bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the frequency of copy number variants
Authors: Ionita-Laza Iuliana , Laird Nan M. , Raby Benjamin A. , Weiss Scott T. , Lange Christoph 
Published: August 2008

Abstract
Motivation: Estimating the frequency distribution of copy number variants (CNVs) is an important aspect of the effort to characterize this new type of genetic variation. Currently, most studies report a strong skew toward low-frequency CNVs. In this article, our goal is to investigate the frequencies of CNVs. We employ a two-step procedure for the CNV frequency estimation process. We use family information a posteriori to select only the most reliable CNV regions, i.e. those showing high rates of Mendelian transmission.
Results: Our results suggest that the current skew toward low-frequency CNVs may not be representative of the true frequency distribution, but may be due, among other reasons, to the non-negligible false negative rates that characterize CNV detection methods. Moreover, false positives are also likely, as low-frequency CNVs are hard to detect with small sample sizes and technologies that are not ideally suited for their detection. Without appropriate validation methods, such as incorporation of biologically relevant information (for example, in our case, the transmission of heritable CNVs from parents to offspring), it is difficult to assess the validity of specific CNVs, and even harder to obtain reliable frequency estimates.
Availability: Software implementing the methods described in this article is available for download at the following address: http://www.isites.harvard.edu/icb/icb.do?keyword=k36162
Contact: iionita@hsph.harvard.edu
Supplementary informantion: Supplementary data are available at Bioinformatics online.
An investigation into the relationship between apical root Impedance and canal anatomy
Authors: Ardeshna S. M. , Flanagan M. , Ng Y.‐L. , Gulabivala K. 
Published: August 2008

Aim  To investigate a possible relationship between apical root impedance and canal anatomy.Methodology  Twenty‐three roots from human extracted teeth (mostly single rooted but also from molars) with different apical anatomy were selected. The apical anatomy was initially classified by staining the root tip to identify number of canal exits; after impedance measurements, the anatomy was confirmed by staining and clearing the dentine. The roots were divided into two groups; 12 had simple (S) anatomy (Vertucci type 1 with a single exit) and 11 had complex (C) anatomy (various Vertucci canal types with multiple exist). Impedance measurements were taken using a frequency response analyser at seven levels in the root (0.0, 0.5, 1.0, 2.0, 3.0, 4.0 and 5.0 mm short of the apical terminus) at 14 frequencies ranging from 1120 to 100 000 Hz. Care was taken to control the temperature and other variables that could confound measurement accuracy. The impedance characteristics of individual roots were compared with 37 equivalent circuits (based on a pool created from a previous study); the best fitting equivalent circuit was selected. The equivalent circuits were used as the single outcome measure describing the impedance characteristics and correlated with the canal anatomy (S/C). Generalized estimating equations were used to perform logistic regression to analyse the data.Results  Canal anatomy had a significant (P = 0.046) effect on the equivalent circuit model. One circuit (model 10) was found to be the commonest and occurred significantly more commonly in the simple canals. The odds of prevalence of circuit model 10 were 2.2 times (odds ratio 2.17, 95% confidence interval 1.01–4.63) higher in canals with simple anatomy compared with canals with complex anatomy.Conclusions  Canal anatomy had a significant effect on the equivalent circuit describing its impedance characteristics. It should be possible to use impedance spectroscopy to clinically predict and image apical canal complexities.
Biofilm disruption by root canal irrigants and potential irrigants
Authors: Bryce G. , Ready D. , Donnell D. O’. , Ng P. , Pratten J. , Gulabivala K. 
Published: August 2008

Aim  To investigate the disruption and bactericidal effect of root canal irrigants on single and dual‐species biofilms.Methodology  Single‐species (Streptococcus sanguis, Enterococcus faecalis, Fusobacterium nucleatum, Porphymonas gingivalis) and dual‐species (S. sanguis and F. nucleatum) biofilms were grown on nitro‐cellulose membranes and immersed in either a commonly used root canal irrigant; (NaOCl, EDTA, Corsodyl®, iodine) or potential root canal irrigant [sodium dodecyl sulphate (SDS), cetyl trimethyl ammonium bromide (CTAB) and Tween®80] for 1, 5 or 10 min. The number of viable and nonviable bacteria disrupted from the biofilm and those remaining attached to the biofilm were determined using a viability stain in conjunction with fluorescent microscopy. In addition, confocal laser scanning microscopy (CLSM) was used to allow a visual assessment of the disruptive effects of selected agents on the stained biofilms.Results  Gram‐negative species were more susceptible to cell removal than their Gram‐positive counterparts, S. sanguis being the least susceptible. The majority of the cell disruption occurred after the first minute of exposure as all of the agents exerted some effect on bacterial disruption and viability; however, the extent varied according to the agent. The most effective root canal irrigant for disrupting biofilms was NaOCl whilst in contrast iodine was generally effective at bacterial killing but not disruption. Of the potential root canal irrigants, CTAB and SDS were both effective in disrupting the biofilm and at bacterial cell‐killing.Conclusions  Biofilm disruption and cell viability were influenced by the species, their co‐association in dual‐species biofilms and the test agent. The effectiveness of NaOCl as an endodontic irrigant was reinforced.
A survey on the experience of UK endodontists and general dental practitioners in the management of intra‐canal fractured endodontic files
Authors: Madarati A. , Watts D. C. , Qualtrough A. J. E. 
Published: August 2008

Aim To investigate the attitudes of general dental practitioners (GDPs) and endodontists in the UK towards management of fractured endodontic file (SEF).Methodology A questionnaire was sent to 330 systemically selected GDPs and all endodontic specialists working in the UK (170). It was accompanied by a covering letter explaining the aims of the study and indicating that all information given would remain confidential. Those who did not respond to the first mailing were sent another two mailings comprising a differently worded covering letter and another copy of the questionnaire. Data were analysed using chi‐squared test at the 0.05 level of significance.Results The overall response rate was 75% (82.82% for endodontists and 70.92% for GDPs). 18.5% of respondents reported they would retrieve files located in the apical third of root canals with a significantly higher proportion of endodontists (25.9%) compared with that of GDPs (14%) doing so. A significantly higher proportion of endodontists (98.5%) used ultrasonics for removal of SEF compared with GDPs (75.8%). The most common complication of SEF retrieval was excessive removal of dentine (67%). The majority of respondents (88.5%) reported that they would leave the un‐removed file in situ and obturate the root canal.Conclusion This study showed that both endodontists and GDPs are aware of the limitations of root canal anatomy when removal of separated instruments is considered. Excessive removal of dentine, which was the most common complication associated with the removal process, suggests the need for more conservative techniques. Both endodontists and GDPs demonstrated a conservative approach towards unsuccessful management of SEF. Further studies regarding attitudes of GDPs and endodontists towards some specific aspects of management of SEF are required.
Serum contamination affects the surface hardness of Portland‐type cements
Authors: Mahmoud O. , Whitworth J. M. , McCabe J. F. 
Published: August 2008

Aim  To compare the surface hardness of cured mineral trioxide aggregates (MTAs), Portland cements (PC) and a dental gypsum product (die stone) after mixing with the recommended solution alone or incorporating serum.Methodology  Samples (n = 3) of white MTAs (ProRoot and Angelus), white PCs (Lafarge) and dental die stone (BPB) were mixed to standard consistency with recommended solution or 50 : 50 (v/v) recommended solution : defibrinated horse serum, packed into 15 mm × 2mm Perspex moulds and stored at 37 °C/100% humidity. Vickers hardness (3/specimen: 200 g at 0.05 mm mm‐1) was determined at 1 or 4 h (depending on setting time), 1, 2, 3, 7, 14, 28 and 56 days. Differences in surface hardness between materials and mixing solutions and changes over time were compared with anova and paired sample t‐tests (P < 0.05).Results  Die stone attained full hardness within 1 day and remained constant thereafter. White PC and MTAs became significantly harder with time. Serum contamination greatly reduced the 1‐day hardness of white PC and ProRoot MTA, significantly increased the 56‐day hardness of PC and all MTAs.Conclusions  The Vickers hardness of white PC and MTAs increased for extended periods after initial hardening. Portland‐type cements appeared to cure in a dissimilar manner to a gypsum‐based dental stone. The hardness of white PC was greater than that of white MTAs at all times after initial hardening. Significant serum contamination may retard the early hardening of some Portland‐type cements, but uniformly produced a significantly harder material at 56 days. The mechanisms of this action are incompletely understood. Clinically, assessing the set of MTAs at 24 h may not be warranted.
Additive partitioning of diversity including species differences: a comment on Hardy & Senterre (2007)
Authors: Villéger Sébastien , Mouillot David 
Published: August 2008

Summary

The distribution of biodiversity at multiple spatial scales has been traditionally investigated through the additive partitioning of γ‐biodiversity (regional) into α‐(within‐site) and β‐(among‐site) components.
However, this decomposition is almost exclusively applied using species turnover among communities while two communities with no species in common can be very similar because they share some ‘biological’ similarity.
To overcome this limitation, Hardy & Senterre (2007) (J. Ecol., 95, 493–506) presented a new statistical framework partitioning the phylogenetic diversity into α‐ and β‐components using the Rao's quadratic entropy.
We show that their decomposition is correct only when sites have the same total abundance, otherwise it may lead to negative β‐diversity values. As an alternative, we provided a general decomposition of the quadratic entropy into α‐, β‐ and γ‐diversities.
Synthesis. We suggest that the ‘biological’ turnover quantified by the β‐component of the regional quadratic entropy may help, at least, to disentangle dispersal vs. niche influences on biodiversity patterns.
Relationship between severity of blackleg (Leptosphaeria maculans/L. biglobosa species complex) and subsequent primary inoculum production on oilseed rape stubble
Authors: Lô‐Pelzer E. , Aubertot J. N. , David O. , Jeuffroy M. H. , Bousset L. 
Published: August 2008

The relationship between severity of blackleg, or phoma stem canker (Leptosphaeria maculans/L. biglobosa), and subsequent primary inoculum production on oilseed rape (Brassica napus) stubble was investigated at two sites in France over 3 years. The quantity of primary inoculum produced in the following year increased with canker severity, from 1·9 to 10·8 pseudothecia cm−2 on stubble with the least and most severe cankers, respectively. Stubble incubated at Le Rheu (cooler, more rain) had 1·7 times more pseudothecia than stubble incubated at Grignon. Stubble collected at Grignon had 2·7 times more pseudothecia than that collected at Le Rheu. The use of Darmor, a cultivar with a good level of quantitative resistance, reduced the severity of canker in the field, but not the subsequent inoculum production for stubble of the same canker severity class. At both sites, maturation of pseudothecia occurred after 63–75 days of incubation and increased with canker severity with a mean of 0·5 and 3% mature pseudothecia appearing per favourable day, on stubble with the least and most severe cankers, respectively. A simplified procedure for pseudothecial quantification proved satisfactory: for all three observers, most (91–96%) of the fructifications counted as pseudothecia were real pseudothecia. Only a few (4–14%) of the fructifications considered as non‐pseudothecia were in fact pseudothecia of L. maculans. The total area occupied by pseudothecia, which was simpler and faster to evaluate, was correlated (coefficient of determination, R2 = 71%) with the number of counted pseudothecia. The results presented here make it possible to forecast the quantity of available primary inoculum for a given disease severity.
Three‐dimensional architecture and development of Danian bryozoan mounds at Limhamn, south‐west Sweden, using ground‐penetrating radar
Authors: NIELSEN LARS , VON BROCKDORFF ADAM SCHACK , BJERAGER MORTEN , SURLYK FINN 
Published: August 2008

AbstractBryozoan mounds from the middle Danian (Lower Palaeocene) of the Danish Basin represent a possibly new class of non‐cemented skeletal mounds. The sedimentology and palaeoecology of the mounds have recently been studied in detail. Three‐dimensional images of middle Danian bryozoan mound structures in the Limhamn limestone quarry, south‐west Sweden, obtained from combined reflected ground‐penetrating radar signals and outcrop analysis provide new information about the architecture and growth development of such mounds. The mounds are composed of bryozoan limestone and dark‐grey to black flint bands which outline mound geometries. Ground‐penetrating radar data sections are collected over a 120 m by 60 m grid of data lines with trace spacing of 0·25 m, providing a depth penetration of 7 to 12 m and a vertical resolution of ca 0·30 m. The ground‐penetrating radar images outline the geometry of the internal layering of the mounds which, typically, have widths and lengths of 30 to 60 m and heights of 5 to 10 m. Mound architecture and growth show great variability in the ground‐penetrating radar images. Small‐scale mound structures with a palaeorelief of only a few metres may constitute the basis for growth of larger mounds. The outermost beds of the individual mounds are commonly characterized by sub‐parallel to parallel reflections which have a circular to slightly oval appearance in map view. The mounds are mainly aggrading and do not show clear signs of pronounced lateral migration during growth, although some mound structures indicate a preferential growth direction towards the south. Growth patterns interpreted from the ground‐penetrating radar images suggest that the palaeocurrents in the study area may have shown great variability, even on a small scale. This observation is in contrast to results from studies of extensive, slightly older early Danian mound complexes exposed in coastal cliffs at Stevns Klint and Karlby Klint located 50 and 200 km away from the study area, respectively. At these locations the mounds show a remarkably uniform development and typically are asymmetrical, clearly showing migration directions towards the south. These differences in mound geometry may be the result of differences in the current systems and water depths that existed during formation of the early and middle Danian mounds, respectively. The mounds at Limhamn were located closer to the basin margin in shallower water than those at Stevns Klint and Karlby Klint. In addition, the difference in mound architecture may be due to the occurrence of non‐layered, irregular coral mounds intercalated with the bryozoan mounds at Limhamn.
The 14 bp deletion polymorphisms in HLA‐G gene play an important role in the expression of soluble HLA‐G in plasma
Authors: Chen X.‐Y. , Yan W.‐H. , Lin A. , Xu H.‐H. , Zhang J.‐G. , Wang X.‐X. 
Published: August 2008

AbstractSoluble human leukocyte antigen‐G (sHLA‐G) functions as a multiple immunoregulator. A 14 bp insertion (+14 bp)/deletion (−14 bp) polymorphism in exon 8 of the HLA‐G gene has been proposed to be associated with HLA‐G mRNA stability and the expression of HLA‐G. In the current study, a total of 150 normal Chinese Han population had been genotyped for the +14 bp/−14 bp polymorphism, and the expression of plasma sHLA‐G was determined with enzyme‐linked immunosorbent assay in these case‐matched plasma. Data showed that genotype of 14 bp polymorphism was significantly associated with sHLA‐G expression. Plasma sHLA‐G level with the +14 bp/+14 bp genotype was dramatically lower than that with +14 bp/−14 bp (P = 0.004) and −14 bp/−14 bp genotypes (P = 0.003), while no dramatic difference was observed between the +14 bp/−14 bp and −14 bp/−14 bp genotypes (P > 0.05). In both males and females, plasma sHLA‐G with the +14 bp/+14 bp genotype was also significantly lower when compared with other two respective 14 bp genotypes. Data also showed that sHLA‐G expression was unrelated to gender. This study suggests that the 14 bp deletion polymorphism in the HLA‐G gene plays an important role in sHLA‐G expression and that interpretation of the potential biological functions of sHLA‐G should be made with caution, taking the polymorphism into consideration.
Dietary phytate (inositol hexaphosphate) regulates the activity of intestinal mucosa phytase
Authors: Onyango E. M. , Adeola O. 
Published: August 2008

SummaryThe role of dietary phytate (inositol hexaphosphate) in the regulation of intestinal mucosa phytase was investigated in chicks. Seven‐day‐old chicks were grouped by weight into six blocks of three cages with six birds per cage. Three purified diets [a chemically defined casein diet, a chemically defined casein diet plus sodium phytate (20 g/kg diet) and a chemically defined casein diet plus sodium phytate (20 g/kg diet) and microbial phytase (1000 units/kg diet)] were randomly assigned to cages within each block. Chicks were fed experimental diets from 8 to 22 days of age then killed, and duodenal mucosa and left tibia removed. Phytase activity in duodenal mucosa, growth performance and bone ash content were determined. Addition of phytate to the chemically defined casein diet reduced (p < 0.05) the Vmax of the duodenal brush border phytase, but the Km of the enzyme was not affected. Addition of phytate also reduced (p < 0.05) weight gain, feed intake, feed efficiency and percentage ash. Addition of microbial phytase fully restored the feed efficiency (p < 0.05), but Vmax and body weight gain were only partially restored (p < 0.05). In conclusion, it would seem that dietary phytates non‐competitively inhibit intestinal mucosa phytase.
Effect of increased methionine level on performance and apparent ileal digestibility of amino acids in ducks
Authors: Jamroz D. , Wiliczkiewicz A. , Lemme A. , Orda J. , Skorupińska J. , Wertelecki T. 
Published: August 2008

SummaryThe experiment was conducted with 960 one‐day‐old ducklings fed mixtures (I control – 0.28% methionine) additionally supplemented with DL‐methionine (DL‐Met) at amounts: 0.03% (group II), 0.07% (III), 0.12% (IV) and 0.18% (V). The performance, carcass quality and apparent ileal digestibility of amino acids as the criterions of methionine (Met) effectivity were considered. The analysis of growth and development of ducks as an effect of diversified DL‐Met supplements indicate that increased content of this amino acid in the diets has not affected clearly the performance parameters. The body weight of 21‐day‐old ducklings was significantly affected only by the level of 0.12% of added Met in comparison to control group. On day 42, the differences among groups were negligible; only the addition of 0.12% DL‐Met has increased the body weight by 2.4% when compared with control (p > 0.05). Feed conversion estimated for a period of 1–42 days has not been influenced by Met supplementation. The indistinct, however, visible tendency of better ileal amino acids’ apparent digestibility (for Asp.a.,Thr, Ser, Glu, Lys) was noted in the groups fed supplemented diets. Application of 0.07% and 0.18% of DL‐met, has significantly (p < 0.05) improved the coefficient of cysteine (Cys) apparent ileal digestibility; however, the improvement of Met apparent ileal digestibility has been achieved by the addition of 0.18% Met. The mortality of ducklings in the experiment was very low and varied between 3.15% (II) and 0.0% (groups I and III). In general, application of 0.12% of DL‐Met to mixture containing 0.28% Met had positive effect on the productive output of birds and also improved the apparent ileal digestibility of Cys and Met.
Development of number combination skill in the early school years: when do fingers help?
Authors: Jordan Nancy C. , Kaplan David , Ramineni Chaitanya , Locuniak Maria N. 
Published: August 2008

Abstract Children's change over time in frequency of finger use on number combinations was examined in relation to their change in accuracy. Performance was tracked longitudinally over 11 time points, from the beginning of kindergarten (mean age = 5.7 years) to the end of second grade (n= 217). Accuracy in number combinations increased steadily during the time period while frequency of finger use declined. Correlations between finger use and accuracy decreased gradually, ranging from 0.60 in kindergarten to −0.15 at the end of second grade. Low‐income children showed linear growth in frequency of finger use while middle‐income children slowed down by second grade and even started to decline. Although girls and boys showed similar growth patterns in frequency and accuracy, boys used their fingers less often than girls and were more accurate. The findings indicate that finger use is most adaptive when children are first learning number combinations, but this benefit lessens over time.
To see or not to see: infants prefer to follow the gaze of a reliable looker
Authors: Chow Virginia , Poulin‐Dubois Diane , Lewis Jessica 
Published: August 2008

AbstractIn two experiments, we examined whether 14‐month‐olds understand the subjective nature of gaze. In the first experiment, infants first observed an experimenter express happiness as she looked inside a container that either contained a toy (reliable looker condition) or was empty (unreliable looker condition). Then, infants had to follow the same experimenter's gaze to a target object located either behind or in front of a barrier. Infants in the reliable looker condition followed the experimenter's gaze behind the barrier more often than infants in the unreliable looker condition, whereas both groups followed the experimenter's gaze to the target object located in front of the barrier equally often. In the second experiment, infants did not generalize their knowledge about the unreliability of a looker to a second ‘naïve’ looker. These findings suggest that 14‐month‐old infants adapt their gaze following as a function of their past experience with the looker.