bluuebunny/crossref_metadata_2025 huggingface dataset:
Incremental cost of non‐invasive prenatal diagnosis versus invasive prenatal diagnosis of fetal sex in England
Authors: Hill Melissa , Taffinder Sally , Chitty Lyn S. , Morris Stephen
Published: January 2011

Objectives

Fetal sex determination is performed for women who carry X‐linked conditions, for example Duchenne muscular dystrophy (DMD), or those associated with ambiguous genitalia, for example congenital adrenal hyperplasia (CAH). Non‐invasive prenatal diagnosis (NIPD) using cell‐free fetal DNA (cffDNA) in maternal plasma is an alternative to invasive prenatal diagnosis (IPD), which carries a 1% risk of miscarriage. This study aimed to evaluate the incremental cost of NIPD compared with IPD of fetal sex.

Methods

Diagnostic accuracy, invasive testing rate, and pregnancy outcome following NIPD were ascertained from an audit of all cases referred to two laboratories in 2006 to 2009. Care pathways for DMD and CAH were established and key cost drivers for IPD and NIPD identified using costs derived from published estimates and local laboratory values.

Results

The differences in mean costs per pregnancy for NIPD versus IPD were small for DMD [mean difference − £87, 95% confidence interval (CI) − £303 to £131] and CAH (−£193, 95% CI − £301 to − £84). Testing costs associated with NIPD were offset by fewer women requiring invasive testing.

Conclusions

The costs of NIPD and IPD of fetal sex are similar. NIPD can provide benefits for many women by avoiding the risks of invasive testing, without incurring additional costs. Copyright © 2011 John Wiley & Sons, Ltd.
MarR homologs with urate‐binding signature
Authors: Perera Inoka C. , Grove Anne
Published: January 2011

Bacteria that associate with living hosts require intricate mechanisms to detect and respond to host defenses. Part of the early host defense against invading bacteria is the production of reactive oxygen species, and xanthine oxidase is one of the main producers of such agents. The end‐product of the enzymatic activity of xanthine oxidase, urate, was previously shown to be the natural ligand for Deinococcus radiodurans‐encoded HucR and it was shown to attenuate DNA binding by Agrobacterium tumefaciens‐encoded PecS and Burkholderia thailandensis‐encoded MftR, all members of the multiple antibiotic resistance regulator (MarR) family. We here show that residues involved in binding urate and eliciting the DNA binding antagonism are conserved in a specific subset of MarR homologs. Although HucR controls endogenous urate levels by regulating a uricase gene, almost all other homologs are predicted to respond to exogenous urate levels and to regulate a transmembrane transport protein belonging to either the drug metabolite transporter (DMT) or the major facilitator superfamily (MFS), as further evidenced by the presence of conserved binding sites for the cognate transcription factor within the respective promoter regions. These data suggest the use of orthologous genes for different regulatory purposes. We propose the designation UrtR (urate responsive transcriptional regulator) for this distinct subfamily of MarR homologs based on their common mechanism of urate‐mediated attenuation of DNA binding.
Modeling GPCR active state conformations: The β2‐adrenergic receptor
Authors: Simpson Lisa M. , Wall Ian D. , Blaney Frank E. , Reynolds Christopher A.
Published: January 2011

The recent publication of several G protein‐coupled receptor (GPCR) structures has increased the information available for homology modeling inactive class A GPCRs. Moreover, the opsin crystal structure shows some active features. We have therefore combined information from these two sources to generate an extensively validated model of the active conformation of the β2‐adrenergic receptor. Experimental information on fully active GPCRs from zinc binding studies, site‐directed spin labeling, and other spectroscopic techniques has been used in molecular dynamics simulations. The observed conformational changes reside mainly in transmembrane helix 6 (TM6), with additional small but significant changes in TM5 and TM7. The active model has been validated by manual docking and is in agreement with a large amount of experimental work, including site‐directed mutagenesis information. Virtual screening experiments show that the models are selective for β‐adrenergic agonists over other GPCR ligands, for (R)‐ over (S)‐β‐hydroxy agonists and for β2‐selective agonists over β1‐selective agonists. The virtual screens reproduce interactions similar to those generated by manual docking. The C‐terminal peptide from a model of the stimulatory G protein, readily docks into the active model in a similar manner to which the C‐terminal peptide from transducin, docks into opsin, as shown in a recent opsin crystal structure. This GPCR‐G protein model has been used to explain site‐directed mutagenesis data on activation. The agreement with experiment suggests a robust model of an active state of the β2‐adrenergic receptor has been produced. The methodology used here should be transferable to modeling the active state of other GPCRs. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Molecular dynamics of EF‐G during translocation
Authors: Li Wen , Trabuco Leonardo G. , Schulten Klaus , Frank Joachim
Published: January 2011

Elongation factor G (EF‐G) plays a crucial role in two stages of mRNA‐(tRNA)2 translocation. First, EF‐G•GTP enters the pre‐translocational ribosome in its intersubunit‐rotated state, with tRNAs in their hybrid (P/E and A/P) positions. Second, a conformational change in EF‐G's Domain IV induced by GTP hydrolysis disengages the mRNA‐anticodon stem‐loops of the tRNAs from the decoding center to advance relative to the small subunit when the ribosome undergoes a backward inter‐subunit rotation. These events take place as EF‐G undergoes a series of large conformational changes as visualized by cryo‐EM and X‐ray studies. The number and variety of these structures leave open many questions on how these different configurations form during the dynamic translocation process. To understand the molecular mechanism of translocation, we examined the molecular motions of EF‐G in solution by means of molecular dynamics simulations. Our results show: (1) rotations of the super‐domain formed by Domains III–V with respect to the super‐domain formed by I–II, and rotations of Domain IV with respect to Domain III; (2) flexible conformations of both 503‐ and 575‐loops; (3) large conformational variability in the bound form caused by the interaction between Domain V and the GTPase‐associated center; (4) after GTP hydrolysis, the Switch I region seems to be instrumental for effecting the conformational change at the end of Domain IV implicated in the disengagement of the codon‐anticodon helix from the decoding center. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Triathlon for energy functions: Who is the winner for design of protein–protein interactions?
Authors: Sharabi Oz , Dekel Ayelet , Shifman Julia M.
Published: January 2011

Computational prediction of stabilizing mutations into monomeric proteins has become an almost ordinary task. Yet, computational stabilization of protein–protein complexes remains a challenge. Design of protein–protein interactions (PPIs) is impeded by the absence of an energy function that could reliably reproduce all favorable interactions between the binding partners. In this work, we present three energy functions: one function that was trained on monomeric proteins, while the other two were optimized by different techniques to predict side‐chain conformations in a dataset of PPIs. The performances of these energy functions are evaluated in three different tasks related to design of PPIs: predicting side‐chain conformations in PPIs, recovering native binding‐interface sequences, and predicting changes in free energy of binding due to mutations. Our findings show that both functions optimized on side‐chain repacking in PPIs are more suitable for PPI design compared to the function trained on monomeric proteins. Yet, no function performs best at all three tasks. Comparison of the three energy functions and their performances revealed that (1) burial of polar atoms should not be penalized significantly in PPI design as in single‐protein design and (2) contribution of electrostatic interactions should be increased several‐fold when switching from single‐protein to PPI design. In addition, the use of a softer van der Waals potential is beneficial in cases when backbone flexibility is important. All things considered, we define an energy function that captures most of the nuances of the binding energetics and hence, should be used in future for design of PPIs. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Indefinite noncooperative self‐association of chicken deoxy hemoglobin D
Authors: Rana Mitra S. , Riggs Austen F.
Published: January 2011

The minor tetrameric hemoglobin (Hb), Hb D, of chicken red blood cells self‐associates upon deoxygenation. This self‐association enhances the cooperativity of oxygen binding. The maximal Hill coefficient is greater than 4 at high Hb concentrations. Previous measurements at low Hb concentrations were consistent with a monomer‐to‐dimer equilibrium and an association constant of ∼1.3–1.6 × 104
M−1. Here, the Hb tetramer is considered as the monomer. However, new results indicate that the association extends beyond the dimer. We show by combination of Hb oligomer modeling and sedimentation velocity analyses that the data can be well described by an indefinite noncooperative or isodesmic association model. In this model, the deoxy Hb D associates noncooperatively to give a linear oligomeric chain with an equilibrium association constant of 1.42 × 104
M−1 at 20°C for each step. The data are also well described by a monomer–dimer–tetramer equilibrium model with monomer‐to‐dimer and dimer‐to‐tetramer association constants of 1.87 and 1.03 × 104
M−1 at 20°C, respectively. A hybrid recombinant Hb D was prepared with recombinant αD‐globin and native β‐globin to give a Hb D tetramer (αβ2). This rHb D undergoes decreased deoxygenation‐dependent self‐association compared with the native Hb D. Residue glutamate 138 has previously been proposed to influence intertetramer interactions. Our results with recombinant Hb D show that Glu138 plays no role in deoxy Hb D intertetramer interactions. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Modeling of the conformational flexibility and E/Z isomerism of thiazoximic acid and cefotaxime
Authors: Lerner Dan A. , Berthomieu Dorothée , Maia Elaine R.
Published: January 2011

The conformational flexibility of the Z and E isomers of cefotaxime (CFX) and thiazoximic acid, their ground‐state isomerization path and transition state, were all analyzed in depth. The modeling was carried at the semiempirical and DFT‐BLYP level with geometry optimization for gas phase conditions. That approach was used after a thorough analysis using classical molecular dynamics to initially define large families of conformers. The lowest energy conformers always have an E configuration, in contradiction to the behavior observed in solution, and the Z–E isomerization mechanism is a rotation. These results reveal the remarkable flexibility of these molecules, allow anticipating the role of water and of their target proteins in the redistribution of the conformers population, and provide the best geometry known for CFX. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Stable complex C2H4Al4Li3− and its similarity with bicyclo[2.2.0]hex‐2‐ene: A DFT study
Authors: Satpati Priyadarshi
Published: January 2011

We propose that complexation of all metal antiaromatic Al4Li with C2H4 may lead to stable C2H4Al4Li species [II(b)]. Complexation leads to the electron transfer from Al4Li moiety to C2H4 and development of aromatic character in the Al4 ring. Our proposed compound C2H4Al4Li [II(b)] is very similar to the existing organic compound bicyclo[2.2.0]hex‐2‐ene [I(b)]. The complex C2H4Al4Li [II(b)] can be imagined as an analogue of bicyclo[2.2.0]hex‐2‐ene [I(b)] achieved by a simple replacement of C4H4 in the later with π‐isoelectronic Al4Li moiety in the former. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Properties of hydrogen molecular ion with static screened coulomb and exponential cosine screened coulomb potentials
Authors: Ghoshal Arijit , Ho Y. K.
Published: January 2011

We have investigated the properties of hydrogen molecular ion (H) interacting with screened Coulomb potentials. Two types of potentials have been considered, namely, static screened Coulomb potential and exponential cosine‐screened Coulomb potential. Simulating the localized motion of the nuclei by using high powers of the internuclear coordinate in the generalized Hylleraas‐type wave function we have been able to obtain reasonably accurate binding energies for 11S(J = 0, ν = 0) and 21S(J = 0, ν = 1) states for various values of the screening parameter within the frame work of Ritz variational method. Borromean bindings are found to exist in the ion for a wide range of the screening parameter. Furthermore, expectation values for various operators and cusp condition have been calculated. Results for the unscreened case are in nice agreement with some of the accurate results available in the literature. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Electronic structure of the ground and low‐lying electronic states of MoB and MoB+
Authors: Borin Antonio Carlos , Gobbo João Paulo
Published: January 2011

Multiconfigurational second‐order perturbation theory (CASSCF//CASPT2) and quadruple‐ζ ANO‐RCC basis sets were employed to investigate the ground and low‐lying electronic states of MoB and MoB+. Spectroscopic constants, potential energy curves, wavefunctions, Mulliken population analyses, and ionization energies are given. The ground state of MoB is of X6Π symmetry (Re = 1.968 Å, ωe = 664 cm−1, and μ = 2.7 D), giving rise to a Ω = 7/2 ground state after including spin‐orbit coupling. For MoB+, the ground state is computed to be of X7 Σ+ symmetry (Re = 2.224 Å, ωe = 141 cm−1, and μ = 1.2 D), with an adiabatic ionization energy of 7.19 eV and a vertical one of 7.53 eV. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111:3362–3370, 2010
Symbolic missing data imputation in principal component analysis
Authors: Zuccolotto Paola
Published: January 2011

The concept of symbolic data has been developed with the aim of representing variables whose measurement is affected by some internal variation. This idea has been mainly concerned with the need of aggregating individuals in order to summarize large datasets into smaller matrices of manageable size, retaining as much of the original knowledge as possible. Nevertheless it is often applied also with variables structured from their outset as symbolic variables, although measured on single individuals. This paper deals with the latter framework, and aims at showing that symbolic data analysis techniques can be applied to the field of missing values treatment. The algorithm for a symbolic imputation technique in principal component analysis is presented as a generalization of the basic strategy called interval imputation. An illustrative example and a real data case study show how the proposed technique works. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 171–183, 2011
Trellis display for modeling data from designed experiments
Authors: Fuentes Montserrat , Xi Bowei , Cleveland William S.
Published: January 2011

Visualizing data by graphing a response against certain factors, and conditioning on other factors, has arisen independently in many contexts. One is the interaction plots used in the analysis of data from designed experiments; these plots show conditional dependence based on the output of methods and models applied to the data. Trellis display, a framework for the visualization of multivariable data, allows conditioning to be readily carried out in a general way. It was developed initially in the context of data sets with a moderate or large number of observations to support the conditioning. This article demonstrates through examples that trellis display is also a highly useful visualization framework for designed experiments with a small number of runs. Trellis allows the visualization of conditional dependence, not only based on the output of models and methods, but also based on the raw data directly, which greatly aids the model building process. Trellis can even succeed for highly fractionated designs. The reason appears to be that for success, such designs require an engineering practice that keeps error variability small, which allows interpretable patterns to emerge on conditioning displays with a limited number of plotted points. © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 133–145 2011
Videobased lesson analysis: Effective science PD for teacher and student learning
Authors: Roth Kathleen J. , Garnier Helen E. , Chen Catherine , Lemmens Meike , Schwille Kathleen , Wickler Nicole I.Z.
Published: January 2011

The Science Teachers Learning from Lesson Analysis (STeLLA) project is a videobased analysis‐of‐practice PD program aimed at improving teacher and student learning at the upper elementary level. The PD program developed and utilized two “lenses,” a Science Content Storyline Lens and a Student Thinking Lens, to help teachers analyze science teaching and learning and to improve teaching practices in this year‐long program. Participants included 48 teachers (n = 32 experimental, n = 16 control) and 1,490 students. The STeLLA program significantly improved teachers' science content knowledge and their ability to analyze science teaching. Notably, the STeLLA teachers further increased their classroom use of science teaching strategies associated with both lenses while their students increased their science content knowledge. Multi‐level HLM analyses linked higher average gains in student learning with teachers' science content knowledge, teachers' pedagogical content knowledge about student thinking, and teaching practices aimed at improving the coherence of the science content storyline. This paper highlights the importance of the science content storyline in the STeLLA program and discusses its potential significance in science teaching and professional development more broadly. © 2011 Wiley Periodicals, Inc., J Res Sci Teach 48: 117–148, 2011
A novel halogen‐free intumescent flame retardant containing phosphorus and nitrogen and its application in polypropylene systems
Authors: Xiang Haiwang , Sun Caiying , Jiang Dawei , Zhang Qingbo , Dong Chunmei , Liu Lei
Published: January 2011

A novel halogen‐free intumescent flame retardant, pentaerythritol spirobisphosphoryl‐dicyandiamide (SPDC), was synthesized and characterized by FTIR, 1H NMR, and 31P NMR spectra. The new flame retardant was used in polypropylene (PP) to prepare flame‐retardant materials whose flammability and thermal behavior were studied by the limiting oxygen index (LOI) method, thermogravimetric analysis (TGA), and cone calorimetry (CONE). The mechanical properties were also investigated. The results indicated that when the addition of SPDC reached 30 wt%, the material showed both excellent flame retardancy and anti‐dripping abilities for PP. Moreover, the LOI value of the PP‐IFR(30%) was 32.5, and it passed the UL‐94 V‐0 rating test. The CONE results revealed that in PP, SPDC(30%) significantly decreased the peak heat release, total heat release, and smoke relative to their values for pure PP. The morphological structures observed by SEM demonstrated that SPDC could promote the formation of a homogeneous and compact intumescent char layer. The TGA data showed that SPDC could enhance the thermal stability of PP and effectively increase the char residue formation. J. VINYL ADDIT. TECHNOL., 2010. © 2010 Society of Plastics Engineers
Model‐free data screening and cleaning
Authors: Tarter Michael E.
Published: January 2011

Categories of data screening and cleaning issues are reviewed and discussed. Bivariate model‐free approaches, specialized model‐free regression techniques, together with order statistic‐based (OSB) approaches are illustrated and shown to be of particular value for a variety of data screening and cleaning applications. It is shown how a combination of curve estimation with OSB approaches can help screen a progression to AIDS data set.WIREs Comp Stat2011 3 168–176 DOI: 10.1002/wics.140

This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Density Estimation

Statistical and Graphical Methods of Data Analysis > Data Reduction, Smoothing, and Filtering

Statistical and Graphical Methods of Data Analysis > Nonparametric Methods
A Comparison of Prognosis between Patients with Hepatitis B and C Virus‐related Hepatocellular Carcinoma Undergoing Resection Surgery
Authors: Kao Wei‐Yu , Su Chien‐Wei , Chau Gar‐Yang , Lui Wing‐Yiu , Wu Chew‐Wun , Wu Jaw‐Ching
Published: January 2011

Background

The impact of viral factors on the prognosis of hepatocellular carcinoma (HCC) remains controversial because of heterogeneous populations included in previous reports. This study aims to compare clinicopathologic features and prognoses between patients with hepatitis B‐ and hepatitis C‐related HCC who underwent resection surgery.

Methods

We enrolled 609 patients with positive serum hepatitis B virus (HBV) surface antigen (HBsAg) and negative serum antibody against hepatitis C virus (anti‐HCV) as the B‐HCC group and 206 patients with negative serum HBsAg and positive anti‐HCV as the C‐HCC group. The overall survival rates and cumulative recurrence rates were compared between these two groups.

Results

B‐HCC patients were significantly younger, predominantly male, had better liver functional reserve, but more advanced tumor stage than C‐HCC patients. After a median follow‐up period of 40.6 months, 427 patients had died. Furthermore, 501 patients had tumor recurrence after surgery. The postoperative overall survival rates (p = 0.640) and recurrence rates (p = 0.387) of the two groups were comparable. However, the overall survival rate was higher in the B‐HCC group than in the C‐HCC group in the cases of transplantable HCC (p = 0.021) and Barcelona‐Clinic Liver Cancer stage A HCC (p = 0.040).

Conclusions

Viral etiologies were not apparent in determining outcomes of HCC patients who underwent resection due to heterogeneous studied populations. In early‐stage HCC, B‐HCC patients had better outcomes than C‐HCC patients did because of better liver reserve and less hepatic inflammation.
Factors Influencing Career Choice After Initial Training in Surgery
Authors: McHugh Seamus , Corrigan Mark , Sheikh Athar , Lehane Elaine , Tanner William , Hill Arnold
Published: January 2011

Introduction

Irish general surgery faces a recruitment crisis with only 87 of 145 (60%) basic surgical training (BST) places filled in 2009. We assessed basic surgical trainees to identify objective, and potentially modifiable, factors that influence ultimate recruitment into a general surgical career.

Methods

Candidates commencing BST training during a 5‐year period between 2004 and 2008 were included in a quantitative study. In addition a total of 2,536 candidates, representing all those who commenced surgical training in Ireland since 1960 were identified through the Royal College of Surgeons in Ireland (RCSI) database and invited to complete an online survey. Statistical analysis was performed using SPSS version 15, with p < 0.05 considered significant.

Results

During the 5‐year quantitative study period there were 381 BST trainees. Gender was a significant predictor of career choice with women more likely to ultimately choose a nonsurgical career after initial surgical training (p = 0.049). Passing surgical membership examinations (MRCS) also was predictive of remaining in surgery (p = 0.005). Training region was not a significant predictor of ultimate career choice. There were 418 survey respondents. The influence of role models was most commonly cited as influencing candidates in choosing to commence surgical training. Candidates who rated “academic opportunity” (p = 0.023) and “intellectual challenge” (p = 0.047) as factors that influenced their decision to commence surgical training were more likely to ultimately continue their careers in a surgical speciality.

Conclusions

This study describes the career pathway of surgical trainees and confirms the importance of academic achievement in discriminating between candidates applying for surgical training schemes.
Improvement of sexual function after transobturator tape procedure in women with stress urinary incontinence
Authors: Arts-de Jong M. , van Altena A. M. , Aalders C. I. M. , Dijkhuizen F. P. H. L. J. , van Balken M. R.
Published: January 2011

Sling procedures are a widely proven treatment for stress urinary incontinence. The aim of this prospective study was to evaluate the effect of the transobturator tape on female sexual functioning. Fifty-four women treated for stress urinary incontinence with transobturator tape filled out self-administered questionnaires on quality of life, urinary incontinence, and sexual function prior to surgery and 6 weeks and 12 months postoperatively. Preoperatively, 40 women (78%) were sexually active. There were no significant postoperative changes regarding frequency of sexual activity, sexual desire, and problems with lubrication or orgasm. Preoperatively, 55% reported urinary leakage during sexual activity and after surgery 6.5%. Sexual satisfaction was significantly improved 6 weeks (p = 0.05) and 12 months (p = 0.03) postoperatively. Pain during or after sexual activity was declined, only one patient reported worsening of pain. The transobturator tape procedure has a positive effect on female sexual functioning by reducing urinary leakage and pain during or after sexual activity. It seems to improve the overall sexual satisfaction. Further research is warranted to support these preliminary findings.
Changes in Fatty Acids, Tocochromanols, Carotenoids and Chlorophylls Content During Flaxseed Development
Authors: Herchi Wahid , Sakouhi Faouzi , Boukhchina Sadok , Kallel Habib , Pepe Claude
Published: January 2011

A comparative study was performed to determine tocopherols, tocotrienols, fatty acids, and pigments content during the development of three varieties of flaxseed (H52, O116 and P129). Seed samples were collected at regular intervals from 7 to 56 days after flowering (DAF). The highest content of chlorophyll (89.72–130.5 mg/kg oil) was detected at 7 DAF. The maximum level of carotenoids (52.10–65.55 mg/kg oil) was reached at 21 DAF. During seed development, unsaturated fatty acids are the major component, reaching 85% of the total fatty acids while saturated fatty acids content were about 15%. The maximum level of γ‐tocopherol (585 mg/kg oil) was reached at 42 DAF in P129 variety. These results may be useful for evaluating the flaxseed quality and determining its optimal harvest period.
Lingual and renal lymphoma in a cat
Authors: Bound Nicola J. , Priestnall Simon L. , Cariou Matthieu P.
Published: January 2011

A domestic shorthair cat presented with a progressive history of polydipsia, lingual swelling and ulceration. The tongue was firm and grossly enlarged with associated regional lymphadenopathy. Surgical biopsies revealed lymphoma of the tongue. Following the procedure, the cat developed respiratory distress and was subsequently euthanased. Necropsy confirmed the diagnosis of lingual lymphoma and also identified lymphoma within the left kidney. This is the first report of lymphoma within the feline tongue in the literature.
Size dominance regulates tree spacing more than competition within height classes in tropical Cameroon
Authors: Getzin Stephan , Worbes Martin , Wiegand Thorsten , Wiegand Kerstin
Published: January 2011

Does competition prevail in large size classes of trees in tropical forests? This question is fundamental to our understanding of the demography and dynamics occurring in rain forests. We investigated this question based on an undisturbed late-secondary forest on a 1-ha plot in central Cameroon. Trees were stem-mapped and classified into three size classes: understorey, midstorey and overstorey. The diameter at breast height and yearly biomass increment were determined as measures of plant growth and performance. Spatial statistics such as pair- and mark-correlation functions were used to detect scale-dependent patterns that could be caused by competition within and between the three size classes. The results revealed a random pattern and spatially uncorrelated measures of plant growth of overstorey trees. This suggests that competitive effects are of minor importance in the large size class of overstorey trees. Likewise, only weak evidence for competition between trees was found within the two lower size classes. However, negative distance correlations were found between the different size classes. We suggest that competition within height classes was relatively low due to the diversity of species with their variable niche differentiations and phenotypic plasticity that may compensate for competitive effects.
Fragment quality and distribution of the arboreal primate Propithecus verreauxi in the spiny forest of south Madagascar
Authors: Norscia Ivan , Palagi Elisabetta
Published: January 2011

The increasing proportion of the landscape used by humans has led, and is still leading, to the conversion of the original habitat into numerous small patches, often separated by a matrix of inhospitable land-uses. This habitat fragmentation is a major threat to biological diversity and is considered to be the primary cause of the present species extinction crisis (Aurambout et al. 2005). Survival in fragments is related to both intrinsic factors, such as abundance and sex ratio, and extrinsic factors related to patch quality (Ramanamanjato & Ganzhorn 2001, Rovero & Struhsaker 2007). At first, the fragmentation process can randomly distribute animals among forest patches and across fragmented habitat and surrounding matrix (Marsh 2003, Tischendorf et al. 2005). Local populations can survive only if the colonized forest remnants are adequate and/or dispersal is possible (Marsh 2003). Subsequently, a non-random distribution can result from local populations either remaining connected but distinct (metapopulation) or merging into a single large but patchy population (Harrison & Taylor 1997). Such distribution can be dictated by different aspects of fragment quality, including size and vegetation variables (e.g. tree species diversity, large-tree abundance and food plant availability) (Ramanamanjato & Ganzhorn 2001, Rovero & Struhsaker 2007). The mutual relationship among variables and their linkage to animal abundance have proven difficult to disentangle and mammals largely diverge in their response to different fragment quality aspects (Irwin 2008, Ramanamanjato & Ganzhorn 2001, Rovero & Struhsaker 2007).
Sprouting traits of Fagaceae species in a hill dipterocarp forest, Ulu Gadut, West Sumatra
Authors: Nishimura Sen , Yoneda Tsuyoshi , Fujii Shinji , Mukhtar Erizal , Kanzaki Mamoru , Ohta Seiichi
Published: January 2011

The size distribution of a tree species gives important information about its regeneration strategy. For example, a tree species that regenerates primarily by sprouting will, in theory, have fewer seedlings than species that regenerate from seedlings, which generally form an L-shaped population size structure because of trade-offs in resource allocation between vegetative sprouting and sexual reproduction (Bellingham & Sparrow 2000, Loehle 2000). The results of some field studies suggest that the number of seedlings decreases with increasing dominance of multi-stemmed sprouters (Krugeret al. 1997, Zimmermanet al. 1994). In their study of four co-occurring species ofCastanopsis(Fagaceae), Nanamiet al. (2004) showed that species with a high frequency of sprouting adults had fewer juveniles and vice versa. This suggested that these species were able to co-exist as a result of trade-offs between investment in seedlings and sprouting. In this study, we investigated the sprouting trait of 17 co-occurring Fagaceae species in a Sumatran hill forest. The forest stand at this site shows a varied population structure across species, and hence, should have a varied life history. We tested the correlation between population skewness and proportion of sprouting trees, following the methods of Nanamiet al. (2004). We hypothesized that the species that frequently form multi-stemmed sprouts will show a lower turnover of individuals because multi-stemmed architecture favours persistence (Bellingham & Sparrow 2009).
Caterpillar abundance and parasitism in a seasonally dry versus wet tropical forest of Panama
Authors: Connahs Heidi , Aiello Annette , Van Bael Sunshine , Rodríguez-Castañeda Genoveva
Published: January 2011

Rainfall seasonality can strongly influence biotic interactions by affecting host plant quality, and thus potentially regulating herbivore exposure to natural enemies. Plant defences are predicted to increase from dry to wet forests, rendering wet-forest caterpillars more vulnerable to parasitoids due to the slow-growth-high-mortality hypothesis. We collected and reared caterpillars from the understorey and trail edges of a wet forest and a seasonally dry forest to determine whether wet-forest caterpillars suffered a higher prevalence of parasitism and were less abundant than dry-forest caterpillars. In the two forests, caterpillar abundances (on average 8 h−1) and prevalence of parasitism (18%) were very similar regardless of feeding niche for both parasitism (27% versus 29% in shelter builders, and 16% versus 11% in external feeders) and caterpillar abundances (shelter builders: 1.42 versus 2.39, and external feeders: 8.27 versus 5.49 caterpillars h−1) in the dry and wet forests, respectively. A similar comparative analysis conducted in the canopy and understorey of the dry forest revealed a higher prevalence of parasitism in the canopy (43%) despite caterpillar densities similar to those in the understorey. Overall, shelter builders suffered higher parasitism than external feeders (32% versus 14.9%), and were attacked primarily by flies, whereas external feeders were more vulnerable to attack by parasitoid wasps.
Population size and dispersal ofSulcophanaeus leander(Coleoptera: Scarabaeidae) on riverine beaches in the Amazonian region
Authors: Noriega Jorge Ari , Acosta Alberto
Published: January 2011

Dung beetles are a well-defined guild within the family Scarabaeidae, with distinctive morphological, ecological and behavioural characteristics (Halffter & Matthews 1966). Although this group has been extensively studied (Hanski & Cambefort 1991) due in part to the important role they fulfil in ecosystems (Nicholset al. 2008), little information exists regarding population size and the scale of their dispersal abilities, especially in the Neotropical region. Moreover, few studies have been devoted to exploring the population dynamics of dung beetles (Roslin 1999, 2000).
Forest structure and territory size relationship in the neotropical understorey insectivoreHenicorhina leucosticta
Authors: Vargas Luis Esteban , Sánchez Natalie Viviana , Avalos Gerardo
Published: January 2011

The neotropical terrestrial insectivoreHenicorhina leucosticta(Troglodytidae) maintains long-term territories through vocalizations and forages among leaf litter trapped in the understorey vegetation and ground litter. The relationship between forest structure andH. leucostictaterritory size was studied in La Selva Biological Station, Costa Rica, during the non-breeding season in 2009. Forest structure was measured by assessing canopy openness and leaf area index (LAI) using hemispherical photography, while territory size was estimated with the playback technique using local conspecific vocalizations. Mean territory area was 3.8 ± 2.8 ha (mean ± SD, n = 10). Territory radius length was similar in old-growth forest and abandoned agro-forest plantations. We found thatH. leucostictaterritory size decreased as median LAI increased. We propose that LAI is related to territory size through the amount of leaf fall and subsequent leaf litter accumulation over the understorey plants, which constitutes an important reservoir of arthropod prey and nest materials forH. leucosticta. The long-term supply of food resources is likely to affect territory size in this species, as well as other insectivorous birds with similar foraging behaviour. These results are congruent with the structural cues hypothesis.
Canopy assemblages of ants in a New Guinea rain forest
Authors: Janda Milan , Konečná Martina
Published: January 2011

The ant assemblages in two common tree species in primary lowland forest of New Guinea were explored using direct canopy access and tuna bait traps. The 19 trees investigated were occupied by 21 ant species of which 18 were canopy inhabitants. On average only 3.6 ant species per tree and 3 species per bait were found. Height of bait position was positively related to ant species richness, with the upper parts of the canopy being occupied by the highest number of species. On the other hand, tree species and study site did not have any effect on ant species richness nor on structure of the ant assemblages. Ant species appeared to be distributed randomly and we did not detect any effect of distance on similarity of ant assemblage occurring on the trees. The dominant species (Crematogaster polita) had certain negative effects on the presence of some species at food sources co-occurring at the same tree, but it did co-occur with the other ants to some extent as well. The majority of species found in the canopy were generalist omnivores (depending mainly on trophobionts or plant exudates).
Water
Authors: van Helden Paul
Published: January 2011

Water remains a scarce and valuable resource. Improving technologies for water purification, use and recycling should be a high priority for all branches of science.
Natural healing
Authors: Suran Melissa
Published: January 2011

Few environmental disasters are as indicting of humanity as major oil spills. Yet Nature has sometimes shown a remarkable ability to clean up the oil on its own.
In the womb's shadow
Authors: Nicoletto Silvia Fabiole , Rinaldi Andrea
Published: January 2011

How does the womb determine the future? Scientists have begun to uncover how environmental and maternal factors influence our long‐term health prospects.
Top Doc
Authors: Jacobs Howy
Published: January 2011

Whilst countries compete for recognition in life quality and social development, science and technology tend to take a back seat. Howy asks whether an index of scientific merit could help to raise standards worldwide.
12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era
Authors: Wóycicki Rafał , Witkowicz Justyna , Pawełkowicz Magdalena , Siedlecka Ewa , Gutman Wojciech , Pląder Wojciech , Seroczyńska Anna , Śmiech Mieczysław , Niemirowicz-Szczytt Katarzyna , Karpiński Stanisław , Malepszy Stefan , Przybecki Zbigniew
Published: January 2011

New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length and N50 2’324 Kbp. In the Celera/Arachne method contigs after prior pyrosequencing reads assembly (in the form of ~ 800 nt reads) were used together with the STCs as the input to Arachne assembler. Number of contigs were 15’764 of the length 193 Mbp with N50 23’280 bp. Number of supercontigs were 12’438 with the coverage of 323 Mbp and N50 323’092 bp. Correctness of the assemblies were proven after mapping 95,56% of 63’035 cucumber unigenes with the average identity 97,81%. Additionally 6 BAC/Fosmid cucumber sequences (totally 372’277 bp) had identity of 97,61% to the assembled genome. Average reads coverage of the genome were 14,20x and 98% of the assembled genome had reads coverage higher than 3x.Taking into consideration coverage used in already reported cucumber assemblies (32x by Miller J. et al., 2009 and 72x by Huang S. et al., 2009), as well as no differences in the quality and the best overall quantity statistics of contigs/scaffold lengths, the Celera approach used in this project should be considered the most optimal one to get omics-ready quality draft sequence of highly repeated eukaryotic genome.
A Note On The Denisova Cave mtDNA Sequence
Authors: Caldararo Niccolo , Guthrie Michael
Published: January 2011

The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
The power of “Green” Energy: plant trait influences on microbial competition and greenhouse gas production
Authors: Sutton-Grier Ariana , Megonigal J. Patrick
Published: January 2011

Background/Questions/Methods

Species vary in the eco-physiological traits they possess which means species may differentially influence ecosystem functions such as microbial activity. In wetland ecosystems it is important to understand how different plant species influence microbial competition for resources because competition affects microbial respiration and one of the products of anaerobic microbial respiration is methane, a potent greenhouse gas. Plants influence the availability of substrates for microbial respiration, both available carbon and terminal electron acceptors (such as Fe(III)). Because methanogenic microbes must compete with other microbes for respiration substrates and can be out-competed if conditions are more favorable for other microbes, plants can influence the outcome of microbial competition as well as overall rates of microbial activity by changing substrate availability. In this study, we examined how plant traits related to plant productivity and carbon inputs (belowground and total biomass, and photosynthesis) and plant traits related to oxygen inputs and terminal electron acceptor availability (root porosity and Fe(III) on roots) influence microbial competition and methane production from wetland soils.

Results/Conclusions

Overall microbial respiration rates were positively correlated with plant productivity, but methane production was negatively correlated with plant productivity, suggesting that carbon inputs were not stimulating methanogenesis. Evidence that alternative microbial respiratory pathways were stimulated with higher plant productivity included: (1) higher CO2:CH4 ratios from the microbial communities of plants with higher productivity and (2) greater oxidized iron (Fe(III)) on roots of plants with higher productivity. Both of these results indicate that as plant productivity and belowground biomass increased, microbes used alternative respiration pathways and produced less methane. These results indicate that plant community composition plays an important role in methane production in wetlands. Therefore, human disturbances, such as climate change, invasive species, and eutrophication, which result in shifts in plant community composition are likely to have profound effects on methane production in wetlands.
Pioneer Discovery of secondary gold deposits-unique bacterioforms andplacers in north Goa from deep coremetabiosphere
Authors: Kamat Nandkumar
Published: January 2011

Bacterioform secondary gold deposits were discovered in tilloid overlaying archaean base rock (metagraywacke) in Sanvordem rock formation, at the depth of 65 metres in north Goa , India and were confirmed optically as microbiogenic Gold. Multiple and unique forms were seen. This is claimed to be first report of bacterioform Gold in deep cores in Goa, India and Asia.
Surface modification of carbon nanotubes with dendrimers or hyperbranched polymers
Authors: Sun Jiao-Tong , Hong Chun-Yan , Pan Cai-Yuan
Published: January 2011

The different methods for modification of carbon nanotubes with dendrimers or hyperbranched polymers are summarized, and recent development is highlighted by discussing some representative examples in detail.
Back propagation artificial neural network (BPANN) based performance analysis of diesel engine using biodiesel
Authors: Barma Sumita Deb , Das Biplab , Giri Asis , Majumder S. , Bose P. K.
Published: January 2011

This work deals with the implementation of back propagation based artificial neural network (BPANN) model for prediction of the different diesel engine parameters, i.e., mean effective pressure, mechanical efficiency, fuel consumption, air-fuel ratio, and torque, to overcome the difficulties of practical experimentation and minimization of time and cost in this endeavor. The parameters provided as input to this model were engine speed, load and different biodiesel, and diesel fuel blends. The model has been trained with approximately 85% of the test results, and the rest were kept for prediction. The number of hidden layers and the number of neuron in each layer were varied to achieve the best predicting model. Once the model was ready, it had been used to predict the remaining data where the mean square error was as low as 6.51×10−4 and had a very low total R value. This work hereby shows that the BPANN based model can predict the performance of diesel engine fed with biodiesel and diesel fuel blends.
Solvation force induced by short range, exact dissipative particle dynamics effective surfaces on a simple fluid and on polymer brushes
Authors: Goicochea Armando Gama , Alarcón Francisco
Published: January 2011

The thermodynamic properties of a simple fluid confined by effective wall forces are calculated using Monte Carlo simulations in the grand canonical ensemble. The solvation force produced by polymer brushes of two different lengths is obtained also. For the particular type of model interactions used, known as the dissipative particle dynamics method, we find that it is possible to obtain an exact, simple expression for the effective force induced by a planar wall composed of identical particles that interact with those in the fluid. We show that despite the short range of all forces in the model, the solvation force can be finite at relatively large distances and therefore does not depend only on the range of the interparticle or solvent-surface forces. As for the polymer brushes, we find that the shape of the solvation force profiles is in fair agreement with scaling and self-consistent field theories. The applications and possible extensions of this work are discussed.