bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Approach for Searching Insertions in Bacterial Genes Leading to the Phase Shift of Triplet Periodicity
Authors: Korotkova Maria A. , Kudryashov Nikolay A. , Korotkov Eugene V. 
Published: December 2011

Abstract
The concept of the phase shift of triplet periodicity (TP) was used for searching potential DNA insertions in genes from 17 bacterial genomes. A mathematical algorithm for detection of these insertions has been developed. This approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large DNA fragments (&gt;100 bases). New similarity measure between triplet matrixes was employed to improve the sensitivity for detecting the TP phase shift. Sequences of 17,220 bacterial genes with each consisting of more than 1,200 bases were analyzed, and the presence of a TP phase shift has been shown in ~16% of analysed genes (2,809 genes), which is about 4 times more than that detected in our previous work. We propose that shifts of the TP phase may indicate the shifts of reading frame in genes after insertions of the DNA fragments with lengths that are not multiples of three bases. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.
Layer-by-layer crystallization of Co2FeSi Heusler alloy thin films
Authors: Fleet L R , Cheglakov G , Yoshida K , Lazarov V K , Nakayama T , Hirohata A 
Published: December 2011

Abstract
Grain-size evolution with increasing annealing time has been investigated in polycrystalline Co2FeSi films. The samples were prepared by sputtering giving differing grain sizes. Large grains were formed after annealing at 500 °C, with grains over 200 nm forming in the L21 phase in a layer-by-layer mode. Further annealing causes a decrease in the average grain size, agreeing well with previously reported results for Co2MnSi. Magnetic measurements showed moments with values of up to 75% of those predicted from the Slater–Pauling curve providing further evidence for the formation of the L21 phase.
Giant anomalous Hall effect in Fe-based microwires grown by focused-electron-beam-induced deposition
Authors: Córdoba R , Lavrijsen R , Fernández-Pacheco A , Ibarra M R , Schoenaker F , Ellis T , Barcones-Campo B , Kohlhepp J T , Swagten H J M , Koopmans B , Mulders J J L , Teresa J M De 
Published: December 2011

Abstract
We report the temperature dependence of the resistivity, the anisotropic magnetoresistance and the Hall effect of iron microwires grown by focused-electron-beam-induced deposition. By modifying the growth conditions in a controllable way, we study wires with iron compositions varying from 45% to 70%, which present different electrical conduction mechanisms, with resistivity values differing over three orders of magnitude. The magnetoresistance depends highly on the composition, and it can be understood by a subtle interplay between the anisotropic magnetoresistance and intergrain magnetoresistance due to their complex microstructure, consisting of an iron–carbon–oxygen amorphous matrix. A giant value for the anomalous Hall effect is found, which we explain by a large contribution of the skew scattering mechanism. The present results emphasize the correlation between the exotic microstructure of the microwires, and their magnetotransport properties.
Tuning of the size and the lattice parameter of ion-beam synthesized Pb nanoparticles embedded in Si
Authors: Wang Huan , Cuppens J , Biermans E , Bals S , Fernandez-Ballester L , Kvashnina K O , Bras W , Van Bael M J , Temst K , Vantomme A 
Published: December 2011

Abstract
The size and lattice constant evolution of Pb nanoparticles (NPs) synthesized by high fluence implantation in crystalline Si have been studied with a variety of experimental techniques. Results obtained from small-angle x-ray scattering showed that the Pb NPs grow with increasing implantation fluence and annealing duration. The theory of NP growth kinetics can be applied to qualitatively explain the size evolution of the Pb NPs during the implantation and annealing processes. Moreover, the lattice constant of the Pb NPs was evaluated by conventional x-ray diffraction. The lattice dilatation was observed to decrease with increasing size of the Pb NPs. Such lattice constant tuning can be attributed to the pseudomorphism caused by the lattice mismatch between the Pb NPs and the Si matrix.
Correlation between space charge accumulation in polyethylene and its fluorinated surface layer characteristics
Authors: An Zhenlian , Liu Chenxia , Chen Xuan , Zheng Feihu , Zhang Yewen 
Published: December 2011

Abstract
Polyethylene (PE) samples were surface fluorinated by the F2/N2 mixture for 30, 60, 120 or 240 min to investigate the influence of the fluorinated layer characteristics on space charge accumulation. After polarization at 50 kV mm−1 dc electrical field and 40 °C for 240 min, the charge amounts of the samples fluorinated for the different times, normalized to the charge amount of the original sample, are 1.17, 0.51, 0.49 and 0.22, respectively, showing significant suppression of the charge accumulation by the longer treatments, especially for the 240 min treatment. Infrared analyses and SEM cross-section images of the fluorinated samples indicate the increases in degree of fluorination and thicknesses of the fluorinated layer with the treatment time, and the fluorinated layer thicknesses were determined to be 0.39, 0.45, 0.65 and 0.80 µm. Surface energy calculations show that the polar component increased from 2.9 to 14.7 mJ m−2 after the 30 min treatment, and subsequently decreased to 11.8, 11.5 and 9.5 mJ m−2 for the longer treatments of 60, 120 and 240 min. This suggests a similar change in surface layer permittivity with the treatment time. The fluorinations led to the shift of thermally stimulated discharge current peak from 156 °C of the original sample to 145, 142, 144 and 149 °C of the fluorinated samples, and thus reduced the trap depth of the surface layer. But, the longer treatments of 60, 120 and 240 min significantly improved the barrier properties of the surface layer to the diffusion of the chemical species from the semi-conductive electrode to the PE by the decrease in free volume of the surface layer. The chemical species diffused into the sample surface layer reduced the depth of surface traps. The decrease in free volume is more important in suppressing the charge accumulation than the increase in surface layer permittivity and the change in surface trap, because it would reduce the charge transport in the surface layer and the charge direct injection at both electrodes.
Effectiveness of three instrumentation systems to remove Enterococcus faecalis from root canals
Authors: Matos Neto M. , Santos S. S. F. , Leão M. V. P. , Habitante S. M. , Rodrigues J. R. D. D. , Jorge A. O. C. 
Published: December 2011

Matos Neto M, Santos SSF, Leão MVP, Habitante SM, Rodrigues JRDD, Jorge AOC. Effectiveness of three instrumentation systems to remove Enterococcus faecalis from root canals. International Endodontic Journal, 45, 435–438, 2012.AbstractAim  To assess the effectiveness of three systems of mechanical preparation to reduce Enterococcus faecalis within root canals.Methodology  Twenty‐four human single‐rooted canine teeth were standardized to a length of 17 mm and the canal contents removed using a size 20 K‐file, as the last apical file. After irrigation and sterilization, the canals were contaminated with E. faecalis and incubated for 21 days at 37 °C with 5% CO2. Then, the teeth were divided into three groups for mechanical preparation with: ProTaper rotary system, ProTaper manual system and manual K‐files. Samples of the root canal contents, before and after the debridement, were collected with sterile paper points for 1 min. Then, the samples were diluted and plated in Brain Heart Infusion (BHI) agar. The colony‐forming units were counted and the percentage reduction calculated. The reduction and log CFU mL−1 were compared between groups using Wilcoxon nonparametric test and two‐way analysis of variance, respectively.Results  There was a significant reduction in the number of CFU/mL (P = 0.000) before and after debridement for all the systems used. However, there was no significant difference between the systems.Conclusion  All the three instrumentation systems reduced E. faecalis counts to a similar degree.
Speciation in the White‐breasted Nuthatch (Sitta carolinensis): a multilocus perspective
Authors: WALSTROM V. WOODY , KLICKA JOHN , SPELLMAN GARTH M. 
Published: December 2011

AbstractInferring the evolutionary and ecological processes that have shaped contemporary species distributions using the geographic distribution of gene lineages is the principal goal of phylogeographic research. Researchers in the field have recognized that inferences made from a single gene, often mitochondrial, can be informative regarding the pattern of diversification but lack conclusive information regarding the evolutionary mechanisms that led to the observed patterns. Here, we use a multilocus (20 loci) data set to explore the evolutionary history of the White‐breasted Nuthatch (Sitta carolinensis). A previous single‐locus study found S. carolinensis is comprised of four reciprocally monophyletic clades geographically restricted to the pine and oak forests of: (i) eastern North America, (ii) southern Rocky Mountain and Mexican Mountain ranges, (iii) Eastern Sierra Nevada and Northern Rocky Mountains and (iv) Pacific slope of North America. The diversification of the clades was attributed to the fragmentation of North American pine and oak woodlands in the Pliocene with subsequent divergences owing to the Pleistocene glacial cycles. Principal component, clustering and species tree analyses of the multilocus data resolved the same four groups or lineages found in the single‐locus study. Coalescent analyses and hypothesis testing of nested isolation and migration models indicate that isolation and not gene flow has been the major evolutionary mechanism responsible for shaping genetic variation, and all the divergence events within S. carolinensis have occurred in response to the Pleistocene glacial cycles.
Association of variants in innate immune genes with asthma and eczema
Authors: Sharma Sunita , Poon Audrey , Himes Blanca E. , Lasky‐Su Jessica , Sordillo Joanne E. , Belanger Kathleen , Milton Donald K. , Bracken Michael B. , Triche Elizabeth W. , Leaderer Brian P. , Gold Diane R. , Litonjua Augusto A. 
Published: December 2011

To cite this article: Sharma S, Poon A, Himes BE, Lasky‐Su J, Sordillo JE, Belanger K, Milton DK, Bracken MB, Triche EW, Leaderer BP, Gold DR, Litonjua AA. Association of variants in innate immune genes with asthma and eczema. Pediatric Allergy Immunology 2012: 23: 315–323.AbstractBackground:  The innate immune pathway is important in the pathogenesis of asthma and eczema. However, only a few variants in these genes have been associated with either disease. We investigate the association between polymorphisms of genes in the innate immune pathway with childhood asthma and eczema. In addition, we compare individual associations with those discovered using a multivariate approach.Methods:  Using a novel method, case control based association testing (C2BAT), 569 single nucleotide polymorphisms (SNPs) in 44 innate immune genes were tested for association with asthma and eczema in children from the Boston Home Allergens and Asthma Study and the Connecticut Childhood Asthma Study. The screening algorithm was used to identify the top SNPs associated with asthma and eczema. We next investigated the interaction of innate immune variants with asthma and eczema risk using Bayesian networks.Results:  After correction for multiple comparisons, 7 SNPs in 6 genes (CARD25, TGFB1, LY96, ACAA1, DEFB1, and IFNG) were associated with asthma (adjusted p‐value<0.02), while 5 SNPs in 3 different genes (CD80, STAT4, and IRAKI) were significantly associated with eczema (adjusted p‐value < 0.02). None of these SNPs were associated with both asthma and eczema. Bayesian network analysis identified 4 SNPs that were predictive of asthma and 10 SNPs that predicted eczema. Of the genes identified using Bayesian networks, only CD80 was associated with eczema in the single‐SNP study. Using novel methodology that allows for screening and replication in the same population, we have identified associations of innate immune genes with asthma and eczema. Bayesian network analysis suggests that additional SNPs influence disease susceptibility via SNP interactions.Conclusion:  Our findings suggest that innate immune genes contribute to the pathogenesis of asthma and eczema, and that these diseases likely have different genetic determinants.
Tuberculosis, bacillus Calmette–Guérin vaccination, and allergic disease: Findings from the International Study of Asthma and Allergies in Childhood Phase Two
Authors: Flohr Carsten , Nagel Gabriele , Weinmayr Gudrun , Kleiner Andrea , Williams Hywel C. , Aït‐Khaled Nadia , Strachan David P. ,   the ISAAC Phase Two Study Group
Published: December 2011

To cite this article: Flohr C, Nagel G, Weinmayr G, Kleiner A, Williams HC, Aït‐Khaled N, Strachan DP, the ISAAC Phase Two Study Group. Tuberculosis, bacillus Calmette–Guérin vaccination, and allergic disease: Findings from the International Study of Asthma and Allergies in Childhood Phase Two. Pediatric Allergy Immunology 2012: 23: 324–331.AbstractSome have suggested a protective effect of tuberculosis (TB) infection on allergic disease risk, but few studies have examined the association between the two. We therefore investigated whether TB disease and bacillus Calmette–Guérin (BCG) vaccination in early life protect against allergic disease. Information on allergic disease symptoms, past TB disease, and BCG vaccination as well as potential confounding factors was gathered by parental questionnaire from a randomly selected subset of 23,901 8‐ to 12‐yr‐old schoolchildren in 20 centers in both developed and developing countries. Children were also physically examined for flexural eczema and underwent skin prick testing. Pooled odds ratio (OR) estimates and corresponding 95% confidence intervals (CIs) across study centers were calculated, using random effects meta‐analysis models. There were 245 (1.0%) reported cases of TB disease, and 66.3% (15,857) of all children received the BCG vaccine. Asthma, hay fever, and flexural eczema symptoms in the past year as well as flexural eczema on skin examination were all positively linked to a history of TB (adjusted pooled OR ‘wheeze in the past year’ = 2.27, 95% CI 1.52–3.41; adjusted pooled OR ‘hay fever symptoms in the past year’ = 2.23, 1.22–4.09; adjusted pooled OR ‘flexural eczema symptoms in the past year’ = 3.21, 2.01–5.12; adjusted pooled OR ‘flexural eczema on skin examination’ = 4.04, 1.71–9.56). Even higher risk estimates were seen for severe asthma and eczema symptoms [adjusted OR = 4.02 (2.17–7.47) and adjusted OR = 6.31 (2.19–18.17), respectively]. There was no significant association between past TB and skin prick test positivity (adjusted pooled OR = 1.32, 0.87–2.02). BCG vaccination during the first year of life was also not associated with any of the allergy outcomes. We found a uniform positive association between TB and all allergic disease outcomes, including eczema on skin examination. As this was a cross‐sectional study, it is unclear whether this positive association is attributable to a causal relationship, and further longitudinal studies are required.
Propofol reduces early post‐operative pain after gynecological laparoscopy
Authors: LI M. , MEI W. , WANG P. , YU Y. , QIAN W. , ZHANG Z. G. , TIAN Y. K. 
Published: December 2011

BackgroundThere is some evidence that propofol may reduce post‐operative pain. However, the results on the analgesic effects of propofol are inconsistent. Thus, we hypothesized that propofol reduces acute pain if confounding factors like opioids are avoided.MethodsIn this prospective, randomized, subject‐ and assessor‐blind, parallel‐group, head‐to‐head comparative study, 90 American Society of Anesthesiologists I or II females underwent elective laparoscopies were randomized to receive either propofol‐based (PR), or sevoflurane‐based (SR), or sevoflurane‐propofol‐based anesthesia (SPR). Pain score at rest assessed by a numerical rating scale at 0.5 h after surgery was the primary outcome. The secondary outcomes included pain score at 1 and 24 h post‐operatively, duration of post‐anesthesia care units stay (PACU), incidence of post‐operative nausea and vomiting, incidence of shivering, and post‐operative quality of recovery score (QoR‐40) within the first 24 h post‐operatively.ResultsNo patients received rescue analgesia. The pain score at 0.5 h post‐operatively was less in group PR when compared with group SR (0.7 ± 1.4 vs. 2.1 ± 1.8; P = 0.010) or group SPR (0.7 ± 1.4 vs. 2.1 ± 2.2; P = 0.008). Group PR was also associated with shorter PACU stay than group SR (21.8 ± 5.7 vs. 26.2 ± 6.9; P = 0.050) or group SPR (21.8 ± 5.7 vs. 27.8 ± 8.9; P = 0.005). Intraoperative bispectral index values, hemodynamic values and post‐operative QoR‐40 scores did not differ among the three groups.ConclusionsPropofol anesthesia was associated with significantly less pain at 0.5 and 1 h after surgery in patients undergoing gynecological laparoscopies with planned opioid‐free post‐operative analgesia.
Residents and ICU nurses get reliable static and dynamic haemodynamic assessments with aortic oesophageal Doppler
Authors: ROBERT J. M. , FLOCCARD B. , CROZON J. , BOYLE E. M. , LEVRAT A. , GUILLAUME C. , BENATIR F. , FAURE A. , MARCOTTE G. , HAUTIN E. , ALLAOUCHICHE B. 
Published: December 2011

BackgroundAortic oesophageal Doppler (ODM) allows continuous non‐invasive haemodynamic monitoring. We tested to confirm if residents and nurses were able to reposition oesophageal probe (OP), obtain aortic blood flow of good quality and so perform reliable static and dynamic haemodynamic assessments.MethodsProspective observational study assessing ODM measurements were obtained by six residents and three nurses after they have participated in training. Measured (aortic diameter) and calculated haemodynamic data [indexed stroke volume (SVI), cardiac index] were directly obtained from ODM, after residents and nurses repositioned the OP. In a second group of patients, we tested the ability of residents and nurses to detect rapid haemodynamic changes after a passive leg raising. SVI comparison was the primary end point. Statistical analysis was performed using the method of Bland and Altman.ResultsSixty‐six haemodynamic measurements were performed on 42 patients. Mean bias for SVI between the skilled physician and residents, and between the skilled physician and nurses were −0.9 ± 5.2 ml/m2 (P = 0.15), with a percentage error of 31%, and 0.9 ± 5.1 ml/m2 (P = 0.14), with a percentage error of 33%, respectively. There was an excellent correlation for SVI between the physician and residents (r = 0.9; P < 0.0001) and between the physician and nurses (r = 0.9; P < 0.0001). Induced changes in SVI measured by residents and nurses strongly followed those of our skilled physician.ConclusionResidents and nurses get reliable static and dynamic haemodynamic assessments with ODM compared to our skilled physician.
Reversed Sex Change in The Haremic Protogynous Hawkfish Cirrhitichthys falco in Natural Conditions
Authors: Kadota Tatsuru , Osato Jun , Nagata Ken , Sakai Yoichi 
Published: December 2011

AbstractBi‐directional sex change has recently been reported in a range of reef fishes, including haremic species that were earlier thought to be protogynous (female to male). However, the occurrence of this phenomenon and the social conditions driving the reversion of males to females (reversed sex change) have been poorly documented under natural conditions. Reversed sex change is predicted to occur in low‐density populations where facultative monogamy is common. However, few studies have evaluated this over a long period in such populations. We documented the occurrence of bi‐directional sex change during a 3‐yr demographic survey of a population characterised by small harem sizes in haremic hawkfish Cirrhitichthys falco. New males were derived following a change in sex of functional females (secondary males; n = 3) and juveniles always matured first as females (n = 3). Thus, C. falco exhibited a typical protogynous sexual pattern, consistent with a range of haremic fish species. We observed reversed sex change in two males. In both cases, all the females disappeared from their harems and the neighbouring males expanded their territories to encompass the territories of the sex changers. However, bachelor males did not always revert to females. A dominant male experienced bachelor status twice but regained mating opportunities following the immigration of a female into his territory or by taking a female from a neighbouring harem. Thus, we conclude that bachelor males use reversed sex change as a facultative tactic to regain reproductive status in a haremic mating system. In addition, we discuss the influence of harem size upon occurrence of reversed sex change.
Fathering and mothering in the family system: linking marital hostility and aggression in adopted toddlers
Authors: Stover Carla Smith , Connell Christian M. , Leve Leslie D. , Neiderhiser Jenae M. , Shaw Daniel S. , Scaramella Laura V. , Conger Rand , Reiss David 
Published: December 2011

Background:  Previous studies have linked marital conflict, parenting, and externalizing problems in early childhood. However, these studies have not examined whether genes account for these links nor have they examined whether contextual factors such as parental personality or financial distress might account for links between marital conflict and parenting. We used an adoption design to allow for a clear examination of environmental impact rather than shared genes of parents and children, and assessments of parental personality and financial strain to assess the effects of context on relationships between marriage and parenting of both mothers and fathers.Method:  Participants were 308 adoption‐linked families comprised of an adopted child, her/his biological mother (BM), adoptive mother (AM) and adoptive father (AF). BMs were assessed 3–6 and 18 months postpartum and adoptive families were assessed when the child was 18 and 27 months old. Structural equations models were used to examine associations between marital hostility, fathers’ and mothers’ parenting hostility, and child aggressive behavior at 27 months of age. In addition, the contribution of financial strain and adoptive parent personality traits was examined to determine the associations with the spillover of marital hostility to hostile parenting.Results:  A hostile marital relationship was significantly associated with hostile parenting in fathers and mothers, which were associated with aggressive behavior in toddlers. Subjective financial strain was uniquely associated with marital hostility and child aggression. Antisocial personality traits were related to a more hostile/conflicted marital relationship and to hostile parenting.Conclusions:  Results clarify mechanisms that may account for the success of early parent–child prevention programs that include a focus on parental economic strain and personality in addition to parent training.
Lecithoceridae (Lepidoptera: Gelechioidea) of New Guinea, Part VI:Lecithocera sublunataspecies complex
Authors: PARK Kyu‐Tek 
Published: December 2011

AbstractThis is the sixth part in a series on the family Lecithoceridae (Lepidoptera: Gelechioidea) of New Guinea. The complex of five sibling species ofLecithocera sublunataDiakonoff is defined, describing further three new species:L. pseudolunatasp. nov.,L. fascitialasp. nov. andL. niptanensissp. nov., and comparing them to another related species,L. tenella(Turner), comb. nov. from Australia. Images of adults, labial palpi, and male and female genitalia are given. A key to species related toL. sublunatais provided.