bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prescont: Predicting protein‐protein interfaces utilizing four residue properties
Authors: Zellner Hermann , Staudigel Martin , Trenner Thomas , Bittkowski Meik , Wolowski Vincent , Icking Christian , Merkl Rainer 
Published: September 2011

AbstractAn important task of computational biology is to identify those parts of a polypeptide chain, which are involved in interactions with other proteins. For this purpose, we have developed the program PresCont, which predicts in a robust manner amino acids that constitute protein‐protein interfaces (PPIs). PresCont reaches state‐of‐the‐art classification quality on the basis of only four residue properties that can be readily deduced from the 3D structure of an individual protein and a multiple sequence alignment (MSA) composed of homologs. The core of PresCont is a support vector machine, which assesses solvent‐accessible surface area, hydrophobicity, conservation, and the local environment of each amino acid on the protein surface. For training and performance testing, we compiled three nonoverlapping datasets consisting of permanently formed or transient complexes, respectively. A comparison with SPPIDER, ProMate, and meta‐PPISP showed that PresCont compares favorably with these highly sophisticated programs, and that its prediction quality is less dependent on the type of protein complex being considered. This balance is due to a mutual compensation of classification weaknesses observed for individual properties: For PPIs of permanent complexes, solvent‐accessible surface and hydrophobicity contribute most to classification quality, for PPIs of transient complexes, the assessment of the local environment is most significant. Moreover, we show that for permanent complexes a segmentation of PPIs into core and rim residues has only a moderate influence on prediction quality. PresCont is available as a web service at http://www‐bioinf.uni‐regensburg.de/. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Urbach tail and bandgap analysis in near stoichiometric LiNbO3 crystals
Authors: Bhatt R. , Bhaumik I. , Ganesamoorthy S. , Karnal A. K. , Swami M. K. , Patel H. S. , Gupta P. K. 
Published: September 2011

AbstractEnergy of the indirect and direct optical bandgap of near‐stoichiometric lithium niobate (nSLN) crystals is evaluated by optical absorption measurement. The value of the indirect bandgap (3.95 eV) is consistent with the earlier reports. However, the direct bandgap energy of 4.12 eV is higher than the previously reported experimental value (3.68 eV). The direct bandgap energy obtained here is closer to the recent theoretical value estimated by Thierfelder et al. [Phys. Status Solidi C 7, 362 (2010)] in comparison to the previously predicted value by Ching et al. [Phys. Rev. B 50, 1992 (1994)]. The phonons involved in the indirect allowed transitions have energies ∼85 meV (685 cm−1) and are identified as the E(TO9) and E(LO8) optical phonon modes from the Raman scattering measurement.
Evidence for Fe2+ in Wurtzite Coordination: Iron Doping Stabilizes ZnO Nanoparticles
Authors: Xiao Jianping , Kuc Agnieszka , Pokhrel Suman , Schowalter Marco , Parlapalli Satyam , Rosenauer Andreas , Frauenheim Thomas , Mädler Lutz , Pettersson Lars G. M. , Heine Thomas 
Published: September 2011

AbstractFirst‐principles calculations are used to investigate the structural and electronic properties of Fe‐doped ZnO nanoparticles. Based on extensive validation studies surveying various density functionals, the hybrid functional PBE0 is employed to calculate the structures, formation energies, and electronic properties of Fe in ZnO with Fe concentrations of 6.25, 12.5, and 18.75 at%. Substitution of Zn by Fe, zinc vacancies, and interstitial oxygen defects is studied. High‐resolution inner‐shell electron energy loss spectroscopy measurements and X‐ray absorption near‐edge structure calculations of Fe and O atoms are performed. The results show that Fe‐doped ZnO nanoparticles are structurally and energetically more stable than the isolated FeO (rocksalt) and ZnO (wurtzite) phases. The Fe dopants distribute homogeneously in ZnO nanoparticles and do not significantly alter the host ZnO lattice parameters. Simulations of the absorption spectra demonstrate that Fe2+ dominates in the Fe‐doped ZnO nanoparticles reported recently, whereas Fe3+ is present only as a trace.
Nanodiamond as a Vector for siRNA Delivery to Ewing Sarcoma Cells
Authors: Alhaddad Anna , Adam Marie‐Pierre , Botsoa Jacques , Dantelle Géraldine , Perruchas Sandrine , Gacoin Thierry , Mansuy Christelle , Lavielle Solange , Malvy Claude , Treussart François , Bertrand Jean‐Rémi 
Published: September 2011

AbstractThe ability of diamond nanoparticles (nanodiamonds, NDs) to deliver small interfering RNA (siRNA) into Ewing sarcoma cells is investigated with a view to the possibility of in‐vivo anticancer nucleic‐acid drug delivery. siRNA is adsorbed onto NDs that are coated with cationic polymer. Cell uptake of NDs is demonstrated by taking advantage of the NDs’ intrinsic fluorescence from embedded color‐center defects. Cell toxicity of these coated NDs is shown to be low. Consistent with the internalization efficacy, a specific inhibition of EWS/Fli‐1 gene expression is shown at the mRNA and protein level by the ND‐vectorized siRNA in a serum‐containing medium.
A Preoperative Predictive Scoring System for Postoperative Pancreatic Fistula after Pancreaticoduodenectomy
Authors: Yamamoto Yusuke , Sakamoto Yoshihiro , Nara Satoshi , Esaki Minoru , Shimada Kazuaki , Kosuge Tomoo 
Published: September 2011

AbstractBackgroundPostoperative pancreatic fistula (POPF) remains a leading cause of morbidity after pancreaticoduodenectomy (PD). In the present study we sought to establish a preoperative scoring system with which to predict this complication.Patients and methodsThe clinical records of 387 consecutive patients who underwent PD for periampullary tumor between 2004 and 2009 were reviewed retrospectively. Patients were divided into two groups; 279 consecutive patients constituted the study group and the next 108 patients constituted the validation group. Univariate and multivariate logistic regression analyses were performed using preoperative and surgical factors potentially influencing grade B or C POPF in the study group, and a score to predict POPF was constructed. This score was confirmed in the validation group.ResultsIn the study group, grade A POPF was recognized in 45 patients (16%), grade B in 98 (35%), and grade C in 5 (2%). A preoperative predictive scoring system for POPF (0‐7 points) was constructed using the following 5 factors; main pancreatic duct index <0.25 (2 points), away from portal vein on computed tomography (2 points), disease other than pancreatic cancer (1 point), male (1 point), and intra‐abdominal thickness >65 mm (1 point). The nomogram showed an area under the curve (AUC) of 0.808. This scoring system was highly predictive for grade B or C POPF in the validation group (AUC = 0.834).ConclusionsThe present scoring system satisfactorily predicted the occurrence of POPF and thus will be useful for the perioperative risk management of patients undergoing PD in a high‐volume center hospital.
Dietary plasma proteins attenuate the innate immunity response in a mouse model of acute lung injury
Authors: Maijó Mònica , Miró Lluïsa , Polo Javier , Campbell Joy , Russell Louis , Crenshaw Joe , Weaver Eric , Moretó Miquel , Pérez-Bosque Anna 
Published: September 2011

We examined whether oral plasma protein supplements affect the innate immune response in a model of acute lung inflammation. Mice were fed diets supplemented with 8 % spray-dried plasma (SDP) or 2 % plasma Ig concentrate (IC) from day 19 (weaning) until day 34. The mice were challenged with intranasal lipopolysaccharide (LPS) at day 33 (and killed 24 h later for cytokine and leucocyte analyses) or at day 34 (and killed 6 h later for cytokine determinations). In bronchoalveolar lavage fluid (BALF), LPS increased the number of leucocytes by twenty-sevenfold, an effect that was partly prevented by both SDP and IC, and by twentyfold the percentage of activated monocytes, which was partly prevented by SDP. In the lung tissue, LPS increased the infiltrated leucocytes, and this effect was prevented in part by SDP. In unchallenged mice, both SDP and IC diets reduced the percentage of resident neutrophils and monocytes (P < 0·05). In the blood, both SDP and IC completely prevented LPS-dependent monocyte activation (CD14+; P < 0·05). LPS dramatically increased the concentration of cytokines (TNF-α, IL-1α, IL-6, granulocyte-macrophage colony-stimulating factor and granulocyte colony-stimulating factor) and chemokines (CXCL1, CCL2, CCL3 and CCL4) in BALF. The acute response of cytokine production was reduced by 20–80 % by both SDP and IC. For chemokines, plasma supplements had no effect on LPS-induced CXCL1 expression but significantly reduced CCL2, CCL3 and CCL4 production (P < 0·05). The results support the view that dietary plasma proteins can be used to attenuate endotoxin-associated lung inflammation.
Measurement and error of hoof horn growth rate in sheep
Authors: SHELTON J. , USHERWOOD N. M. , WAPENAAR W. , BRENNAN M. L. , GREEN L. E. 
Published: September 2011

SUMMARYDetermining the rate of hoof horn growth in sheep is important for understanding the physiology and pathology of the foot and the impact of the environment and the treatment of diseased feet on foot health. It could lead to improved understanding of the interaction between hoof horn and pasture/barn floor characteristics and in methods for prevention and treatment of ovine foot diseases. In the current study, the hoof horn was measured using a previously tested protocol on all eight digits of 21 healthy yearling mule ewes on a farm in North Wales on four occasions over a period of 53 days. The mean hoof horn growth rate was 0·11 mm (s.e.m. 0·02) per day; the residual error variance was 0·024 and the R2 was 0·245. There were no significant differences between hoof horn growth rates in front and hind feet or between medial and lateral claws or over time.
Stability and change in the intergenerational family: a convoy approach
Authors: ANTONUCCI TONI C. , BIRDITT KIRA S. , SHERMAN CAREY W. , TRINH SARAH 
Published: September 2011

ABSTRACTThere have been fundamental changes in the intergenerational family, and yet families continue to be an important part of people's lives. We use the convoy model to describe the factors that influence supportive relations within intergenerational families, beginning with a description of the changing structure of the intergenerational family. We next outline support exchanges, detailing how personal characteristics, especially gender, race, age and socio-economic status, and situational characteristics, in particular family structure and intergenerational context, influence support exchanges. Instrumental and emotional family exchanges are described, with special attention to the unique circumstances of care-giving in intergenerational families. We also examine the importance of recognising differences in the quality of intergenerational relations, again noting the influence of personal and situational characteristics. Variations in support quality,e.g. positive, negative and ambivalent, and its influence on wellbeing are discussed. As families and individuals change, differences emerge at the individual, family and societal levels. We consider the implications of changes and stability in intergenerational relations and make recommendations about how best to envisage and plan future intergenerational family support. Societies with fewer resources as well as individuals and families with diverse individual histories must be innovative and creative in meeting the needs of older people as well as those of all family members.
Adjusting the cut: fashion, the body and age on the UK high street
Authors: TWIGG JULIA 
Published: September 2011

ABSTRACTThe article explores the interplay between bodily and cultural ageing in the provision of clothing for older women, examining how design directors of UK clothing retailers act as cultural mediators, shaping the ways in which later years are imagined, experienced and performed at an embodied level. Based on interviews with clothing retailers with a significant involvement with the older market: Marks & Spencer, George at Asda, Jaeger, Viyella and Edinburgh Woollen Mill, it analyses the contexts in which they design, discussing: the potential of the grey market; the association of fashion and youthfulness; and the tensions between lifestyle and age in the formation of the market. It explores the ways in which they adjust the cut, colour and style of clothes to meet the requirements of older bodies and the changing cultural interpretations of these, addressing debates around the interplay of bodily and cultural ageing, and the role of consumption in the constitution of age. Reflecting both the cultural and material turns, it argues for the need to expand the social gerontology imaginary to encompass wider sources shaping the meanings of later years.
The language features and architecture of B-Prolog
Authors: ZHOU NENG-FA 
Published: September 2011

AbstractB-Prolog is a high-performance implementation of the standard Prolog language with several extensions including matching clauses, action rules for event handling, finite-domain constraint solving, arrays and hash tables, declarative loop constructs, and tabling. The B-Prolog system is based on the Tree-Oriented Abstract Machine (TOAM) architecture which differs from the Warren Abstract Machine (WAM) mainly in that (1) arguments are passed old fashionedly through the stack, (2) only one frame is used for each predicate call, and (3) instructions are provided for encoding matching trees. The most recent architecture, called TOAM Jr., departs further from the WAM in that it employs no registers for arguments or temporary variables, and provides variable-size instructions for encoding predicate calls. This paper gives an overview of the language features and a detailed description of the TOAM Jr. architecture, including architectural support for action rules and tabling.
(−)‐Epigallocatechin gallate suppresses adipocyte differentiation through the MEK/ERK and PI3K/Akt pathways
Authors: Kim Hyojung , Sakamoto Kazuichi 
Published: September 2011

AbstractEGCG [(−)‐epigallocatechin gallate], tea catechin, is one of the compounds that has been reported to act against obesity and diabetes. To determine the effect of EGCG on adipocyte differentiation, we treated 3T3‐L1 preadipocytes with different catechins. Oil Red O staining showed significantly reduced intracellular lipid accumulation, especially with EGCG. Cell cycle analysis showed that EGCG inhibited cell proliferation by disturbing the cell cycle during the clonal expansion of 3T3‐L1. RT‐PCR (real‐time PCR) demonstrated that EGCG noticeably reduced mRNA expression of PPARα (peroxisome proliferator‐activated receptor α), C/EBPα (CCAAT/enhancer‐binding protein α) and FoxO1 (forkhead box class O1). EGCG also caused a significant decrease in the transcription of FoxO1 – the forkhead transcription factor class O1 involved in adipocyte differentiation – via the PI3K (phosphoinositide 3‐kinase)/Akt and MEK [MAPK (mitogen‐activated protein kinase)/ERK (extracellular‐signal‐regulated kinase) kinase] pathways. These results suggest that EGCG suppresses the clonal expansion of adipocytes by inactivating FoxO1 via insulin signalling and stress‐dependent MAPK pathways.
Atomic force microscopy at ambient and liquid conditions with stiff sensors and small amplitudes
Authors: Wutscher Elisabeth , Giessibl Franz J. 
Published: September 2011

We report on atomic force microscopy (AFM) in ambient and liquid environments with the qPlus sensor, a force sensor based on a quartz tuning fork with an all-electrical deflection measurement scheme. Small amplitudes, stiff sensors with bulk diamond tips and high Q values in air and liquid allow to obtain high resolution images. The noise sources in air and liquid are analyzed and compared for standard silicon cantilevers and qPlus sensors. First, epitaxial graphene was imaged in air, showing atomic steps with 3 Å height and ridges. As a second sample system, measurements on calcite (CaCO3) in liquids were performed in water and polyethylenglycol (PEG). We demonstrate high resolution images of steps in PEG on calcite and nanolithography processes, in particular with frequency-modulation AFM the controlled dissolution of calcite monolayers.
Four polymorphisms of the CAPN 10 gene and their relationship to polycystic ovary syndrome susceptibility: a meta‐analysis
Authors: Huang Miaoling , Xiao Jianpeng , Zhao Xiaomiao , Liu Changhao , Chen Qing 
Published: September 2011

SummaryObjective  To investigate the association between CAPN 10 gene polymorphism and polycystic ovary syndrome (PCOS) susceptibility.Design Meta‐analysis of published case–control studies of four single nucleotide polymorphisms (SNPs) in CAPN 10 and PCOS susceptibility.Patients  Women with PCOS.Measurements  Odds ratios (ORs) and 95% confidence intervals (CIs) for heterozygous, homozygous, dominant model, recessive model and allele.Results  A total of 11 studies were involved in the meta‐analysis. UCSNP‐63 was significantly associated with PCOS, with homozygous carriers (TT vs CC: OR = 0·64; 95% CI: 0·45–0·90) and recessive model (TT vs CC and CT: OR = 0·64; 95% CI: 0·45–0·90) being protective factors. In addition, UCSNP‐19 was significantly associated with PCOS, with recessive model (ins/ins vs del/del and del/ins: OR = 0·72, 95% CI: 0·59–0·88) and insert allele (ins vs del: OR = 0·85, 95% CI: 0·76–0·96) being protective factors, while heterozygous carriers (del/ins vs del/del: OR = 1·56, 95% CI: 1·24–1·94) and deletion allele (del vs ins: OR = 1·18, 95% CI: 1·04–1·32) being risk factors. However, no significant associations were found between UCSNP‐44, ‐43 and PCOS. Moreover, the results of the Rotterdam criteria subgroup analysis were similar with that of overall analysis.Conclusions  This is the first report on the association between CAPN 10 UCSNP‐63 and PCOS in genotype, with homozygous carriers and recessive model being protective factors. Additionally, insert allele and recessive model of UCSNP‐19 are protective factors, while deletion allele and heterozygous genotype are risk factors for PCOS development.
Increased vitamin D supplementation recommended during summer season in the gulf region: a counterintuitive seasonal effect in vitamin D levels in adult, overweight and obese Middle Eastern residents
Authors: Al‐Daghri Nasser M. , Al‐Attas Omar S. , Alokail Majed S. , Alkharfy Khalid M. , El‐Kholie Emad , Yousef Mansour , Al‐Othman Abdulaziz , Al‐Saleh Yousef , Sabico Shaun , Kumar Sudhesh , Chrousos George P. 
Published: September 2011

SummaryPurpose  Seasonal variations in circulating vitamin D levels provide vital information as to the most appropriate time to either start or increase vitamin D supplementation to maintain optimal vitamin D levels. In this follow‐up study, we determined seasonal differences in serum 25(OH)‐vitamin D (25(OH)D) levels, as well as parallel changes in metabolic parameters, in a cohort of adult, overweight and obese Saudis.Methods  A total of 121 adult, overweight, obese, and consenting Saudis aged 18–70 years were randomly recruited from four Primary Health Care Centers in Riyadh, Saudi Arabia. They were divided according to the season when baseline measurements were made [74 summer (April–October); 47 winter (November–March)]. Anthropometrics were obtained, and fasting blood samples were taken at baseline and every 3 months for 1 year. Fasting blood glucose, corrected calcium levels, and lipid profiles were measured routinely. Serum 25(OH)‐vitamin D was quantified using a specific enzyme‐linked immunosorbent assay (ELISA).Results  Age‐ and BMI‐matched mean 25(OH)‐vitamin D levels from the winter group were significantly higher than those of the summer group (P < 0·001). In both groups, HDL‐C levels improved significantly as 25(OH)‐vitamin D levels increased with subsequent follow‐ups, even after adjusting for age, gender and BMI (P < 0·001).Conclusion  Seasonal differences in serum 25(OH)‐vitamin D levels in Saudi Arabia are counterintuitive, with circulating levels being higher during the winter than the summer season. Increased vitamin D supplementation is thus recommended to maintain optimal serum 25(OH)‐vitamin D levels during the summer season.
Resolving uncertainty and creating value from the exercise of e‐commerce investment options
Authors: Otim Sam , Grover Varun 
Published: September 2011

AbstractThis study examines the effect of the resolution of uncertainty on real options exercise decisions with respect to three e‐commerce investment options: scale‐up, stage and joint investment, and the relationship between exercise of these options and firm performance. The results of a study of 172 public e‐commerce investment announcements show that resolution of external (exogenous) and internal (endogenous) uncertainty has a significant effect on option exercise decisions. However, the results also imply that simply waiting without investment in active learning does not create significant value from real options. The key differentiator is how a firm resolves endogenous uncertainty as this endows it with the ability to successfully undertake the information technology investment and exploit the economic opportunity implied by the resolution of exogenous uncertainty. Furthermore, our results imply that different options should be used to manage situations involving certainty of loss on one hand and severity of loss on the other hand. Thus, it is important for firms to make the right choices when using options‐based investing to manage risk. We suggest that, perhaps, managers need to maintain a portfolio of options to manage the two dimensions of risk simultaneously.
Biogenic amine receptor gene expression in the ovarian tissue of the honey bee Apis mellifera
Authors: Vergoz V. , Lim J. , Oldroyd B. P. 
Published: September 2011

AbstractIn the honey bee Apis mellifera loss of the queen from a colony induces increased levels of the biogenic amine dopamine in the brain of workers, and this elevation is correlated with ovary activation. In the present study we use real‐time quantitative PCR to investigate expression of five biogenic amine receptor genes. We show that biogenic amine receptors are expressed in ovarian tissue, and that their expression is strongly influenced by the presence or absence of a queen in the colony. In contrast to the brain, where all three dopamine receptors are expressed, only two dopamine receptors are expressed in the ovaries, and their expression is strongly correlated with the reproductive status of workers. We conclude that biogenic amine receptors are expressed in the ovaries and are likely to be directly influential in the regulation of worker sterility in honey bees.