bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controllable ring‐opening copolymerization of L‐lactide and (3S)‐benzyloxymethyl‐(6S)‐methyl‐morpholine‐2,5‐dione initiated by a biogenic compound creatinine acetate
Authors: Pang Zibo , Li Hong , He Peiru , Wang Yuqin , Ren Hongxia , Wang Hao , Zhu X.X. 
Published: June 2012

AbstractRing‐opening copolymerization (ROCP) of L‐lactide (L‐LA) and (3S)‐benzyloxymethyl‐(6S)‐methyl‐morpholine‐2,5‐dione [(3S, 6S)‐BMMD] initiated by creatinine acetate, a biogenic organic compound, was performed in the bulk at 130 °C. The copolymerization was well controlled as evidenced by that both the measured values of number‐average molecular weight (Mn,NMR(OH) and Mn,NMR(COOH)) and serine molar fraction (FBz.ser) of synthesized copolymers were close to the corresponding theoretical values; and that the higher isotacticity of synthesized copolymers (85–86%) and lower racemization degree of the ROCP. After removing O‐benzyls of the copolymers with Et3SiH/Et3N/CH2Cl2 under catalysis of PdCl2, functional biodegradable copolymers of L‐lactic acid (L‐Lac) and L‐Ser with designed molar fraction of serine (Fser 1.35%, 3.57%, 5.41%), narrow molecular weight distribution (polydispersity index 1.10–1.36), and improved hydrophilicity (θstat 82.3–89.6°) were finally obtained. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
What is the relationship between trait anxiety and depressive symptoms, fatigue, and low sleep quality following breast cancer surgery?
Authors: Lockefeer J. P. M. , De Vries J. 
Published: June 2012

AbstractBackgroundDepressive symptoms, fatigue, and low sleep quality are common symptoms during and after breast cancer (BC) treatment. In the present study, the relationship between trait anxiety and these symptoms in a long follow‐up period was examined.MethodsThis was a prospective study. Participants, composed of 163 women with BC and 224 women with benign breast problems (BBPs), completed questionnaires on depressive symptoms, fatigue, and sleep quality before diagnosis and 1, 3, 6, 12, and 24 months after diagnosis (BBP group) or surgical treatment (BC group). In addition, patients completed a questionnaire on trait anxiety before diagnosis.Results and ConclusionsTrait anxiety was the most significant predictor for depressive symptoms (p < 0.001) and lower sleep quality (p = 0.040) at 2‐year follow‐up. For fatigue, fatigue at baseline and trait anxiety together was the most important predictor (p < 0.001). Linear mixed model analyses showed that there was an interaction effect of time with trait anxiety and with diagnosis for depressive symptoms (p = 0.001 and p < 0.001) and fatigue (p = 0.004 and p < 0.001). There was no interaction effect of time with trait anxiety or diagnosis for sleep quality (p = 0.055 and p = 0.225). Together with diagnosis, trait anxiety was an important determinant of depressive symptoms, fatigue, and low sleep quality following diagnosis of BBP or BC and seemed to be a common factor in these persisting symptoms. Copyright © 2012 John Wiley & Sons, Ltd.
Improved microphysical parametrization of drizzle and fog for operational forecasting using the Met Office Unified Model
Authors: Wilkinson Jonathan M. , Porson Aurore N. F. , Bornemann F. Jorge , Weeks Mark , Field Paul R. , Lock Adrian P. 
Published: June 2012

AbstractIn order to improve the forecasting of fog, visibility and drizzle within the Met Office Unified Model, three parametrizations are included in high‐resolution, limited‐area versions of the model. These are (i) improved rainfall speeds; (ii) linking aerosol to the autoconversion scheme; and (iii) a taper curve for cloud droplets near the surface. The results show a better representation of low‐visibility conditions in winter. There is a general reduction in drizzle and a better representation of drizzle depending on whether the air mass is clean or polluted. Summertime occurrences of fog are also reduced and are now under‐forecast, which will require a further investigation to correct. The package described in the paper has been made operational in the 4 and 1.5 km operational forecast versions of the Unified Model during the spring and summer of 2011, showing an improvement in model performance and a reduction in model error. This demonstrates the ability to improve operational NWP forecasts by coupling cloud and aerosol processes. Copyright © 2012 British Crown copyright, the Met Office. Published by John Wiley & Sons Ltd.
E-cadherin and, in Its Absence, N-cadherin Promotes Nanog Expression in Mouse Embryonic Stem Cells via STAT3 Phosphorylation
Authors: Hawkins Kate , Mohamet Lisa , Ritson Sarah , Merry Catherine L. R. , Ward Christopher M. 
Published: June 2012

Abstract
We have recently shown that loss of E-cadherin in mouse embryonic stem cells (mESCs) results in significant alterations to both the transcriptome and hierarchy of pluripotency-associated signaling pathways. Here, we show that E-cadherin promotes kruppel-like factor 4 (Klf4) and Nanog transcript and protein expression in mESCs via STAT3 phosphorylation and that β-catenin, and its binding region in E-cadherin, is required for this function. To further investigate the role of E-cadherin in leukemia inhibitory factor (LIF)-dependent pluripotency, E-cadherin null (Ecad−/−) mESCs were cultured in LIF/bone morphogenetic protein supplemented medium. Under these conditions, Ecad−/− mESCs exhibited partial restoration of cell–cell contact and STAT3 phosphorylation and upregulated Klf4, Nanog, and N-cadherin transcripts and protein. Abrogation of N-cadherin using an inhibitory peptide caused loss of phospho STAT3, Klf4, and Nanog in these cells, demonstrating that N-cadherin supports LIF-dependent pluripotency in this context. We therefore identify a novel molecular mechanism linking E- and N-cadherin to the core circuitry of pluripotency in mESCs. This mechanism may explain the recently documented role of E-cadherin in efficient induced pluripotent stem cell reprogramming.
Fatty Acid Composition of the Brain, Retina, Liver and Adipose Tissue of the Grey Mouse Lemur (Microcebus murinus, Primate)
Authors: Pifferi Fabien , Perret Martine , Guesnet Philippe , Aujard Fabienne , Alessandri Jean‐Marc 
Published: June 2012

AbstractThe particular interest in supplementing human foods with n‐3 fatty acids has arisen from the findings that this series of polyunsaturated fatty acids (PUFA) have an impact on neuronal functions. Indeed vertebrates, including humans, preferentially use docosahexaenoic acid (DHA, 22:6n‐3) over other long‐chain n‐3 PUFA for the genesis of their neuronal and retinal membranes. The grey mouse lemur is a nocturnal prosimian primate originating from Madagascar. The increased use of this omnivorous primate in nutritional studies (chronic caloric restriction, n‐3 fatty acids supplementation), justifies the interest of determining their fatty acids body composition. In the present study, we report the fatty acid composition in lipid classes from the main target tissues (brain, retina, liver and adipose tissue) of six adult mouse lemurs raised under laboratory nutritional conditions. Among the main findings, n‐6‐docosapentaenoic acid (n‐6‐DPA; 22:5n‐6) is very low in the brain cortex and retina, whereas there is a very high accumulation of docosahexaenoic acid (DHA, 22:6n‐3) in the neural tissues compared to liver and plasma. In particular, DHA accounts for about one half of the total fatty acids in the retina ethanolamine glycerophospholipids. This high concentration clearly indicates that DHA is efficiently transferred from blood lipids to the outer segment of the mouse lemur retina. We conclude that the mouse lemur n‐3 PUFA metabolism efficiently drives DHA to neural tissues, through the blood–brain barrier and the blood–retina barrier.
Minimally Invasive Distal Metatarsal Osteotomy in the Treatment of Primary Metatarsalgia
Authors: Tsz-Cheung Wong , Siu-Wah Kong 
Published: June 2012

Introduction Metatarsalgia is a common presentation to orthopaedic surgeons. Primary metatarsalgia is caused by chronic imbalance in weight-bearing distribution across the forefoot or between the forefoot and midfoot. Management of primary matatarsalgia is mainly conservative. Metatarsal osteotomy can be considered if conservative treatment has failed. Minimally Invasive Distal Metatarsal Osteotomy technique can achieve satisfactory outcomes. Method and material From April 2009 to May 2010, we performed distal metatarsal osteotomies using minimally invasive technique in four patients (3 females and 1 male). Stab incision was made, and metatarsal neck osteotomy was achieved with a burr. No internal fixation was performed. Full weight bearing walking was allowed on the first day after operation. Radiographs were taken before and after operations, and forefoot scores were documented by using the American College of Foot and Ankle Surgeons score. Result The average age of the four patients was 55.8 years (range 46–62). The average operation time was 40 minutes (range 24–65). Blood loss was minimal in all patients. The length of hospital stay was 4 days in all patients. All osteotomies healed uneventfully in 4 months. There was no major complication. The average metatarsal index decreased from 3.125 to 2.8 mm, and the average first/second intermetatarsal angle on lateral X-ray decreased from 6° to 2°. The average American College of Foot and Ankle Surgeons score improved from 66.25 (range 56–74) preoperatively to 96.25 (range 93–99) postoperatively. Conclusion Minimally Invasive Distal Metatarsal Osteotomy without internal fixation is a viable alternative to open procedure in the management of recalcitrant metatarsalgia.
PROTO-UTO-AZTECAN AS A MESOAMERICAN LANGUAGE
Authors: Hill Jane H. 
Published: June 2012

AbstractNew evidence is presented in support of the hypothesis that Proto-Uto-Aztecan (PUA) was spoken by a community of cultivators in the northwest quadrant of Mesoamerica. New cognates are presented in support of reconstructions of meanings of PUA words within the maize-cultivation domain. It is argued that some of this vocabulary was borrowed from an Otomanguean language, perhaps Proto-Oto-Chinantecan. In addition, it is argued that PUA included a vocabulary in the domain of pottery. New reconstructions of a pottery lexicon are proposed, and arguments that this vocabulary was borrowed from an Otomanguean language are presented. If PUA speakers were familiar with pottery, then PUA was spoken as late as 4400–4100b.p.and did not begin to break up into its daughter languages until after knowledge of pottery reached its speakers.
Ozone Disinfection of Eggs from Gilthead Seabream Sparus aurata, Sea Bass Dicentrarchus labrax, Red Porgy, and Common Dentex Dentex dentex
Authors: Can Erkan , Karacalar Ulviye , Saka Sahin , Firat Kursat 
Published: June 2012

Abstract
The risk of fish pathogen transmission via eggs can be reduced by disinfection in ozonated seawater. The aim of this study was to determine the suitable conditions for ozone disinfection of the eggs of gilthead seabream Sparus aurata, sea bass Dicentrarchus labrax, red porgy Pagrus pagrus, and common dentex Dentex dentex. The eggs were disinfected with a concentration (C) of 0.5 mg of ozone/L of water at four different exposure times (T = 2, 4, 8, and 16 min). The hatching rate was determined in triplicate for each treatment. Bacterial colonies were counted on tryptic soy agar and thiosulfate–citrate–bile salts–sucrose agar. At the end of the experiment, bacterial load and hatching rate were assessed together to determine the optimal ozone treatment values, which were estimated in CT units (i.e., C [= 0.5 mg/L] × T [min]). Optimal values were CT 2–4 (T = 4–8 min; 18°C) for gilthead seabream and red porgy, CT 2 (T = 4 min; 18°C) for common dentex, and CT 4 (T = 8 min; 15°C) for sea bass.
Received April 12, 2011; accepted February 2, 2012
Role of Ti/Al relative thickness in the formation mechanism of Ti/Al/Ni/Au Ohmic contacts to AlGaN/GaN heterostructures
Authors: Kong Xin , Wei Ke , Liu Guoguo , Liu Xinyu 
Published: June 2012

Abstract
In this work, Ti/Al/Ni/Au Ohmic contacts to AlGaN/GaN heterostructures with different Ti/Al relative thicknesses were fabricated and characterized. A contact with Ti/Al relative thickness of 20/180 nm presented non-linear current–voltage response and bumpy surface morphology, while a contact with Ti/Al relative thickness of 20/120 nm demonstrated low contact resistance and flat surface morphology. We verify the existence of two electron transport mechanisms, namely carrier tunnelling and direct link through a TiN conductive pathway, by scanning transmission electron microscopy and corresponding electron dispersive x-ray spectra. Ti/Al relative thickness exerts a decisive influence on the alloy reaction processing. Superfluous Al consumes Ti, thus impeding the formation of low-resistance TiN and N vacancies. As a result, electron transport is restricted by the low-efficiency tunnelling mechanism. At the same time, the consumption of Ni causes damage to its blocking effect and arouses the free diffusion of metal alloys, which should be responsible for the rough surface.
Numerical simulation for production of O and N radicals in an atmospheric-pressure streamer discharge
Authors: Komuro Atsushi , Ono Ryo , Oda Tetsuji 
Published: June 2012

Abstract
A streamer discharge model is developed to analyse the characteristics of a pulsed positive streamer discharge in point-to-plane electrodes filled with oxygen–nitrogen mixed gas at room temperature and atmospheric pressure. In this paper we study the mechanisms of O and N radical production in an atmospheric-pressure streamer discharge. To confirm the validity of the simulation model, the discharge emission of light and the discharge current are compared with experimental data at several voltages in gas mixtures with 2–20% oxygen concentrations. The calculated streak picture and the axial distribution of streamer luminous intensity are in good agreement with our previous experimental results. After demonstrating the reliability of the model, we performed a numerical study on radical production by the streamer discharge. The experimentally obtained axial distributions of oxygen radical production in O2(20%)/N2 and nitrogen radical production in O2(2%)/N2 are successfully reproduced in our simulation. For the production of nitrogen radicals, two-step dissociation through the vibrationally excited states is predominant.
Guiding microwave radiation using laser-induced filaments: the hollow conducting waveguide concept
Authors: Alshershby Mostafa , Hao Zuoqiang , Lin Jingquan 
Published: June 2012

Abstract
A microwave waveguide that consists of a set of laser plasma filaments produced in air by the propagation of femtosecond laser pulses is investigated according to the hollow conducting waveguide concept. The conductivity, skin depth of the electromagnetic waves in this plasma waveguide and the energy required to excite such a waveguide are calculated for different possible configurations. A hollow conducting plasma waveguide is shown to support guided modes of electromagnetic radiation from millimetre to centimetre wavelength range. Our calculations show that, under the concept of conducting waveguide, it is more suitable to use the TE01 mode rather than TE11 to achieve an extended attenuation length. The attenuation length of the low-loss mode TE01 is shown to be dependent on the geometry of the plasma waveguides, the operating frequency and the plasma effective electron density. The effect of the plasma wall density spread on TE01 propagation is evaluated. Using the hollow conducting plasma waveguide operating in TE01 mode, an enhancement of microwave transmission over both free space propagation and dielectric plasma waveguide is obtained.
The effect of progressively increasing lithium coatings on plasma discharge characteristics, transport, edge profiles and ELM stability in the National Spherical Torus Experiment
Authors: Maingi R. , Boyle D.P. , Canik J.M. , Kaye S.M. , Skinner C.H. , Allain J.P. , Bell M.G. , Bell R.E. , Gerhardt S.P. , Gray T.K. , Jaworski M.A. , Kaita R. , Kugel H.W. , LeBlanc B.P. , Manickam J. , Mansfield D.K. , Menard J.E. , Osborne T.H. , Raman R. , Roquemore A.L. , Sabbagh S.A. , Snyder P.B. , Soukhanovskii V.A. 
Published: June 2012

Abstract
Lithium wall coatings have been shown to reduce recycling, suppress edge-localized modes (ELMs), and improve energy confinement in the National Spherical Torus Experiment (NSTX). Here we document the effect of gradually increasing lithium wall coatings on the discharge characteristics, with the reference ELMy discharges obtained in boronized, i.e. non-lithiated conditions. We observed a continuous but not quite monotonic reduction in recycling and improvement in energy confinement, a gradual alteration of edge plasma profiles, and slowly increasing periods of ELM quiescence. The measured edge plasma profiles during the lithium-coating scan were simulated with the SOLPS code, which quantified the reduction in divertor recycling coefficient from ∼98% to ∼90%. The reduction in recycling and fuelling, coupled with a drop in the edge particle transport rate, reduced the average edge density profile gradient, and shifted it radially inwards from the separatrix location. In contrast, the edge electron temperature (T
e) profile was unaffected in the H-mode pedestal steep gradient region within the last 5% of normalized poloidal flux, ψ
N ; however, the T
e gradient became steeper at the top of the H-mode pedestal for 0.8 < ψ
N < 0.94 with lithium coatings. The peak pressure gradients were comparable during ELMy and ELM-free phases, but were shifted away from the separatrix in the ELM-free discharges, which is stabilizing to the current-driven instabilities thought to be responsible for ELMs in NSTX.
Empirical Bayes conditional independence graphs for regulatory network recovery
Authors: Mahdi Rami , Madduri Abishek S. , Wang Guoqing , Strulovici-Barel Yael , Salit Jacqueline , Hackett Neil R. , Crystal Ronald G. , Mezey Jason G. 
Published: June 2012

AbstractMotivation: Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense regions of a network, a consequence of both computational complexity and unreliable parameter estimation when sample size is small. As a result, identification of hub genes is of special difficulty for these methods.Methods: We present a new algorithm, Empirical Light Mutual Min (ELMM), for large network reconstruction that has properties well suited for recovery of graphs with high-degree nodes. ELMM reconstructs the undirected graph of a regulatory network using empirical Bayes conditional independence testing with a heuristic relaxation of independence constraints in dense areas of the graph. This relaxation allows only one gene of a pair with a putative relation to be aware of the network connection, an approach that is aimed at easing multiple testing problems associated with recovering densely connected structures.Results: Using in silico data, we show that ELMM has better performance than commonly used network inference algorithms including GeneNet, ARACNE, FOCI, GENIE3 and GLASSO. We also apply ELMM to reconstruct a network among 5492 genes expressed in human lung airway epithelium of healthy non-smokers, healthy smokers and individuals with chronic obstructive pulmonary disease assayed using microarrays. The analysis identifies dense sub-networks that are consistent with known regulatory relationships in the lung airway and also suggests novel hub regulatory relationships among a number of genes that play roles in oxidative stress and secretion.Availability and implementation: Software for running ELMM is made available at http://mezeylab.cb.bscb.cornell.edu/Software.aspx.Contact: ramimahdi@yahoo.com or jgm45@cornell.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations
Authors: Gray Vanessa E. , Kukurba Kimberly R. , Kumar Sudhir 
Published: June 2012

Abstract
Summary: Site-directed mutagenesis is frequently used by scientists to investigate the functional impact of amino acid mutations in the laboratory. Over 10 000 such laboratory-induced mutations have been reported in the UniProt database along with the outcomes of functional assays. Here, we explore the performance of state-of-the-art computational tools (Condel, PolyPhen-2 and SIFT) in correctly annotating the function-altering potential of 10 913 laboratory-induced mutations from 2372 proteins. We find that computational tools are very successful in diagnosing laboratory-induced mutations that elicit significant functional change in the laboratory (up to 92% accuracy). But, these tools consistently fail in correctly annotating laboratory-induced mutations that show no functional impact in the laboratory assays. Therefore, the overall accuracy of computational tools for laboratory-induced mutations is much lower than that observed for the naturally occurring human variants. We tested and rejected the possibilities that the preponderance of changes to alanine and the presence of multiple base-pair mutations in the laboratory were the reasons for the observed discordance between the performance of computational tools for natural and laboratory mutations. Instead, we discover that the laboratory-induced mutations occur predominately at the highly conserved positions in proteins, where the computational tools have the lowest accuracy of correct prediction for variants that do not impact function (neutral). Therefore, the comparisons of experimental-profiling results with those from computational predictions need to be sensitive to the evolutionary conservation of the positions harboring the amino acid change.
Contact: s.kumar@asu.edu
Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior
Authors: Osorio Sonia , Alba Rob , Nikoloski Zoran , Kochevenko Andrej , Fernie Alisdair R. , Giovannoni James J. 
Published: June 2012

AbstractIntegrative comparative analyses of transcript and metabolite levels from climacteric and nonclimacteric fruits can be employed to unravel the similarities and differences of the underlying regulatory processes. To this end, we conducted combined gas chromatography-mass spectrometry and heterologous microarray hybridization assays in tomato (Solanum lycopersicum; climacteric) and pepper (Capsicum chilense; nonclimacteric) fruits across development and ripening. Computational methods from multivariate and network-based analyses successfully revealed the difference between the covariance structures of the integrated data sets. Moreover, our results suggest that both fruits have similar ethylene-mediated signaling components; however, their regulation is different and may reflect altered ethylene sensitivity or regulators other than ethylene in pepper. Genes involved in ethylene biosynthesis were not induced in pepper fruits. Nevertheless, genes downstream of ethylene perception such as cell wall metabolism genes, carotenoid biosynthesis genes, and the never-ripe receptor were clearly induced in pepper as in tomato fruit. While signaling sensitivity or actual signals may differ between climacteric and nonclimacteric fruit, the evidence described here suggests that activation of a common set of ripening genes influences metabolic traits. Also, a coordinate regulation of transcripts and the accumulation of key organic acids, including malate, citrate, dehydroascorbate, and threonate, in pepper fruit were observed. Therefore, the integrated analysis allows us to uncover additional information for the comprehensive understanding of biological events relevant to metabolic regulation during climacteric and nonclimacteric fruit development.