection but interobserver variation in both acquisition and image interpretation is still a concern. The objective was to assess if a short collegiate consensus would improve inter‐observer reliability in scoring of synovitis.MethodsEight rheumatologists (Singapore) participated in a 1‐day consensus meeting divided into: (i) still‐image interpretation and consensus followed by; (ii) image acquisition and interpretation, according to definitions and synovitis scoring rules endorsed by Outcome Measures in Rheumatology (OMERACT) and TUI (Targeted Ultrasound Initiative). Interobserver reliability of semiquantitative scoring in B‐mode, Power Doppler (PDUS) and European League Against Rheumatism (EULAR)‐OMERACT PDUS composite score was assessed by intraclass correlation co‐efficient (ICC). Agreement at the joint region level was calculated using prevalence‐adjusted‐biased‐adjusted‐kappa (PABAK).ResultsFor B‐mode still images, ICC was good at 0.75 (95% CI 0.66–0.82) while for PDUS images this was excellent at ICC = 0.88 (95% CI 0.83–0.92) with ICC improving by 12% for B‐mode and 13% for PDUS respectively. During image acquisition and interpretation, B‐mode scoring showed ICC = 0.75 (95% CI 0.66–0.84) while for PDUS the ICC was lower at 0.59 (95% CI 0.48–0.72). The ICC for OMERACT PDUS composite synovitis scoring was good at 0.77 (95% CI 0.68–0.85). At the joint level, agreement varied with PABAK being excellent in the small joints of the hands but poor to fair in the wrists, elbows, ankles and metatarsophalangeal joints, and no agreement at the knees (PABAK range −0.34 to 0.85).ConclusionA consensus meeting was useful in improving interobserver variation in US synovitis scoring of still images, but image acquisition and interpretation especially in non‐hand joints require further standardization.
Predicting local and non‐local effects of resources on animal space use using a mechanistic step selection model
Authors: Potts Jonathan R. , Bastille‐Rousseau Guillaume , Murray Dennis L. , Schaefer James A. , Lewis Mark A. 
Published: December 2013

Summary

Predicting space use patterns of animals from their interactions with the environment is fundamental for understanding the effect of habitat changes on ecosystem functioning. Recent attempts to address this problem have sought to unify resource selection analysis, where animal space use is derived from available habitat quality, and mechanistic movement models, where detailed movement processes of an animal are used to predict its emergent utilization distribution. Such models bias the animal's movement towards patches that are easily available and resource‐rich, and the result is a predicted probability density at a given position being a function of the habitat quality at that position. However, in reality, the probability that an animal will use a patch of the terrain tends to be a function of the resource quality in both that patch and the surrounding habitat.

We propose a mechanistic model where this non‐local effect of resources naturally emerges from the local movement processes, by taking into account the relative utility of both the habitat where the animal currently resides and that of where it is moving. We give statistical techniques to parametrize the model from location data and demonstrate application of these techniques to GPS location data of caribou (Rangifer tarandus) in Newfoundland.

Steady‐state animal probability distributions arising from the model have complex patterns that cannot be expressed simply as a function of the local quality of the habitat. In particular, large areas of good habitat are used more intensively than smaller patches of equal quality habitat, whereas isolated patches are used less frequently. Both of these are real aspects of animal space use missing from previous mechanistic resource selection models.

Whilst we focus on habitats in this study, our modelling framework can be readily used with any environmental covariates and therefore represents a unification of mechanistic modelling and step selection approaches to understanding animal space use.