bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparison of the bioaccumulation potential of three freshwater organisms exposed to sediment-associated contaminants under laboratory conditions
Authors: Van Geest Jordana L , Poirier David G , Solomon Keith R , Sibley Paul K
Published: December 2010

In the field of sediment quality assessment, increased support has been expressed for using multiple species that represent different taxa, trophic levels, and potential routes of exposure. However, few studies have compared the bioaccumulation potential of various test species over a range of sediment contaminants (hydrophobic organics and metals). As part of the development and standardization of a laboratory bioaccumulation method for the Ontario Ministry of the Environment, the oligochaete Lumbriculus variegatus, mayfly nymph Hexagenia spp., and juvenile fathead minnow Pimephales promelas were exposed to a variety of field-contaminated sediments (n = 10) to evaluate their relative effectiveness for accumulating different contaminants (e.g., dichlorodiphenyltrichloroethane [DDT] and metabolites, polychlorinated biphenyls [PCBs), polycyclic aromatic hydrocarbons [PAHs), polychlorinated dibenzo-p-dioxins and dibenzofurans [PCDD/Fs), and heavy metals). Bioaccumulation was usually highest in L. variegatus but also most variable within and (relative measures) between sediments. Bioaccumulation was similar between L. variegatus and Hexagenia spp. in most of the sediments tested. Significant differences in bioaccumulation between species were observed for DDT, dichlorodiphenyldichloroethane (DDD), PAHs, and PCDD/Fs. The present study indicates that species-specific differences in bioaccumulation may, but do not always, exist and can vary with contaminant and sediment type. The choice of test species or combination to use in a standard test method may depend on the objectives of the sediment quality assessment and data requirements of an ecological risk assessment. The results of the present study provide insight for selection of test species and validation of laboratory methods for assessing bioaccumulation with these species, as well as valuable information for interpreting results of bioaccumulation tests. Environ. Toxicol. Chem. 2011; 30:939–949. © 2010 SETAC
Effect of 2,4-dihydroxybenzophenone (BP1) on early life-stage development of the marine copepod Acartia tonsa at different temperatures and salinities
Authors: Kusk Kresten Ole , Avdolli Manola , Wollenberger Leah
Published: December 2010

Benzophenone (BP)-type ultraviolet (UV) filters are widely used in cosmetic and sunscreen products and can enter the aquatic environment. Therefore, we investigated the subchronic toxicity of 2,4-dihydroxybenzophenone (BP1) on the marine calanoid copepod Acartia tonsa in an early life-stage development study. Since developmental endpoints depend on environmental conditions, a preceding study of A. tonsa development was performed at three temperatures, four salinities, four light:dark regimes, six food densities, and four culture densities. Times elapsed until 50% of the population had reached a copepodite stage (DT½) at the different conditions were calculated. The DT½ values decreased from 296 h at 15°C to 89 h at 25°C and were also affected by salinity (126 h at 15‰ and 167 h at 30‰), whereas the light:dark regime and culture density influenced development only to a minor extent. BP1 was found acutely toxic at 2.6 mg/L (48-h median lethal concentration [LC50]). The toxicity of BP1 on early life-stage development was studied in combinations of three temperatures (15, 20, 25°C) and three salinities (15, 20, 25‰) using five toxicant concentrations between 0.051 and 2 mg/L in each scenario. Concentrations causing 10 and 50% inhibition of development (EC10 and EC50) were determined. Acartia tonsa was most resistant towards BP1 at 20°C where an EC50 of 1.1 mg/L was found, whereas EC50 values were significantly lower at 15°C (0.49 mg/L) and 25°C (0.77 mg/L), respectively. The EC50 also decreased with increasing salinity. Our results demonstrate that environmental conditions do influence toxicity test results; thus, they need to be considered carefully when developing test protocols as well as for environmental risk assessments of chemicals. Environ. Toxicol. Chem. 2011; 30:959–966. © 2010 SETAC
Predicting multiallelic genes using unphased and flanking single nucleotide polymorphisms
Authors: Li Shuying S. , Wang Hongwei , Smith Anajane , Zhang Bo , Zhang Xinyi (Cindy) , Schoch Gary , Geraghty Daniel , Hansen John A. , Zhao Lue Ping
Published: December 2010

Recent advances in genotyping technologies have enabled genomewide association studies (GWAS) of many complex traits including autoimmune disease, infectious disease, cancer and heart disease. To facilitate interpretations and establish biological basis, it could be advantageous to identify alleles of functional genes, beyond just single nucleotide polymorphisms (SNPs) within or nearby genes. Leslie et al. ([2008] Am J Hum Genet 82:48–56) have proposed an Identity‐by‐Decent method (IBD‐based) for predicting human leukocyte antigen (HLA) alleles (multiallelic and highly polymorphic) with SNP data, and predictions have achieved a satisfactory accuracy on the order of 97%. Building upon their success, we introduce a complementary method for predicting highly polymorphic alleles using unphased SNP data as the training data set. Due to its generality and flexibility, the new method is readily applicable to large population studies. Applying it to HLA genes in a cohort of 630 healthy individuals as a training set, we constructed predictive models for HLA‐A, B, C, DRB1 and DQB1. Then, we performed a validation study with another cohort of 630 healthy individuals, and the predictive models achieved predictive accuracies for HLA alleles defined at intermediate or high resolution ranging as high as (100%, 97%) for HLA‐A, (98%, 96%) for B, (98%, 98%) for C, (97%, 96%) for DRB1 and (98%, 95%) for DQB1, respectively. These preliminary results suggest the feasibility of predicting other polymorphic genetic alleles, since HLA loci are almost certainly among most polymorphic genes. Genet. Epidemiol. 35:85‐92, 2011. © 2010 Wiley‐Liss, Inc.
Assessment of the biocompatibility of two novel, bionanocomposite scaffolds in a rodent model
Authors: Deeken C. R. , Esebua M. , Bachman S. L. , Ramshaw B. J. , Grant S. A.
Published: January 2011

Two novel, bionanocomposite scaffolds were evaluated in a rodent model over the course of three months to determine whether these scaffolds possessed adequate biocompatibility characteristics to warrant further evaluation as possible tissue reconstruction scaffolds. These bionanocomposite scaffolds were comprised of amine‐functionalized gold nanoparticles (AuNP) or silicon carbide nanowires (SiCNW) crosslinked to an acellular porcine diaphragm tendon. It was hypothesized that the addition of nanomaterials to the porcine tendon would also improve its biocompatibility by imparting a nanostructured surface. As early as seven days after implantation, both types of bionanocomposite scaffolds displayed evidence of granulation tissue and the beginning of scaffold remodeling with new collagen deposited by the host, and by ninety‐seven days the bionanocomposite scaffolds were completely remodeled with no evidence of any adverse host tissue reaction or scar tissue formation. The AuNP bionanocomposite scaffolds exhibited accelerated scaffold remodeling compared to the SiCNW scaffolds. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
A 3D numerical simulation of stress distribution and fracture process in a zirconia‐based FPD framework
Authors: Kou Wen , Li Decong , Qiao Jiyan , Chen Li , Ding Yansheng , Sjögren Göran
Published: January 2011

In this study, a numerical approach to the fracture behavior in a three‐unit zirconia‐based fixed partial denture (FPD) framework was made under mechanical loading using a newly developed three‐dimensional (3D) numerical modeling code. All the materials studied were treated heterogeneously and Weibull distribution law was applied to describe the heterogeneity. The Mohr‐Coulomb failure criterion with tensile strength cut‐off was utilized to judge whether the material was in an elastic or failed state. For validation, the fracture pattern obtained from the numerical modeling was compared with a laboratory test; they largely correlated with each other. Similar fracture initiation sites were detected both in the numerical simulation and in an earlier fractographic analysis. The numerical simulation applied in this study clearly described the stress distribution and fracture process of zirconia‐based FPD frameworks, information that could not be gained from the laboratory tests alone. Thus, the newly developed 3D numerical modeling code seems to be an efficient tool for prediction of the fracture process in ceramic FPD frameworks. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration
Authors: Bruckner Stefan , Boresch Stefan
Published: December 2010

We attempt to optimize the efficiency of thermodynamic integration, as defined by the minimal number of unphysical intermediate states required for the computation of accurate and precise free energy differences. The suitability of various numerical quadrature methods is tested. In particular, we compare the trapezoidal rule, Simpson's rule, Gauss‐Legendre, Gauss‐Kronrod‐Patterson, and Clenshaw‐Curtis integration, as well as integration based on a cubic spline approximation of the integrand. We find that Simpson's rule and spline integration are already significantly more efficient that the trapezoidal rule, i.e., correct free energy differences can be obtained using fewer λ‐states. We demonstrate that Simpson's rule can be used advantageously with nonequidistant values of the abscissa, which increases the flexibility of the method. Efficiency is enhanced even further if higher order methods, such as Gauss‐Legendre, Gauss‐Kronrod‐Patterson, or Clenshaw‐Curtis integration, are used; no more than seven λ‐states, which in the case of Clenshaw‐Curtis integration include the physical end states, were required for accurate results in all test problems studied. Thus, the performance of thermodynamic integration can equal that of Bennett's acceptance ratio method. We also show, however, that the high efficiency found here relies on the particular functional form of the soft‐core potential used; overall, thermodynamic integration is more susceptible to the details of the hybrid Hamiltonian used than Bennett's acceptance ratio method. Therefore, we recommend Bennett's acceptance ratio method as the most robust method to compute alchemical free energy differences; nevertheless, scenarios when thermodynamic integration may be preferable are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Combination of the CHARMM27 force field with united‐atom lipid force fields
Authors: Sapay Nicolas , Tieleman D. Peter
Published: December 2010

Computer simulations offer a valuable way to study membrane systems, from simple lipid bilayers to large transmembrane protein complexes and lipid‐nucleic acid complexes for drug delivery. Their accuracy depends on the quality of the force field parameters used to describe the components of a particular system. We have implemented the widely used CHARMM22 and CHARMM27 force fields in the GROMACS simulation package to (i) combine the CHARMM22 protein force field with two sets of united‐atom lipids parameters; (ii) allow comparisons of the lipid CHARMM27 force field with other lipid force fields or lipid‐protein force field combinations. Our tests do not show any particular issue with the combination of the all‐atom CHARMM22 force field with united‐atoms lipid parameters, although pertinent experimental data are lacking to assess the quality of the lipid‐protein interactions. The conversion utilities allow automatic generation of GROMACS simulation files with CHARMM nucleic acids and protein parameters and topologies, starting from pdb files using the standard GROMACS pdb2gmx method. CMAP is currently not implemented. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Regional differences in hyoid muscle activity and length dynamics during mammalian head shaking
Authors: Wentzel Sarah E. , Konow Nicolai , German Rebecca Z.
Published: December 2010

The sternohyoid (SH) and geniohyoid (GH) are antagonist strap muscles that are active during a number of different behaviors, including sucking, intraoral transport, swallowing, breathing, and extension/flexion of the neck. Because these muscles have served different functions through the evolutionary history of vertebrates, it is quite likely they will have complex patterns of electrical activity and muscle fiber contraction. Different regions of the SH exhibit different contraction and activity patterns during a swallow. We examined the dynamics of the SH and GH muscles during an unrestrained, and vigorous head shaking behavior in an animal model of human head, neck, and hyolingual movement. A gentle touch to infant pig ears elicited a head shake of several revolutions. Using sonomicrometry and intramuscular EMG, we measured regional (within) muscle strain and activity in SH and GH. We found that EMG was consistent across three regions (anterior, belly, and posterior) of each muscle. Changes in muscle length, however, were more complex. In the SH, mid‐belly length‐change occurred out‐of‐phase with the anterior and posterior end regions, but with a zero lag timing; the anterior region shortened before the posterior. In the GH, the anterior region shortened before and out‐of‐phase with the mid‐belly and posterior regions. Head shaking is a relatively simple reflex behavior, yet the underlying patterns of muscle length dynamics and EMG activity are not. The regional complexity in SH and GH, similar to regionalization of SH during swallowing, suggests that these anatomically simple hyoid strap muscles have more complex function than textbooks often suggest. J. Exp. Zool. 315:111–120, 2011. © 2010 Wiley‐Liss, Inc.
Temperature affects brain and pituitary gene expression related to reproduction and growth in the male blue gouramis, Trichogaster trichopterus
Authors: David Dalia , Degani Gad
Published: December 2010

This study examined the effect of temperature on reproduction and growth‐related factors in blue gourami males under nonreproductive and reproductive conditions. Males that were maintained under nonreproductive conditions did not build nest and the gonado‐somatic index (% GSI) was significantly higher in fish maintained at 27°C compared with fish maintained at 23°C. The relative mRNA levels of brain gonadotropin‐releasing hormone 3 (GnRH3), pituitary adenylate cyclase‐activating polypeptide (PACAP), insulin‐like growth factor‐1(IGF‐1), pituitary β‐luteinizing hormone (βLH), and prolactin were significantly higher when the fish were maintained at 27°C than at 23°C or 31°C. β‐Follicle‐stimulating hormone (βFSH) mRNA levels were significantly lower when maintained at 31°C than at the other temperatures. Nests were observed only in males under reproductive conditions. In these fish, higher mRNA levels of GnRH3, PACAP, βFSH, βLH and prolactin were detected at 27°C, and higher mRNA levels of IGF‐1 were detected at 23°C, when compared with other temperature of maintenance or with fish that did not build nest. In conclusion, we propose that temperature has more effect on the transcription of genes, associated with reproduction, than on those pertaining to growth. J. Exp. Zool. 315A:203–214, 2011. © 2011 Wiley‐Liss, Inc.
New insights on ctenophore neural anatomy: Immunofluorescence study in Pleurobrachia pileus (Müller, 1776)
Authors: Jager Muriel , Chiori Roxane , Alié Alexandre , Dayraud Cyrielle , Quéinnec Eric , Manuel Michaël
Published: December 2010

Ctenophores are non‐bilaterian animals sharing with cnidarians and bilaterians the presence of sensory receptors, nerve cells, and synapses, absent in placozoans and sponges. Although recent immunofluorescence studies have renewed our knowledge of cnidarian neuro‐anatomy, ctenophores have been much less investigated despite their importance to understanding the origin and early evolution of the nervous system. In this study, the neuro‐anatomy of the ctenophore Pleurobrachia pileus (Müller, 1776) was explored by whole‐mount fluorescent antibody staining using antibodies against tyrosylated α‐tubulin, FMRFamide, and vasopressin. We describe the morphology of nerve nets and their local specializations, and the organization of the aboral neuro‐sensory complex comprising the apical organ and polar fields. Two distinct nerve nets are distinguished: a mesogleal nerve net, loosely organized throughout body mesoglea, and a much more compact “nerve net” with polygonal meshes in the ectodermal epithelium. The latter is organized as a plexus of short nerve cords. This epithelial nervous system contains distinct sub‐populations of dispersed FMRFamide and vasopressin immunoreactive nerve cells. In the aboral neuro‐sensory complex, our most significant observations include specialized nerve nets underlying the apical organ and polar fields, a tangential bundle of actin‐rich fibers (interpreted as a muscle) within the polar fields, and distinct groups of neurons labeled by anti‐FMRFamide and anti‐vasopressin antibodies, within the apical organ floor. These results are discussed in a comparative perspective. J. Exp. Zool. (Mol. Dev. Evol.) 316:171–187, 2011. © 2010 Wiley‐Liss, Inc.
Aging and training and development willingness: Employee and supervisor mindsets
Authors: Van Vianen Annelies E. M. , Dalhoeven Betty A. G. W. , De Pater Irene E.
Published: January 2011

In this study, we examined individual and situational factors that impact the relationship between age and employee training and development willingness. We proposed that the relationship between age and training and development willingness would be moderated by employees' entity self‐theory and perceived developmental support. Furthermore, we investigated supervisors' beliefs about the avoidance orientations of older employees and whether these beliefs would moderate the relationship between employee age and training and development willingness. The proposed moderation effects were found. Moreover, it was shown that entity self‐theory beliefs, perceived developmental support, and supervisor avoidance orientation beliefs were related to the training and development willingness of older subordinates. Copyright © 2010 John Wiley & Sons, Ltd.
Screening for fetal aneuploidies at 11 to 13 weeks
Authors: Nicolaides Kypros H.
Published: January 2011

Effective screening for major aneuploidies can be provided in the first trimester of pregnancy. Screening by a combination of fetal nuchal translucency and maternal serum free‐β‐human chorionic gonadotrophin and pregnancy‐associated plasma protein‐A can identify about 90% of fetuses with trisomy 21 and other major aneuploidies for a false‐positive rate of 5%. Improvement in the performance of first‐trimester screening can be achieved by firstly, inclusion in the ultrasound examination assessment of the nasal bone and flow in the ductus venosus, hepatic artery and across the tricuspid valve, and secondly, carrying out the biochemical test at 9 to 10 weeks and the ultrasound scan at 12 weeks. Copyright © 2011 John Wiley & Sons, Ltd.
Challenges in the diagnosis of fetal non‐chromosomal abnormalities at 11–13 weeks
Authors: Syngelaki Argyro , Chelemen Teodora , Dagklis Themistoklis , Allan Lindsey , Nicolaides Kypros H.
Published: January 2011

Objective

To examine the performance of the 11–13 weeks scan in detecting non‐chromosomal abnormalities.

Methods

Prospective first‐trimester screening study for aneuploidies, including basic examination of the fetal anatomy, in 45 191 pregnancies. Findings were compared to those at 20–23 weeks and postnatal examination.

Results

Aneuploidies (n = 332) were excluded from the analysis. Fetal abnormalities were observed in 488 (1.1%) of the remaining 44 859 cases; 213 (43.6%) of these were detected at 11–13 weeks. The early scan detected all cases of acrania, alobar holoprosencephaly, exomphalos, gastroschisis, megacystis and body stalk anomaly, 77% of absent hand or foot, 50% of diaphragmatic hernia, 50% of lethal skeletal dysplasias, 60% of polydactyly, 34% of major cardiac defects, 5% of facial clefts and 14% of open spina bifida, but none of agenesis of the corpus callosum, cerebellar or vermian hypoplasia, echogenic lung lesions, bowel obstruction, most renal defects or talipes. Nuchal translucency (NT) was above the 95th percentile in 34% of fetuses with major cardiac defects.

Conclusion

At 11–13 weeks some abnormalities are always detectable, some can never be and others are potentially detectable depending on their association with increased NT, the phenotypic expression of the abnormality with gestation and the objectives set for such a scan. Copyright © 2011 John Wiley & Sons, Ltd.
Prediction of miscarriage and stillbirth at 11–13 weeks and the contribution of chorionic villus sampling
Authors: Akolekar Ranjit , Bower Sarah , Flack Nicola , Bilardo Caterina M. , Nicolaides Kypros H.
Published: January 2011

Objectives

To derive models for estimating risk of miscarriage and stillbirth from maternal characteristics and findings of first‐trimester screening for aneuploidies and to define the procedure‐related risk of chorionic villus sampling (CVS) after adjusting for these factors.

Method

We examined 33 856 singleton pregnancies at 11+0 to 13+6 weeks, and in 2396 CVS was carried out. Logistic regression analysis was used to examine the factors contributing to miscarriage and stillbirth.

Results

There were 33 310 (98.4%) livebirths, 404 (1.2%) miscarriages and 142 (0.4%) stillbirths. Models combining maternal characteristics, nuchal translucency, pregnancy‐associated plasma protein‐A (PAPP‐A) and flow in the ductus venosus detected 36.9% of miscarriages and 35.2% of stillbirths, at a 10% false‐positive rate. The risk of miscarriage and stillbirth increased with maternal age and weight, in women of African racial origin, in those with previous miscarriages or stillbirths and in those with low serum PAPP‐A and reversed A‐wave in the ductus venosus. The risk of miscarriage increased in women with pre‐existing diabetes mellitus, in those conceiving on ovulation‐induction drugs and in those with high fetal nuchal translucency, and the risk of stillbirth increased in women with chronic hypertension and in cigarette smokers. The expected number of miscarriages and stillbirths in the CVS group and the models derived from the non‐CVS group were 45 (95% prediction intervals 32–58) and 18 (95% prediction intervals 9–26), respectively. These expected numbers were not significantly different from the observed 44 and 15 cases (p = 0.881 and 0.480), respectively.

Conclusion

A high proportion of fetal losses can be predicted at 11 to 13 weeks. A model for such predictions can be used to assess the procedure‐related risks from CVS. Copyright © 2011 John Wiley & Sons, Ltd.
Prediction of spontaneous preterm delivery from maternal factors, obstetric history and placental perfusion and function at 11–13 weeks
Authors: Beta Jarek , Akolekar Ranjit , Ventura Walter , Syngelaki Argyro , Nicolaides Kypros H.
Published: January 2011

Objective

To develop a model for prediction of spontaneous delivery before 34 weeks based on maternal factors, placental perfusion and function at 11–13 weeks' gestation.

Methods

Two groups of studies: first, screening study of maternal characteristics, serum pregnancy‐associated plasma protein‐A (PAPP‐A), free β‐human chorionic gonadotrophin (β‐hCG) and uterine artery pulsatility index (PI). Second, case‐control studies of maternal serum or plasma concentration of placental growth factor (PlGF), placental protein 13 (PP13), a disintegrin and metalloprotease 12 (ADAM12), inhibin‐A and activin‐A. Regression analysis was used to develop a model for the prediction of spontaneous early delivery.

Results

Spontaneous early delivery occurred in 365 (1.1%) of the 34 025 pregnancies. A model based on maternal factors could detect 38.2% of the preterm deliveries in women with previous pregnancies at or beyond 16 weeks and 18.4% in those without, at a false positive rate (FPR) of 10%. In the preterm delivery group, compared with unaffected pregnancies there were no significant differences in the markers of placental perfusion or function, except for PAPP‐A which was reduced.

Conclusions

Patient‐specific risk of preterm delivery is provided by maternal factors and obstetric history. Placental perfusion and function at 11–13 weeks are not altered in pregnancies resulting in spontaneous early delivery. Copyright © 2011 John Wiley & Sons, Ltd.
Interstitial iron concentrations across multicrystalline silicon wafers via photoluminescence imaging
Authors: Liu AnYao , Fan Yang‐Chieh , Macdonald Daniel
Published: January 2011

We present high‐resolution images of the lateral distribution of interstitial iron across wafers from various positions along the length of a directionally solidified multicrystalline silicon ingot. Iron images were taken on wafers in the as‐cut state and also after two different phosphorus gettering steps performed at 845°C for 30 min, one with an additional anneal at 600°C for 5 h (referred to as extended gettering). The iron images were obtained by taking calibrated photoluminescence (PL) images of the low injection carrier lifetimes, before and after dissociation of iron–boron pairs via strong illumination. The iron images clearly reveal the internal gettering of iron during ingot cooling to grain boundaries and dislocation clusters, resulting in much lower dissolved iron concentrations at those features. In contrast, the PL images of gettered wafers exhibit a reversed distribution of dissolved iron compared to the as‐cut wafers, in other words, with higher interstitial iron concentrations at the grain boundaries than within the grains, most probably owing to the precipitated iron at the grain boundaries partly dissolving during the high‐temperature gettering process. Phosphorus gettering was found to result in a significant reduction of interstitial iron both inside the grains and at grain boundaries. The extended gettering resulted in a further significant reduction in all parts of the wafers and along all sections of the ingot. Copyright © 2011 John Wiley & Sons, Ltd.
Clinical observational gait analysis to evaluate improvement of balance during gait with vibrotactile biofeedback
Authors: Janssen Maurice , Pas Rianne , Aarts Jos , Janssen‐Potten Yvonne , Vles Hans , Nabuurs Christine , van Lummel Rob , Stokroos Robert , Kingma Herman
Published: January 2011

Background and Purpose. This study explores the effect of vibrotactile biofeedback on gait in 20 patients with bilateral vestibular areflexia using observational gait analysis to score individual balance. Methods. A tilt sensor mounted on the head or trunk is used to detect head or body tilt and activates, via a microprocessor, 12 equally distributed vibrators placed around the waist. Two positions of the tilt sensor were evaluated besides no biofeedback in three different gait velocity tasks (slow/fast tandem gait, normal gait on foam) resulting in nine different randomized conditions. Biofeedback activated versus inactivated was compared. Twenty patients (10 males, 10 females, age 39–77 years) with a bilateral vestibular areflexia or severe bilateral vestibular hyporeflexia, severe balance problems and frequent falls participated in this study. Results. Significant improvements in balance during gait were shown in our patients using biofeedback and sensor on the trunk. Only two patients showed a significant individual gait improvement with the biofeedback system, but in the majority of our patients, it increased confidence and a feeling of balance. Conclusion. This study indicates the feasibility of vibrotactile biofeedback for vestibular rehabilitation and to improve balance during gait. Copyright © 2011 John Wiley & Sons, Ltd.
Influenza A virus infection kinetics: quantitative data and models
Authors: Smith Amber M. , Perelson Alan S.
Published: December 2010

Influenza A virus is an important respiratory pathogen that poses a considerable threat to public health each year during seasonal epidemics and even more so when a pandemic strain emerges. Understanding the mechanisms involved in controlling an influenza infection within a host is important and could result in new and effective treatment strategies. Kinetic models of influenza viral growth and decay can summarize data and evaluate the biological parameters governing interactions between the virus and the host. Here we discuss recent viral kinetic models for influenza. We show how these models have been used to provide insight into influenza pathogenesis and treatment, and we highlight the challenges of viral kinetic analysis, including accurate model formulation, estimation of important parameters, and the collection of detailed data sets that measure multiple variables simultaneously. WIREs Syst Biol Med 2011 3 429–445 DOI: 10.1002/wsbm.129

This article is categorized under:

Analytical and Computational Methods > Computational Methods
A multifaceted approach to modeling the immune response in tuberculosis
Authors: Marino Simeone , Linderman Jennifer J. , Kirschner Denise E.
Published: December 2010

Tuberculosis (TB) is a deadly infectious disease caused byMycobacterium tuberculosis(Mtb). No available vaccine is reliable and, although treatment exists, approximately 2 million people still die each year. The hallmark of TB infection is the granuloma, a self‐organizing structure of immune cells forming in the lung and lymph nodes in response to bacterial invasion. Protective immune mechanisms play a role in granuloma formation and maintenance; these act over different time/length scales (e.g., molecular, cellular, and tissue scales). The significance of specific immune factors in determining disease outcome is still poorly understood, despite incredible efforts to establish several animal systems to track infection progression and granuloma formation. Mathematical and computational modeling approaches have recently been applied to address open questions regarding host–pathogen interaction dynamics, including the immune response to Mtb infection and TB granuloma formation. This provides a unique opportunity to identify factors that are crucial to a successful outcome of infection in humans. These modeling tools not only offer an additional avenue for exploring immune dynamics at multiple biological scales but also complement and extend knowledge gained via experimental tools. We review recent modeling efforts in capturing the immune response to Mtb, emphasizing the importance of a multiorgan and multiscale approach that has tuneable resolution. Together with experimentation, systems biology has begun to unravel key factors driving granuloma formation and protective immune response in TB.WIREs Syst Biol Med2011 3 479–489 DOI: 10.1002/wsbm.131

This article is categorized under:

Models of Systems Properties and Processes > Cellular Models

Models of Systems Properties and Processes > Mechanistic Models

Physiology > Mammalian Physiology in Health and Disease
Layers of epistasis: genome‐wide regulatory networks and network approaches to genome‐wide association studies
Authors: Cowper‐Sal·lari Richard , Cole Michael D. , Karagas Margaret R. , Lupien Mathieu , Moore Jason H.
Published: December 2010

The conceptual foundation of the genome‐wide association study (GWAS) has advanced unchecked since its conception. A revision might seem premature as the potential of GWAS has not been fully realized. Multiple technical and practical limitations need to be overcome before GWAS can be fairly criticized. But with the completion of hundreds of studies and a deeper understanding of the genetic architecture of disease, warnings are being raised. The results compiled to date indicate that risk‐associated variants lie predominantly in noncoding regions of the genome. Additionally, alternative methodologies are uncovering large and heterogeneous sets of rare variants underlying disease. The fear is that, even in its fulfillment, the current GWAS paradigm might be incapable of dissecting all kinds of phenotypes. In the following text, we review several initiatives that aim to overcome these limitations. The overarching theme of these studies is the inclusion of biological knowledge to both the analysis and interpretation of genotyping data. GWAS is uninformed of biology by design and although there is some virtue in its simplicity, it is also its most conspicuous deficiency. We propose a framework in which to integrate these novel approaches, both empirical and theoretical, in the form of a genome‐wide regulatory network (GWRN). By processing experimental data into networks, emerging data types based on chromatin immunoprecipitation are made computationally tractable. This will give GWAS re‐analysis efforts the most current and relevant substrates, and root them firmly on our knowledge of human disease.WIREs Syst Biol Med2011 3 513–526 DOI: 10.1002/wsbm.132

This article is categorized under:

Laboratory Methods and Technologies > Genetic/Genomic Methods
Ischemic kidney injury and mechanisms of tissue repair
Authors: Sabbahy Marwa El , Vaidya Vishal S.
Published: December 2010

Acute kidney injury (AKI) may result from ischemia or by the use of nephrotoxic agents. The incidence of AKI is variable, depends on comorbidities, and ranges from 5 to 35% in all hospitalized patients. The mechanisms of kidney injury exist within a large network of signaling pathways driven by interplay of inflammatory cytokines/chemokines, reactive oxygen species (ROS), and apoptotic factors. The effects and progression of injury overlap extensively with the remarkable ability of the kidney to repair itself both by intrinsic and extrinsic mechanisms that involve specific cell receptors/ligands as well as possible paracrine influences. The fact that kidney injury is usually part of a generalized comorbid condition makes it all the more challenging in terms of assessment of severity. In this review, we attempt to analyze the mechanisms of ischemic injury and repair in acute and chronic kidney disease from the perspectives of both preclinical and human studies.WIREs Syst Biol Med2011 3 606–618 DOI: 10.1002/wsbm.133

This article is categorized under:

Physiology > Mammalian Physiology in Health and Disease
Whole transcriptome analysis: what are we still missing?
Authors: Saxena Alka , Carninci Piero
Published: December 2010

New technologies such as tag‐based sequencing and tiling arrays have provided unique insights into the transcriptional output of cells. Many new RNA classes have been uncovered in the past decade, despite limitations in current technologies. Even as the repertoire of known functional elements of the transcriptome increases and contemporary technologies become mainstream, inadequacies in conventional protocols for library preparation, sequencing and mapping continue to hamper revelation of the entire transcriptome of cells. In this article, we review current protocols and outline their deficiencies. We also provide our view on what we may be overlooking in the transcriptome, despite exhaustive investigations, and indicate future areas of technological development and research. WIREs Syst Biol Med 2011 3 527–543 DOI: 10.1002/wsbm.135

This article is categorized under:

Laboratory Methods and Technologies > Genetic/Genomic Methods
Functional genomics of the brain: uncovering networks in the CNS using a systems approach
Authors: Konopka Genevieve
Published: December 2010

The central nervous system (CNS) is undoubtedly the most complex human organ system in terms of its diverse functions, cellular composition, and connections. Attempts to capture this diversity experimentally were the foundation on which the field of neurobiology was built. Until now though, techniques were either painstakingly slow or insufficient in capturing this heterogeneity. In addition, the combination of multiple layers of information needed for a complete picture of neuronal diversity from the epigenome to the proteome requires an even more complex compilation of data. In this era of high‐throughput genomics though, the ability to isolate and profile neurons and brain tissue has increased tremendously and now requires less effort. Both microarrays and next‐generation sequencing have identified neuronal transcriptomes and signaling networks involved in normal brain development, as well as in disease. However, the expertise needed to organize and prioritize the resultant data remains substantial. A combination of supervised organization and unsupervised analyses are needed to fully appreciate the underlying structure in these datasets. When utilized effectively, these analyses have yielded striking insights into a number of fundamental questions in neuroscience on topics ranging from the evolution of the human brain to neuropsychiatric and neurodegenerative disorders. Future studies will incorporate these analyses with behavioral and physiological data from patients to more efficiently move toward personalized therapeutics. WIREs Syst Biol Med 2011 3 628–648 DOI: 10.1002/wsbm.139

This article is categorized under:

Laboratory Methods and Technologies > Genetic/Genomic Methods
Human cardiomyogenesis and the need for systems biology analysis
Authors: Adam Young D. , DeQuach Jessica A. , Christman Karen L.
Published: December 2010

Cardiovascular disease remains the leading cause of death in the Western world and myocardial infarction is one of the primary facets of this disease. The limited natural self‐renewal of cardiac muscle following injury and restricted supply of heart transplants has encouraged researchers to investigate other means to stimulate regeneration of damaged myocardium. The plasticity of stem cells toward multiple lineages offers the potential to repair the heart following injury. Embryonic stem cells have been extensively studied for their ability to differentiate into early cardiomyocytes, however, the pathway has only been partially defined and inadequate efficiency limits their clinical applicability. Some studies have shown cardiomyogenesis from adult mesenchymal stem cells, from both bone marrow and adipose tissue, but their differentiation pathway remains poorly detailed and these results remain controversial. Despite promising results using stem cells in animal models of cardiac injury, the driving mechanisms behind their differentiation down a cardiomyogenic pathway have yet to be determined. Currently, there is a paucity of information regarding cardiomyogenesis on the systemic level. Stem cell differentiation results from multiple signaling parameters operating in a tightly regulated spatiotemporal pattern. Investigating this phenomenon from a systems biology perspective could unveil the abstruse mechanisms controlling cardiomyogenesis that would otherwise require extensive in vitro testing. WIREs Syst Biol Med 2011 3 666–680 DOI: 10.1002/wsbm.141

This article is categorized under:

Developmental Biology > Stem Cell Biology and Regeneration
Synthesis, Structure, Luminescent and Thermal Properties of Ytterbium(III) and Dysprosium(III) Complexes with 5‐Sulfoisophthalic Acid Sodium Salt
Authors: Wu Gang , Yin Fu‐Jun , Wei Hao , Liu Zhen‐Feng , Yin Gui
Published: January 2011

Two rare earth metal‐organic framework compounds [Ybsip(H2O)5]·3H2O (1) and [Dysip(H2O)4] (2) (NaH2sip: 5‐sulfoisophthalic acid sodium salt) were synthesized hydrothermally, and characterized by single‐crystal X‐ray diffraction, elemental analysis, and FT‐IR spectroscopy. In complex 1, each YbIII atom is nine‐coordinate with a distorted monocapped tetragonal prismatic arrangement. Two carboxylate groups of each sip3– molecule adopt the same μ1‐η1:η1 chelating coordination model connecting two YbIII atoms. The oxygen atoms of the sulfonate group do not participate in coordination with YbIII. The whole sip3– molecule acts as a μ2 bridge to form an one‐dimensional (1D) chain structure. The 1D chains are linked by hydrogen bonding to generate two‐dimensional layers, and are further combined together to form a three‐dimensional structure. In complex 2, the DyIII atom is nine‐coordinate with a distorted monocapped tetragonal antiprismatic arrangement. In each sip3– anion, two carboxylate groups take the same μ1‐η1:η1 chelating coordination mode, only an oxygen atom of sulfonate group bond to DyIII ion. The whole ligand sip3– acts as a μ3 bridge linking three different DyIII ions to generate a wave‐like two‐dimensional network with (6,3) topological structure. The two‐dimensional networks are further linked by O–H···O hydrogen bonds to form a three‐dimensional structure. The thermal and luminescent properties of both complexes are investigated.
A 3D Nickel(II) Coordination Polymer with cds Nets Constructed from 3‐Pyridin‐4‐yl‐benzoic Acid
Authors: Tang Long , Fu Feng , Gao Loujun , Wu Yapan , Liu Quirui , Gao Xiaoming
Published: January 2011

A new coordination polymer, [Ni(3,4‐pybz)2(H2O)]n (1), was hydrothermally synthesized from Ni(NO3)2·6H2O and an unsymmetrical 3‐pyridin‐4‐yl‐benzoic acid (3,4‐Hpybz). It was characterized by IR spectroscopy, elemental analysis, thermogravimetric analysis, and single‐crystal X‐ray diffraction. In complex 1, the 3,4‐pybz ligands act as linear linkers to join 4‐connected nickel(II) ion nodes, to build a 3D 4‐connected twofold interpenetrated 658‐cds coordination framework. In addition, the magnetic and thermal properties of complex 1 were also investigated.
Synthesis of Dimeric Methylzinc N,N‐Bis(2‐pyridylmethyl)carbamate via Addition of CO2 to a Methylzinc Amide
Authors: Kahnes Marcel , Görls Helmar , Westerhausen Matthias
Published: January 2011

Exposure of a THF solution of bis(methylzinc) tert‐butylamide bis(2‐pyridylmethyl)amide (1) to a carbon dioxide atmosphere leads to formation of dimeric methylzinc bis(2‐pyridylmethyl)carbamate (2). The preparation of 2 from 1 and CO2 is a two‐step reaction and affords ligand redistribution after insertion of CO2 into the Zn–N bonds. The central structural fragment is an eight‐membered (ZnO2C)2 ring with tetracoordinate zinc atoms and planar C2N–CO2 carbamate units in a boat conformation.
Palm Olein and Olive Oil Cause a Higher Increase in Postprandial Lipemia Compared with Lard but Had No Effect on Plasma Glucose, Insulin and Adipocytokines
Authors: Teng Kim‐Tiu , Nagapan Gowri , Cheng Hwee Ming , Nesaretnam Kalanithi
Published: December 2010

Postprandial lipemia impairs insulin sensitivity and triggers the pro‐inflammatory state which may lead to the progression of cardiovascular diseases. A randomized, crossover single‐blind study (n= 10 healthy men) was designed to compare the effects of a high‐fat load (50 g fat), rich in palmitic acid from both plant (palm olein) or animal source (lard) versus an oleic acid‐rich fat (virgin olive oil) on lipemia, plasma glucose, insulin and adipocytokines. Serum triacylglycerol (TAG) concentrations were significantly lower after the lard meal than after the olive oil and palm olein meals (meal effectP= 0.003; time effectP< 0.001). The greater reduction in the plasma non‐esterified free fatty acids levels in the lard group compared to the olive oil meal was mirrored by the changes observed for serum TAG levels (P< 0.05). The magnitude of response for plasma glucose, insulin and adipocytokines [interleukin‐6 (IL‐6), tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β) and leptin] were not altered by the type of dietary fats. A significant difference in plasma IL‐1β was found over time following the three high fat loads (time effectP= 0.036). The physical characteristics and changes in TAG structure of lard may contribute to the smaller increase in postprandial lipemia compared with palm olein. A high fat load but not the type of fats influences concentrations of plasma IL‐1β over time but had no effect on other pro‐inflammatory markers tested in the postprandial state.
Lumbopelvic fusion with a new fixation technique in lumbosacral agenesis: Three cases
Authors: Yazici Muharrem , Akel Ibrahim , Demirkiran Halil Gokhan
Published: December 2010

Purpose

Patients with lumbosacral agenesis characteristically sit on their iliac wings with their torsos bent forward, which yields an increase in intra-abdominal pressure and, subsequently, negative effects on their diaphragm. The sacrum is not available as an anchor point for instrumentation. Dunn-McCarthy rods or Galveston fixations cannot be performed due to these limited anatomic properties. On the other hand, the absence of necessary bone mass for fusion anteriorly limits the fusion interventions to the posterior. Therefore, a secure and rigid fixation is essential to preclude the need for an external support. There are limited publications discussing different techniques due to the relatively rare incidence of the disease. We report the clinical and radiological results of a new technique applied to three patients in which previously recommended methods are modified.

Methods

Two 6-year-old female patients and one 5-year-old male patient with lumbosacral agenesis underwent posterior lumbopelvic instrumentation and fusion. Together with standard pedicle screw spinal instrumentation, pelvic fixation is obtained with a combination of supero-inferior directed rod and/or screw to overcome deforming forces created at the flexion–extension pivot points of the lumbopelvic junction. Autogenic anterior tibial cortical structural graft is used for laminopelvic bridging, and demineralized bone matrix is used for the augmentation of osteoinduction. A single leg hip spica is applied for 4 months to protect the fixation.

Results

Total correction yielded an aligned spine with a posture that allows for sitting on the ischial spines for all three patients. Solid fusion was observed to maintain this correction at the final follow-up.

Conclusion

The use of new-generation pediatric spinal instrumentation systems with a new technique without knee disarticulation provides a safe and effective fixation and fusion in lumbosacral agenesis.
The function of bone morphogenetic proteins in the human ovary
Authors: Yoshino Osamu , Shi Jia , Osuga Yutaka , Harada Miyuki , Nishii Osamu , Yano Tetsu , Taketani Yuji
Published: January 2011

The gonadotropins, follicle‐stimulating hormone (FSH), and luteinizing hormone (LH), are of particular importance in ovarian physiology. However, FSH receptors and LH receptors are not expressed until the secondary follicle stage, indicating that initiation of follicular growth is independent of the gonadotropins. Among many intra‐ovarian growth factors, many studies have shown that bone morphogenetic proteins (BMPs) play pivotal roles in regulating the early phases of follicular growth. The BMP system induces the gonadotropin system by modulating gonadotropin receptors in early‐stage follicles. Interestingly, the BMP system also prevents precocious maturation of the follicle by suppressing luteinization. Signals provoked by the preovulatory LH surge eliminate BMPs, enabling luteinization to progress. Thus, the BMP system and the gonadotropin system seem to cooperate in regulating follicular development, maturation, and luteinization.
Implementation of Environmental Sustainability in Business: Suggestions for Improvement
Authors: Brennan Linda , Binney Wayne , McCrohan Janelle , Lancaster Narelle
Published: December 2010

This paper discusses the options for implementing ‘sustainable’ environmental business strategies that are acceptable to a multiplicity of stakeholders. To evaluate the current situation in Australia a content analysis of the web pages for leading companies indicates that there is little tangible evidence that sustainable business practices are being implemented. The authors propose several directions for research into substantive issues between ethical behaviour, corporate social responsibility and environmentally sustainable behaviour for business. Each of these areas is developing research in relative isolation. However, we argue that this paradigmatic divide is limiting the opportunities for research to provide real insight into seemingly intractable problems.