bluuebunny/crossref_metadata_2025 huggingface dataset:
Automatic assignment of 1H‐NMR spectra of small molecules
Authors: Cobas C. , Seoane F. , Vaz E. , Bernstein M. A. , Dominguez S. , Pérez M. , Sýkora S.
Published: August 2013

A novel data‐evaluation procedure for the automatic atom to peak or multiplet assignment of 1H‐NMR spectra of small molecules has been developed using a fast and robust expert system. The applicability and reliability of the method are demonstrated by comparison of a manually assigned database of 1H‐NMR spectra with the assignments produced by the automatic procedure. The results of this analysis show an excellent success ratio, indicating that this new algorithm can have a major impact as a time saving tool for the organic chemist. A new graphical feature used to illustrate both the stability and quality of the elementary assignments is also introduced. Copyright © 2013 John Wiley & Sons, Ltd.
Management of cognitive radio ad hoc networks using a congestion‐based metric
Authors: Potier Paul , Qian Lijun
Published: August 2013

In this paper, we propose a new network management protocol to address the unique challenges of managing cognitive radio ad hoc networks that have distributed, multihop architectures with dynamic spectrum availability. We focus on performance management for these networks, and address the problem of network congestion for secondary users, because of its significant impact on data throughput. Specifically, we define a performance metric, the average congestion level of the network, and derive it analytically as a function of the primary users’ activities and the secondary users’ strategy. For practical implementation, we further propose a cluster‐based management architecture that utilizes a designated central manager and cluster heads that function as distributed managers. The cluster heads collect information from multiple layers of the protocol stack using new MIB (management information base) variables to capture the characteristics of cognitive radio ad hoc networks, such as the location‐dependent spectrum availability. The objective of the management action is to utilize a network‐level view of the congestion situation in the network by directing the secondary users to select the highest‐quality links available and avoid congested clusters. This hierarchical networkmanagement design allows us to take advantage of its scalability to achieve near‐real‐time management. Numerical results demonstrate the effectiveness of the proposed scheme. Copyright © 2013 John Wiley & Sons, Ltd.
Outcome of patients with stage II/favorable histology wilms tumor with and without local tumor spill: A report from the National Wilms Tumor Study Group
Authors: Green Daniel M. , Breslow Norman E. , D'Angio Giulio J. , Malogolowkin Marcio H. , Ritchey Michael L. , Evans Audrey E. , Beckwith J. Bruce , Perlman Elizabeth J. , Shamberger Robert C. , Peterson Susan , Grundy Paul E. , Dome Jeffrey S. , Thomas Patrick R.M. , Kalapurakal John A.
Published: August 2013

Background

Intra‐operative tumor spill increases the risk of local recurrence of Wilms tumor, and adversely impacts relapse‐free (RFS) and overall survival (OS) rates.

Methods

Surgical checklists, operative notes, institutional pathology reports, central pathology review and flow sheets of 602 patients registered between August 1986 and September 1994 on National Wilms Tumor Study—4 as randomized, followed or switched and coded as Final Stage II, favorable histology (FH) were reviewed. RFS and OS were estimated using the Kaplan–Meier method. Hazard ratios (HRs) were estimated using the Cox model and tested for statistical significance by the log‐rank test.

Results

Four hundred ninety‐nine patients were found after review to have Stage II, FH Wilms tumor. The 8‐year RFS percentages were 85.0% (95% confidence interval (CI): 81.1%, 88.1%) for those with no spill compared to 75.7% (65.8%, 83.2%) for those with spill. The 8‐year OS percentages were 95.6% (93.1%, 97.3%) for those with no spill compared to 90.3% (82.2%, 94.9%) for those with spill. The HR for relapse among those with spill was 1.55 ((95%CI: 0.97,2.51),P = 0.067) and the HR for death was 1.94 ((0.92,4.09),P = 0.077).

Conclusions

RFS and OS were lower for patients who had intra‐operative tumor spill. The majority of NWTS Stage II, FH patients with intra‐operative tumor spill have an overall excellent outcome when treated with two drug chemotherapy (vincristine and actinomycin D) and no abdominal irradiation. Pediatr Blood Cancer 2014;61:134–139. © 2013 Wiley Periodicals, Inc.
Malformations, genetic abnormalities, and wilms tumor
Authors: Dumoucel S. , Gauthier‐Villars M. , Stoppa‐Lyonnet D. , Parisot P. , Brisse H. , Philippe‐Chomette P. , Sarnacki S. , Boccon‐Gibod L. , Rossignol S. , Baumann C. , Aerts I. , Bourdeaut F. , Doz F. , Orbach D. , Pacquement H. , Michon J. , Schleiermacher G.
Published: August 2013

Background

Wilms Tumor (WT) can occur in association with tumor predisposition syndromes and/or with clinical malformations. These associations have not been fully characterized at a clinical and molecular genetic level. This study aims to describe clinical malformations, genetic abnormalities, and tumor predisposition syndromes in patients with WT and to propose guidelines regarding indications for clinical and molecular genetic explorations.

Procedure

This retrospective study analyzed clinical abnormalities and predisposition syndromes among 295 patients treated for WT between 1986 and 2009 in a single pediatric oncological center.

Results

Clinically identified malformations and predisposition syndromes were observed in 52/295 patients (17.6%). Genetically proven tumor predisposition syndromes (n = 14) frequently observed were syndromes associated with alterations of the chromosome WT1 region such as WAGR (n = 6) and Denys–Drash syndromes (n = 3), syndromes associated with alterations of the WT2 region (Beckwith–Wiedeman syndrome, n = 3), and Fanconi anemia (n = 2). Hemihypertrophy and genito‐urinary malformations (n = 12 and n = 16, respectively) were the most frequently identified malformations. Other different syndromes or malformations (n = 10) were less frequent. Median age of WT diagnosis was significantly earlier for children with malformations than those without (27 months vs. 37 months, P = 0.0009). There was no significant difference in terms of 5‐year EFS and OS between WT patients without or with malformations.

Conclusions

The frequency of malformations observed in patients with WT underline the need of genetic counseling and molecular genetic explorations for a better follow‐up of these patients, with a frequently good outcome. A decisional tree, based on clinical observations of patients with WT, is proposed to guide clinicians for further molecular genetic explorations. Pediatr Blood Cancer 2014;61:140–144. © 2013 Wiley Periodicals, Inc.
Effect of functionalized nanosilica on properties of polyoxymethylene‐matrix nanocomposites
Authors: Guo Liping , Xu Xiangmin , Zhang Yudong , Zhang Zhijun
Published: August 2013

Amino group and methyl group functionalized nano‐silica (coded as RNS and DNS) particulates were separately used as nanofillers to prepare polyxymethylene‐matrix (denoted as POM‐matrix) nanocomposites by melt blending. The tensile strength, Young's modulus, and impact toughness of as‐prepared POM‐matrix nanocomposites were measured, and their thermal decomposition behavior and crystallization behavior were analyzed by means of thermogravimetric measurement and differential scanning calorimetry and polarized light microscope. Moreover, the morphology of as‐prepared POM‐matrix nanocomposites was observed with a transmission electron microscope. Results show that incorporating a proper content of RNS and DNS contributes to improve the tensile strength, Young's modulus and impact toughness of POM, and POM‐DNS nanocomposites with a high content of inorganic filler have better mechanical properties than POM‐RNS counterparts. Besides, POM‐matrix nanocomposites have a higher crystallization onset temperature and a smaller grain size than neat POM, which is due to the heterogeneous nucleation effect of DNS and RNS. Moreover, incorporating RNS containing surface amino group helps to increase the thermal stability of POM‐RNS nanocomposites and leads to an increase of initial decomposition temperature by about 27°C; but the introduction of DNS has little effect on the thermal decomposition behavior of POM. The reason lies in that RNS containing surface amino group can strongly chemically interact with thermal decomposed products of POM (it can absorb formaldehyde and formic acid generated via thermal decomposition of POM) but DNS with surface methyl group cannot absorb formaldehyde and formic acid. POLYM. COMPOS., 35:127–136, 2014. © 2013 Society of Plastics Engineers
Placenta membranacea with placenta accreta: radiologic diagnosis and clinical implications
Authors: Pereira Nigel , Yao Ruofan , Guilfoil Daniel S. , Richard Scott D. , Plante Lauren A.
Published: August 2013

What's already known about this topic?

Placenta membranacea is a rare developmental abnormality of the human placenta associated with abnormal placental adherence.

This placental abnormality is usually diagnosed after post‐delivery pathologic examination of the placenta.

What does this study add?

We highlight the utility of magnetic resonance imaging as an adjunct to ultrasonography in the antenatal diagnosis of placenta membranacea.

Magnetic resonance imaging can optimize the diagnosis of abnormal placental adherence in the presence of placenta membranacea, thereby influencing antenatal management, as well as the timing and route of delivery.
Psychological morbidity and stress but not social factors influence level of fear of cancer recurrence in young women with early breast cancer: results of a cross‐sectional study
Authors: Thewes B. , Bell M. L. , Butow P. , Beith J. , Boyle F. , Friedlander M. , McLachlan S. A. ,   the Members of the FCR Study Advisory Committee
Published: August 2013

Background

Fear of cancer recurrence (FCR) is a common problem amongst survivors. Past research has shown that young women with breast cancer are particularly vulnerable to FCR, yet few previous studies have specifically examined FCR in this subgroup.

Aims

The aim of the study is to explore the relationship between FCR, psychological morbidity and social factors. A secondary aim was to explore the relationship between clinical levels of FCR and generalised anxiety disorder (GAD) and hypochondriasis.

Method

Two hundred eighteen breast cancer survivors (aged 18–45 years at diagnosis) diagnosed at least 1 year prior were recruited through seven metropolitan oncology clinics and two breast cancer consumer groups. Participants completed a web‐based questionnaire, which assessed FCR, psychological functioning, generalised anxiety, hypochondriasis and items exploring past cancer‐related experiences, attitudes to future childbearing, social support and correlates were identified using linear regression.

Results

Psychological morbidity scales measuring anxiety and psychological functioning and stressful life events were significantly associated with FCR in adjusted and unadjusted models (p < 0.0001). Past cancer experiences, children, social support and attitudes to childrearing were not associated with FCR. Among those with clinical levels of FCR (n = 152), 43% met screening criteria for hypochondriasis, and 36% met screening criteria for GAD.

Conclusions

This study shows psychological morbidity is associated with FCR, but the majority of women with high levels of FCR do not also meet the criteria for a clinical level of GAD or hypochondriasis. Understanding the factors that make young women vulnerable to FCR is important to help guide the development of FCR‐specific interventions for this subgroup. Copyright © 2013 John Wiley & Sons, Ltd.
New Estimates of Permafrost Evolution during the Last 21 k Years in Eurasia using Numerical Modelling
Authors: Kitover D. C. , van Balen R. T. , Roche D. M. , Vandenberghe J. , Renssen H.
Published: August 2013

The evolution of past permafrost since the Last Glacial Maximum (LGM) is simulated using the Vrije Universiteit Amsterdam Permafrost (VAMPER) model. This method is different from a proxy‐based approach which translates reconstructed air temperatures to estimate past permafrost extent and thickness. First, a sensitivity analysis was performed to assess the behaviour of the model. Then five case studies within Eurasia were performed using mean annual ground surface temperatures derived from an Earth system model as the surface forcing. In Central and West Siberia, the simulated LGM permafrost thicknesses of 730–940 m and 365–445 m, respectively, agree well with previous estimates. The LGM and present‐day estimates for South Russia (9–15 m) are underestimated, which is likely due to a highly simplified land‐atmosphere coupling. In West and Central Europe, however, the VAMPER model was not able to produce permafrost during LGM conditions, which is due to previously recognised biases of the Earth system model. A supplementary simulation was then performed, resulting in an LGM permafrost thickness estimate of 260–320 m. Average thawing rates are on the order of 1 to 3 cm/yr except for Central Siberia, where permafrost thawed at rates of 0.3 to 0.4 cm/yr. Overall results of these simulations provide a basis for future improvement in modelling the permafrost‐climate relationship over millennia. Copyright © 2013 John Wiley & Sons, Ltd.
MSMB gene variant alters the association between prostate cancer and number of sexual partners
Authors: Stott‐Miller Marni , Wright Jonathan L. , Stanford Janet L.
Published: August 2013

BACKGROUND

Recently, a genetic variant (rs10993994) in the MSMB gene associated with prostate cancer (PCa) risk was shown to correlate with reduced prostate secretory protein of 94 amino acids (PSP94) levels. Although the biological activity of PSP94 is unclear, one of its hypothesized functions is to protect prostatic cells from pathogens. Number of sexual partners and a history of sexually transmitted infections (STIs) have been positively associated with PCa risk, and these associations may be related to pathogen‐induced chronic prostatic inflammation. Based on these observations, we investigated whether MSMB genotype modifies the PCa‐sexual history association.

METHODS

We estimated odds ratios (ORs) and 95% confidence intervals (CIs) for the association between number of sexual partners and PCa by fitting logistic regression models, stratified by MSMB genotype, and adjusted for age, family history of PCa, and PCa screening history among 1,239 incident cases and 1,232 controls.

RESULTS

Compared with 1–4 female sexual partners, men with ≥15 such partners who carried the variant T allele of rs10993994 were at increased risk for PCa (OR = 1.32; 95% CI, 1.03–1.71); no association was observed in men with the CC genotype (OR = 1.03; 95% CI, 0.73–1.46; P = 0.05 for interaction). Similar estimates were observed for total sexual partners (any T allele OR = 1.37; 95% CI, 1.07–1.77; CC genotype OR = 1.11; 95% CI, 0.79–1.55; P = 0.06 for interaction).

CONCLUSIONS

The rs10993994 genotype in the MSMB gene modifies the association between number of sexual partners and PCa risk. These findings support a hypothesized biological mechanism whereby prostatic infection/inflammation may enhance risk of PCa. Prostate 73:1803–1809, 2013. © 2013 Wiley Periodicals, Inc.
Characterization of endocytic uptake of MK2‐inhibitor peptides
Authors: Brugnano Jamie , McMasters James , Panitch Alyssa
Published: August 2013

Cell penetrating peptides (CPP) have been widely used to increase the cellular delivery of their associated cargo. Multiple modes of uptake have been identified; however, they cannot be predicted a priori. Elucidating these mechanisms is important for understanding peptide function as well as further optimizing cellular delivery. We have developed a class of mitogen activated protein kinase activated protein kinase 2 (MK2) inhibitor peptides, named FAK and YARA that utilize CPP domains to gain cellular access. In this study, we investigate the mechanism of endocytosis of these MK2 inhibitors by examining the uptake of fluorescently labeled peptide in human monocyte (THP‐1) and mesothelial cells, and looking for colocalization with known markers of endocytosis. Our results indicate that uptake of the MK2 inhibitors was minimally enhanced by the addition of the fluorescent label, and that the type of endocytosis used by the inhibitor depends on several factors including concentration, cell type, and which CPP was used. We found that in THP‐1 cells, the uptake of YARA occurred primarily via macropinocytosis, whereas FAK entered via all three mechanisms of endocytosis examined in this study. In mesothelial cells, uptake of YARA occurred via caveolae‐mediated endocytosis, but became less specific at higher concentrations; whereas uptake of FAK occurred through clathrin‐mediated endocytosis. In all cases, the delivery resulted in active inhibition of MK2. In summary, the results support endocytic uptake of fluorescently labeled FAK and YARA in two different cell lines, with the mechanism of uptake dependent on extracellular concentration, cell type, and choice of CPP. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Thermoelectric properties of Au nanoparticle‐supported Sb1.6Bi0.4Te3 synthesized by a γ‐ray irradiation method
Authors: Jung Doyoung , Kurosaki Ken , Seino Satoshi , Ishimaru Manabu , Sato Kazuhisa , Ohishi Yuji , Muta Hiroaki , Yamanaka Shinsuke
Published: August 2013

SbBiTe alloys have been some of the most efficient thermoelectric materials near room temperature. Here we synthesized a complete nanocomposite using γ‐ray irradiation, in which Au/AuTe2 nanoparticles are dispersed uniformly without aggregation in the Sb1.6Bi0.4Te3 matrix. The lattice thermal conductivity was significantly reduced mainly due to the increased number of interfaces for phonon scattering between the nanoparticles and the matrix phase, thereby resulting in clear enhancement of dimensionless figure of merit (ZT). The maximum ZT value of the Au/AuTe2 nanoparticle‐supported Sb1.6Bi0.4Te3 nanocomposite was 1.01 at 423 K, which is about 18% higher than the maximum ZT value of Sb1.6Bi0.4Te3.
Multi‐pin dc glow discharge PECVD for uniform growth of vertically oriented graphene at atmospheric pressure
Authors: Bo Zheng , Ma Wei , Wang Pengxiang , Wu Erka , Yang Weicheng , Yu Kehan , Zhang Xiaopeng , Yan Jianhua , Cen Kefa
Published: August 2013

Atmospheric normal glow discharge plasma‐enhanced chemical vapor deposition (ANGD‐PECVD) holds great potential for the industrial in‐line continuous growth of vertically oriented graphene (VG) nanosheets. However, conventional single‐pin‐to‐plate electrode arrangement owns the drawback of producing a non‐uniform electric field, subsequently leading to a fairly poor uniformity of the as‐grown VG nanosheets. This work offers a proof of concept on a novel multi‐pin ANGD‐PECVD method for the uniform growth of VG nanosheets. Based on the numerical calculation, the dual‐pin ANGD can provide a more uniform electric field compared with the single‐pin counterpart, due to the compensation from adjacent pins and a lower integrated curvature of the discharge electrode. Experimental results demonstrate that ANGD with a four‐pin discharge electrode is able to significantly improve the uniformity of the localized current density at the growth substrate, and further realize the growth of VG nanosheets with excellent homogeneity in terms of morphology and structure. Successful application of the as‐grown VG nanosheets working as the active materials of a supercapacitor is illustrated at the end of this work.
Passivation of black silicon boron emitters with atomic layer deposited aluminum oxide
Authors: Repo Päivikki , Benick Jan , Gastrow Guillaume von , Vähänissi Ville , Heinz Friedemann D. , Schön Jonas , Schubert Martin C. , Savin Hele
Published: August 2013

The nanostructured surface – also called black silicon (b‐Si) – is a promising texture for solar cells because of its extremely low reflectance combined with low surface recombination obtained with atomic layer deposited (ALD) thin films. However, the challenges in keeping the excellent optical properties and passivation in further processing have not been addressed before. Here we study especially the applicability of the ALD passivation on highly boron doped emitters that is present in crystalline silicon solar cells. The results show that the nanostructured boron emitters can be passivated efficiently using ALD Al2O3 reaching emitter saturation current densities as low as 51 fA/cm2. Furthermore, reflectance values less than 0.5% after processing show that the different process steps are not detrimental for the low reflectance of b‐Si. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An inherently mass‐conserving semi‐implicit semi‐Lagrangian discretization of the deep‐atmosphere global non‐hydrostatic equations
Authors: Wood Nigel , Staniforth Andrew , White Andy , Allen Thomas , Diamantakis Michail , Gross Markus , Melvin Thomas , Smith Chris , Vosper Simon , Zerroukat Mohamed , Thuburn John
Published: August 2013

Following previous work on an inherently mass‐conserving semi‐implicit (SI) semi‐Lagrangian (SL) discretization of the two‐dimensional (2D) shallow‐water equations and 2D vertical slice equations, that approach is here extended to the 3D deep‐atmosphere, non‐hydrostatic global equations. As with the reduced‐dimension versions of this model, an advantage of the approach is that it preserves the same basic structure as a standard, non‐mass‐conserving, SISL version of the model. Additionally, the model is simply switchable to hydrostatic and/or shallow‐atmosphere forms. It is also designed to allow simple switching between various geometries (Cartesian, spherical, spheroidal). The resulting mass‐conserving model is applied to a standard set of test problems for such models in spherical geometry and compared with results from the standard SISL version of the model.
The impact of downscaled initial condition perturbations on convective‐scale ensemble forecasts of precipitation
Authors: Kühnlein C. , Keil C. , Craig G. C. , Gebhardt C.
Published: August 2013

A major issue in convective‐scale ensemble prediction systems (EPSs) is the specification of effective initial condition perturbations (ICPs). The present work considers the suitability of downscaled ICPs from a multi‐model global EPS for short‐range regional ensemble forecasts of convective precipitation at convection‐permitting resolution. Previous studies indicated the importance of convective‐scale initial condition uncertainties, with the most pronounced impact in weather conditions characterised by weak versus strong synoptic‐scale forcing of convection. However, the downscaled ICPs do not explicitly represent small‐scale uncertainty, which questions their effectiveness in convective‐scale EPSs. To investigate the issue, the high‐resolution ensemble system of the Deutscher Wetterdienst, COSMO‐DE‐EPS, which includes physics perturbations and lateral boundary condition perturbations in addition to ICPs, is employed. Forecasts are compared with a second EPS, identical but without ICPs, for a period of 3.5 months in the central European warm season. Weakly forced conditions are considered separately from strongly forced conditions, using an objective classification based on the area‐averaged convective adjustment time‐scale.

Generally for all EPSs, forecast quality measures show a distinct behaviour in strong versus weak forcing conditions. However, the impact of the ICPs is found to be similar in the two regimes. The impact of the ICPs is clearly largest and positive (consistently in terms of ensemble variance and probabilistic forecast quality, but negative for the equitable threat score) in the first six forecast hours when the ICPs dominate the physics perturbations and lateral boundary condition perturbations. The ICPs then decay relatively quickly with lead time as the physics perturbations and lateral boundary condition perturbations start to become important and later dominant. Probabilistic precipitation forecasts by the EPSs outperform the deterministic COSMO‐DE at the same convection‐permitting resolution, and this more strongly in the first nine forecast hours with the EPS applying the ICPs.
A marginal‐mean ANOVA approach for analyzing multireader multicase radiological imaging data
Authors: Hillis Stephen L.
Published: August 2013

The correlated‐error ANOVA method proposed by Obuchowski and Rockette (OR) has been a useful procedure for analyzing reader‐performance outcomes, such as the area under the receiver‐operating‐characteristic curve, resulting from multireader multicase radiological imaging data. This approach, however, has only been formally derived for the test‐by‐reader‐by‐case factorial study design. In this paper, I show that the OR model can be viewed as a marginal‐mean ANOVA model. Viewing the OR model within this marginal‐mean ANOVA framework is the basis for the marginal‐mean ANOVA approach, the topic of this paper. This approach (1) provides an intuitive motivation for the OR model, including its covariance‐parameter constraints; (2) provides easy derivations of OR test statistics and parameter estimates, as well as their distributions and confidence intervals; and (3) allows for easy generalization of the OR procedure to other study designs. In particular, I show how one can easily derive OR‐type analysis formulas for any balanced study design by following an algorithm that only requires an understanding of conventional ANOVA methods. Copyright © 2013 John Wiley & Sons, Ltd.
Self‐controlled case series method with smooth age effect
Authors: Ghebremichael‐Weldeselassie Yonas , Whitaker Heather J. , Paddy Farrington C.
Published: August 2013

The self‐controlled case series method, commonly used to investigate potential associations between vaccines and adverse events, requires information on cases only and automatically controls all age‐independent multiplicative confounders while allowing for an age‐dependent baseline incidence.

In the parametric version of the method, we modelled the age‐specific relative incidence by using a piecewise constant function, whereas in the semiparametric version, we left it unspecified. However, mis‐specification of age groups in the parametric version can lead to biassed estimates of exposure effect, and the semiparametric approach runs into computational problems when the number of cases in the study is moderately large. We, thus, propose to use a penalized likelihood approach where the age effect is modelled using splines.

We use a linear combination of cubic M‐splines to approximate the age‐specific relative incidence and integrated splines for the cumulative relative incidence. We conducted a simulation study to evaluate the performance of the new approach and its efficiency relative to the parametric and semiparametric approaches. Results show that the new approach performs equivalently to the existing methods when the sample size is small and works well for large data sets. We applied the new spline‐based approach to data on febrile convulsions and paediatric vaccines. Copyright © 2013 John Wiley & Sons, Ltd.
Oct4 Maintains the Pluripotency of Human Embryonic Stem Cells by Inactivating p53 Through Sirt1-Mediated Deacetylation
Authors: Zhang Zhen-Ning , Chung Sun-Ku , Xu Zheng , Xu Yang
Published: August 2013

Oct4 is critical to maintain the pluripotency of human embryonic stem cells (hESCs); however, the underlying mechanism remains to be fully understood. Here, we report that silencing of Oct4 in hESCs leads to the activation of tumor suppressor p53, inducing the differentiation of hESCs since acute disruption of p53 in p53 conditional knockout (p53CKO) hESCs prevents the differentiation of hESCs after Oct4 depletion. We further discovered that the silencing of Oct4 significantly reduces the expression of Sirt1, a deacetylase known to inhibit p53 activity and the differentiation of ESCs, leading to increased acetylation of p53 at lysine 120 and 164. The importance of Sirt1 in mediating Oct4-dependent pluripotency is revealed by the finding that the ectopic expression of Sirt1 in Oct4-silenced hESCs prevents p53 activation and hESC differentiation. In addition, using knock-in approach, we revealed that the acetylation of p53 at lysine 120 and 164 is required for both stabilization and activity of p53 in hESCs. In summary, our findings reveal a novel role of Oct4 in maintaining the pluripotency of hESCs by suppressing pathways that induce differentiation. Considering that p53 suppresses pluripotency after DNA damage response in ESCs, our findings further underscore the stringent mechanism to coordinate DNA damage response pathways and pluripotency pathways in order to maintain the pluripotency and genomic stability of hESCs. Stem Cells  2014;32:157–165
Irradiation of Juvenile, but not Adult, Mammary Gland Increases Stem Cell Self-Renewal and Estrogen Receptor Negative Tumors
Authors: Tang Jonathan , Fernandez-Garcia Ignacio , Vijayakumar Sangeetha , Martinez-Ruis Haydeliz , Illa-Bochaca Irineu , Nguyen David H. , Mao Jian-Hua , Costes Sylvain V. , Barcellos-Hoff Mary Helen
Published: August 2013

Children exposed to ionizing radiation have a substantially greater breast cancer risk than adults; the mechanism for this strong age dependence is not known. Here we show that pubertal murine mammary glands exposed to sparsely or densely ionizing radiation exhibit enrichment of mammary stem cell and Notch pathways, increased mammary repopulating activity indicative of more stem cells, and propensity to develop estrogen receptor (ER) negative tumors thought to arise from stem cells. We developed a mammary lineage agent-based model (ABM) to evaluate cell inactivation, self-renewal, or dedifferentiation via epithelial-mesenchymal transition (EMT) as mechanisms by which radiation could increase stem cells. ABM rejected cell inactivation and predicted increased self-renewal would only affect juveniles while dedifferentiation could act in both juveniles and adults. To further test self-renewal versus dedifferentiation, we used the MCF10A human mammary epithelial cell line, which recapitulates ductal morphogenesis in humanized fat pads, undergoes EMT in response to radiation and transforming growth factor β (TGFβ) and contains rare stem-like cells that are Let-7c negative or express both basal and luminal cytokeratins. ABM simulation of population dynamics of double cytokeratin cells supported increased self-renewal in irradiated MCF10A treated with TGFβ. Radiation-induced Notch concomitant with TGFβ was necessary for increased self-renewal of Let-7c negative MCF10A cells but not for EMT, indicating that these are independent processes. Consistent with these data, irradiating adult mice did not increase mammary repopulating activity or ER-negative tumors. These studies suggest that irradiation during puberty transiently increases stem cell self-renewal, which increases susceptibility to developing ER-negative breast cancer. Stem Cells  2014;32:649–661
Supporting Boys as Readers
Authors: Serafini Frank
Published: August 2013

The challenges associated with boys and reading are focused on such factors as society's lack of focus on literacy skills, parents failings to inspire reading in boys, and internal motivational factors rather than looking at the environments created for reading in and out of school. In this column, several ideas for helping boys develop a sense of themselves as readers and get the books they want into their hands are offered. Ten instructional strategies are presented for supporting boys as readers.
A Keeper of Books
Authors: Swiney Angie
Published: August 2013

View From the Chalkboard essays share readers’ reflections on teaching experiences, advice for new teachers, and perspectives on current issues.
E‐BEST Principles: Infusing Technology Into the Writing Workshop
Authors: Coskie Tracy L. , Michelle Hornof M.
Published: August 2013

As teachers work to move their writing workshop into the 21st century and to help students meet new standards expectations, they are ramping up their use of technology. This article lays out a set of guiding principles (E‐BEST) to help teachers make reflective choices, so that the digital technologies in their workshops will enhance and extend student learning.
Selecting “App” ealing and “App” ropriate Book Apps for Beginning Readers
Authors: Cahill Maria , McGill‐Franzen Anne
Published: August 2013

Beginning with a brief rationale for selecting quality digital picture book apps for beginning readers, the authors describe the elements of digital picture books and provide a brief review of the instructional benefits of digital picture book use for beginning readers. They then present a detailed taxonomy for selecting quality picture book apps. Examples drawn from actual apps available for young children illustrate the concepts addressed.

Beginning with a brief rationale for selecting quality digital picture book apps for beginning readers, the authors describe the elements of digital picture books and provide a brief review of the instructional benefits of digital picture book use for beginning readers. They then present a detailed taxonomy for selecting quality picture book apps. Examples drawn from actual apps available for young children illustrate the concepts addressed.
“Look What I Did!”
Authors: Young Chase , Stover Katie
Published: August 2013

The authors describe a strategy that empowers students to edit and revise their own writing. Students input their writing in to text‐to‐speech software that rereads the text aloud. While listening, students make necessary revisions and edits.
Cognitive aspects of schizophrenia
Authors: Harvey Philip D.
Published: August 2013

Cognitive impairments are a central feature of schizophrenia and are present in most, if not all, cases. There are multiple domains of impairment seen and the level of severity of impairment is considerable. Impairments can be detected prior to the onset of clinical symptoms and the course of impairments involves some subtle early worsening followed by stability in most cases. Cognitive impairments are associated with functional disability, particularly in domains of vocational functioning and independence of residence. Both pharmacological and cognitive remediation interventions have been employed for the treatment of these impairments, with greater progress to date being made in cognitive remediation interventions. While much is known about cognitive impairments, treatment efforts are still in an early stage of development. WIREs Cogn Sci 2013, 4:599–608. doi: 10.1002/wcs.1253

This article is categorized under:

Psychology > Brain Function and Dysfunction

Neuroscience > Cognition
Regulation of the seed to seedling developmental phase transition by the LAFL and VAL transcription factor networks
Authors: Jia Haiyan , Suzuki Masaharu , McCarty Donald R.
Published: August 2013

In the seed, a fundamental transition between embryo and vegetative phases of plant development is coordinated by the interaction between the AFL and VAL sub‐clades of the plant specific B3 domain transcription factor family. The AFL B3 factors together with LEC1‐type HAP3 transcription factors promote embryo maturation; whereas the VAL B3 factors repress the LEC1/AFL (LAFL) network during seed germination. Recent advances reveal that genes in key developmental programs and hormone signaling pathways are downstream targets of the LAFL network highlighting the central role of the LAFL network in integration of intrinsic developmental and hormonal signals during plant development. The VAL B3 proteins are proposed to mediate repression by recruiting a histone deacetylase complex (HDAC) to LAFL genes that contain the Sph/RY cis‐element recognized by AFL and VAL B3‐DNA‐binding domains. In addition to VAL B3 factors, epigenetic mechanisms are implicated in maintaining repression of LAFL network during vegetative development. WIREs Dev Biol 2014, 3:135–145. doi: 10.1002/wdev.126

This article is categorized under:

Plant Development > Fertilization, Embryogenesis, and Seed Development

Plant Development > Vegetative Development
A brief account of nanoparticle contrast agents for photoacoustic imaging
Authors: Pan Dipanjan , Kim Benjamin , Wang Lihong V. , Lanza Gregory M
Published: August 2013

Photoacoustic imaging (PAI) is a hybrid, nonionizing modality offering excellent spatial resolution, deep penetration, and high soft tissue contrast. In PAI, signal is generated based on the absorption of laser‐generated optical energy by endogenous tissues or exogenous contrast agents leading to acoustic emissions detected by an ultrasound transducer. Research in this area over the years has shown that PAI has the ability to provide both physiological and molecular imaging, which can be viewed alone or used in a hybrid modality fashion to extend the anatomic and hemodynamic sensitivities of clinical ultrasound. PAI may be performed using inherent contrast afforded by light absorbing molecules such as hemoglobin, myoglobin, and melanin or exogenous small molecule contrast agent such as near infrared dyes and porphyrins. However, this review summarizes the potential of exogenous nanoparticle‐based agents for PAI applications including contrast based on gold particles, carbon nanotubes, and encapsulated copper compounds. WIREs Nanomed Nanobiotechnol 2013, 5:517–543. doi: 10.1002/wnan.1227

This article is categorized under:

Diagnostic Tools > In Vivo Nanodiagnostics and Imaging
An interplay between transcription, processing, and degradation determines tRNA levels in yeast
Authors: Wichtowska Dominika , Turowski Tomasz W. , Boguta Magdalena
Published: August 2013

tRNA biogenesis in yeast involves the synthesis of the initial transcript by RNA polymerase III followed by processing and controlled degradation in both the nucleus and the cytoplasm. A vast landscape of regulatory elements controlling tRNA stability in yeast has emerged from recent studies. Diverse pathways of tRNA maturation generate multiple stable and unstable intermediates. A significant impact on tRNA stability is exerted by a variety of nucleotide modifications. Pre‐tRNAs are targets of exosome‐dependent surveillance in the nucleus. Some tRNAs that are hypomodified or bear specific destabilizing mutations are directed to the rapid tRNA decay pathway leading to 5′→3′ exonucleolytic degradation by Rat1 and Xrn1. tRNA molecules are selectively marked for degradation by a double CCA at their 3′ ends. In addition, under different stress conditions, tRNA half‐molecules can be generated by independent endonucleolytic cleavage events. Recent studies reveal unexpected relationships between the subsequent steps of tRNA biosynthesis and the mechanisms controlling its quality and turnover. WIREs RNA 2013, 4:709–722. doi: 10.1002/wrna.1190

This article is categorized under:

RNA Processing > tRNA Processing

RNA Turnover and Surveillance > Regulation of RNA Stability
Coordination Frameworks based on 3,5‐Bis(imidazole‐1‐yl)­pyridine and Aromatic Dicarboxylate Ligands: Synthesis, Crystal Structures, and Photoluminescent Properties
Authors: Xu Jiakun , Sun Xiaochun , Yang Lirong , Yan Xincheng , Bi Caifeng , Sun Mi
Published: August 2013

Three metal coordination polymers [Zn(bdc)(L)(H2O)]n (1), [Co(pta)(L)(H2O)2]n (2), and [Cd(tda)(L)(H2O)]n (3) [H2bdc = 1,2‐benzene dicarboxylate acid, H2pta = terephthalic acid, H2tda = 2,5‐thiophenedicarboxylic acid, L = 3,5‐bis(imidazole‐1‐yl)pyridine] were synthesized and structurally characterized by IR spectroscopy, elemental analysis, X‐ray powder diffraction, and X‐ray single crystal diffraction. Complex 1 shows a three‐dimensional (3D) structure with cco topology with the symbol 65·8, whereas complex 2 features a 3D structure with cds topology with the symbol 65·8. Complex 3 has a 2D network constructed by the cadmium atoms bridged through the ligands tda and L. Their X‐ray powder diffraction patterns were compared with the simulated ones. Moreover, their luminescent properties were investigated in the solid state at room temperature, and the thermogravimetric analyses were carried out to study the thermal stability of the 3D networks.
Synthesis of Large Single Crystals and Thermoelectrical Properties of the Type‐I Clathrate K8Zn4Sn42
Authors: Baran Volodymyr , Fischer Andreas , Scherer Wolfgang , Fässler Thomas F.
Published: August 2013

In order to investigate the thermoelectric transport properties of tin‐based clathrates, highly dense samples are required. Since tin clathrates decompose at temperatures above 550 °C, compacting of samples by hot pressing without the formation of side products is not possible. Large single crystals of the composition K8Zn4Sn42 suitable for physical property measurements can be obtained using the tin liquid metal flux technique. A single crystal structure determination of K8Zn4Sn42 (Pm$\bar{3}$n, a = 12.07164(2) Å) shows Zn/Sn mixed occupancy at the 6c position. According to physical property measurements, K8Zn4Sn42 is a promising semimetallic thermoelectric material.
The Current State of Genetic Counseling Before and After Amniocentesis for Fetal Karyotyping in Japan: A Survey of Obstetric Hospital Clients of a Prenatal Testing Laboratory
Authors: Nishiyama Miyuki , Sawai Hideaki , Kosugi Shinji
Published: August 2013

Pregnant women undergoing prenatal genetic testing should receive genetic counseling so they can make informed decisions. We examined the current state of providing genetic counseling in Japan to pregnant women before they elected amniocentesis for prenatal diagnosis of chromosome abnormalities and after test results were completed, and explored the opportunity for expanding access to certified genetic counselors (CGC) at clinical practices offering amniocentesis. An anonymous survey was mailed to the 298 hospitals that referred amniotic fluid specimens to LabCorp Japan in 2009. Most genetic counseling was provided by the obstetrician alone; 73.8 % (76/103) of pre‐amniocentesis, 82.5 % (85/103) if normal results, and 49.4 % (44/89) if abnormal results. Respondents spent limited time in genetic counseling; 57.3 % spent <10 min for pre‐amniocentesis, 88.3 % spent <10 min for normal results, and 54.0 % spent <20 min for abnormal results. While 45.8 % indicated that CGC do not have an essential role in clinical practice, responses that supported employment of CGC were more likely to come from hospitals that submitted more than ten specimens annually (p < 0.0001), university hospitals (p < 0.0001), and MD geneticists (p = 0.020). Currently, there is limited genetic counseling available in Japan. This indicates there are opportunities for the employment of CGC to improve the quality of genetic counseling.
Crystallization Behavior of High‐Oleic High‐Stearic Sunflower Oil Stearins Under Dynamic and Static Conditions
Authors: Martini S. , Cardona J. A. Rincón , Ye Y. , Tan C. Y. , Candal R. J. , Herrera M. L.
Published: August 2013

Soft (SS) and hard (HS) stearins obtained from high‐oleic high‐stearic sunflower oil were isothermally crystallized under dynamic (with agitation) and static conditions at 16, 17, 18, 19, and 20 °C and 24, 25, 26, 27, and 28 °C, respectively. Both fractions crystallized under the α‐form at early stages of crystallization for all temperatures (Tc) tested. Polymorphic behavior strongly changed with Tc and shear conditions for both fractions. SS fractions were characterized by α, β2 and/or β1 polymorphs at lower Tc and β1 crystals at higher Tc when crystallized under dynamic conditions, while this same fat system was characterized by β2′ crystals at lower Tc and β2 at higher Tc under static conditions. HS samples were mainly characterized by α and β2 crystals at lower Tc and α and β1 crystals at higher Tc when crystallized under dynamic conditions; while the same fat was characterized by β1′ crystals when crystallized at lower Tc and α when crystallized at higher Tc under static conditions after 90 min at Tc. These different polymorphic behaviors, in combination with the different processing and tempering temperatures are translated in specific textural behavior of the samples.
Rationality and Engagement: McDowell, Dreyfus and Zidane
Authors: Smith Nicholas H.
Published: August 2013

The article examines John McDowell's attempt to rehabilitate the classical idea of the rational animal and Hubert Dreyfus's criticisms of that attempt. After outlining the ‘engaged’ conception of rationality which, in McDowell's view, enables the idea of the rational animal to shake off its intellectualist appearance, the objections posed by Dreyfus are presented that such a conception of rationality is inconsistent with the phenomena of everyday coping, characterised by non-conceptual ‘involvement’, and expertise, characterised by non-conceptual ‘absorption’. Drawing on Michael Fried's reflections on the representation of absorption in Douglas Gordon and Philippe Parreno's film Zidane, and invoking other considerations concerning the ‘mindedness’ of skilful activity, the sharp contrast between conceptuality and rationality on the one side and absorption and skilled coping on the other that frames Dreyfus's position in the debate is questioned. The paper concludes by suggesting that in order to see why Dreyfus is so firmly committed to that contrast, we need to widen the lens so that a broader range of philosophical motivations comes into view. For it is not just that there are phenomena that go missing or are mis-described in McDowell's account, according to Dreyfus; there are ideals and excellences that go missing too.
Bodies inProlegomena§13: Noumena or Phenomena?
Authors: Kanterian Edward
Published: August 2013

This article discusses Kant's transcendental idealism in relation to his perplexing use of ‘body’ and related terms inProlegomena§13. Here Kant admits the existence of bodies external to us, although unknown as what they might be in themselves. It is argued that we need to distinguish between a phenomenal and a noumenal use of ‘body’ to make sense of Kant's argument. The most important recent discussions of this passage, i.e., Prauss (1977), Langton (1998) and Bird (2006), are presented and shown to suffer from both systematic and exegetical shortcomings. The article is a contribution to understanding the nature of Kant's transcendental idealism, defending the view, especially against Prauss and Bird, that Kant is committed to the existence of things in themselves.
Hegel as a Theorist of Secularization
Authors: Hammer Espen
Published: August 2013

Hegel's philosophy of religion is characterized by what seems to be a deep tension. On the one hand, Hegel claims to be a Christian thinker, viewing religion, and in particular Christianity, as a manifestation of the absolute. On the other hand, however, he seems to view modernity as largely secular, devoid of authoritative claims to transcendence. Modernity is secular in the political sense of requiring the state to be neutral when it comes to matters of religion. However, it is also secular in the sense of there being no recourse to authoritative representations of a transcendent God. Drawing on Charles Taylor's view of secularization, the article focuses on the second strand of his religious thinking, exploring how Hegel can be thought of as a theorist of secularization. It is claimed that his dialectic of religious development describes a process of secularization. Ultimately, Hegel's system offers a view of the absolute as immanent, suggesting that an adequate account of religion will necessarily have to accept secularization as the end-point of spirit's development. This is how the tension between religion and secularization can be resolved.