bluuebunny/crossref_metadata_2025 huggingface dataset:
Data mining and life sciences applications on the grid
Authors: Cannataro Mario , Guzzi Pietro Hiram , Sarica Alessia
Published: April 2013

Data mining (DM) is increasingly used in the analysis of data generated in life sciences, including biological data produced in several disciplines such as genomics and proteomics, medical data produced in clinical practice, and administrative data produced in health care. The difficulty in mining such data is twofold. First of all, data in life sciences are inherently heterogeneous, spanning from molecular level data to clinical and administrative data. Second, data in life sciences are produced at an increasing rate and data repositories are becoming very large. Thus, the management and analysis of such data is becoming a main bottleneck in biomedical research. The main goal of this paper is to review the main methodologies to mine life sciences data and the ways they are coupled to high‐performance infrastructures and systems that result in an efficient analysis. This paper recalls basic concepts of DM, grids, and distributed DM on grids, and reviews main approaches to mine biomedical data on high‐performance infrastructures with special focus on the analysis of genomics, proteomics, and interactomics data, and the exploration of magnetic resonance images in neurosciences. The paper can be of interest both to bioinformaticians, who can learn how to exploit high performance infrastructures to mine life sciences data, and to computer scientists, who can address the heterogeneity and the high volumes of life sciences data at the data management, algorithm, and user interface layers. © 2013 Wiley Periodicals, Inc.

This article is categorized under:

Algorithmic Development > Biological Data Mining

Application Areas > Data Mining Software Tools

Application Areas > Health Care

Technologies > Computer Architectures for Data Mining
A survey of fuzzy web mining
Authors: Lin Chun‐Wei , Hong Tzung‐Pei
Published: April 2013

The Internet has become an unlimited resource of knowledge, and is thus widely used in many applications. Web mining plays an important role in discovering such knowledge. This mining can be roughly divided into three categories, including Web usage mining, Web content mining, and Web structure mining. Data and knowledge on the Web may, however, consist of imprecise, incomplete, and uncertain data. Because fuzzy‐set theory is often used to handle such data, several fuzzy Web‐mining techniques have been proposed to reveal fuzzy and linguistic knowledge. This paper reviews these techniques according to the three Web‐mining categories above—fuzzy Web usage mining, fuzzy Web content mining, and fuzzy Web structure mining. Some representative approaches in each category are introduced and compared. © 2013 Wiley Periodicals, Inc.

This article is categorized under:

Algorithmic Development > Web Mining

Technologies > Computational Intelligence
The Role of Unilateral Adrenalectomy in Corticotropin‐Independent Bilateral Adrenocortical Hyperplasias
Authors: Xu Yunze , Rui Wenbin , Qi Yicheng , Zhang Chongyu , Zhao Juping , Wang Xiaojing , Wu Yuxuan , Zhu Qi , Shen Zhoujun , Ning Guang , Zhu Yu
Published: April 2013

Background

The objective of the present study was twofold: to demonstrate our experience with unilateral adrenalectomy in the treatment of adrenocorticotropic hormone (ACTH)‐independent Cushing syndrome (CS) caused by bilateral adrenocortical hyperplasias, and to evaluate the long‐term results as evidenced by the main laboratory and clinical findings.

Methods

From February 2000 to August 2009, unilateral adrenalectomy was performed on 27 patients with ACTH‐independent CS and bilateral adrenocortical hyperplasias, including 14 patients with ACTH‐independent macronodular adrenal hyperplasia (AIMAH) and 13 patients with primary pigmented nodular adrenocortical disease (PPNAD). Signs and symptoms of CS, endocrine examinations, and radiographic imaging were evaluated preoperatively and postoperatively.

Results

At a median follow‐up of 69 months (range: 23–120 months) for AIMAH and 47 months (range: 16–113 months) for PPNAD, 25 patients were cured by unilateral adrenalectomy. Serum cortisol level, daily urinary free cortisol (UFC), and plasma ACTH regained the normal range in both AIMAH and PPNAD patients at monthly follow‐up visits; the circadian serum cortisol rhythm returned to normal, and a normal responsiveness to overnight low‐dose dexamethasone administration (LDDST) became obvious. Both systolic and diastolic blood pressure (BP) levels were significantly reduced: 85 % of patients recovered normal BP levels, and the remaining patients need antihypertensive drugs, but at a reduced dose. No surgery‐related morbidity occurred, and there was no sign of further enlargement of the residual adrenal gland after successful unilateral adrenalectomy. One patient with PPNAD and another patient with AIMAH with similar weights and sizes of the bilateral adrenals needed contralateral adrenalectomy.

Conclusions

Unilateral adrenalectomy may be the suitable treatment for selected patients with AIMAH and PPNAD. It can achieve long‐term remission of CS and improve glycemic control and BP values.
Tristetraprolin suppresses AHRR expression through mRNA destabilization
Authors: Lee Hyun Hee , Kim Won-Tae , Kim Dong Hee , Park Jeong Woo , Kang Tae-Hong , Chung Jin Woong , Leem Sun-Hee
Published: April 2013

The aryl hydrocarbon receptor repressor (AHRR) inhibits the transcription of the aryl hydrocarbon receptor (AHR) by binding to XRE. We report that AHRR expression is inhibited by tristetraprolin (TTP), an AU‐rich element (ARE)‐binding protein. Overexpression of TTP decreased the mRNA stability and protein expression of AHRR, and TTP‐overexpressing cells made smaller colonies than the control. Contrarily, inhibition of TTP by siRNA increased AHRR expression. Analyses of point mutants of the AREs demonstrated that AREs were responsible for the TTP‐mediated destabilization of AHRR mRNA. RNA EMSA revealed that TTP directly binds to the AHRR 3′UTR. Taken together, we demonstrate that TTP acts as a negative regulator of AHRR and may affect tumor development through induction of tumor suppressor genes as observed in MDA‐MB435.
Mitochondrial dysfunction and nuclear‐mitochondrial shuttling of TERT are involved in cell proliferation arrest induced by G‐quadruplex ligands
Authors: Zhuang Xin-Ying , Yao Yong-Gang
Published: April 2013

G‐quadruplex ligands DODC and TMPyP4 have different binding modes to quadruplex structure and cause cell proliferation arrest. Here we showed that DODC was more efficient in cell growth inhibition than TMPyP4. Both G‐quadruplex ligands induced nuclear‐cytoplasmic shuttling and accumulation of TERT in mitochondria. This effect was not fully dependent on cellular oxidative stress. DODC induced robust cell apoptosis by perturbing mitochondrial function intensively. Overexpression of TERT could not counteract the effects of DODC on mitochondrial respiratory function. Taken together, our results suggest that interference of mitochondrial function by DODC is one of main targets for its anti‐tumor ability.
Blocking the attachment of cancer cells in vivo with DNA aptamers displaying anti‐adhesive properties against the carcinoembryonic antigen
Authors: Orava Erik W. , Abdul-Wahid Aws , Huang Eric H.-B. , Mallick Amirul Islam , Gariépy Jean
Published: April 2013

The formation of metastatic foci occurs through a series of cellular events, initiated by the attachment and aggregation of cancer cells leading to the establishment of micrometastases. We report the derivation of synthetic DNA aptamers bearing anti‐adhesive properties directed at cancer cells expressing the carcinoembryonic antigen (CEA). Two DNA aptamers targeting the homotypic and heterotypic IgV‐like binding domain of CEA were shown to block the cell adhesion properties of CEA, while not recognizing other IgV‐like domains of CEACAM family members that share strong sequence and structural homologies. More importantly, the pre‐treatment of CEA‐expressing tumour cells with these aptamers prior to their intraperitoneal implantation resulted in the prevention of peritoneal tumour foci formation. Taken together, these results highlight the effectiveness of targeting the cell adhesion properties of cancer cells with aptamers in preventing tumour implantation.
The Undeserving Rich
Authors: McCall Leslie
Published: April 2013

It is widely assumed that Americans care little about income inequality, believe opportunities abound, admire the rich, and dislike redistributive policies. Leslie McCall contends that such assumptions are based on both incomplete survey data and economic conditions of the past and not present. In fact, Americans have desired less inequality for decades, and McCall's book explains why. Americans become most concerned about inequality in times of inequitable growth, when they view the rich as prospering while opportunities for good jobs, fair pay and high quality education are restricted for everyone else. As a result, they favor policies to expand opportunity and redistribute earnings in the workplace, reducing inequality in the market rather than redistributing income after the fact with tax and spending policies. This book resolves the paradox of how Americans can express little enthusiasm for welfare state policies and still yearn for a more equitable society, and forwards a new model of preferences about income inequality rooted in labor market opportunities rather than welfare state policies.
Experimental study of parametric subharmonic instability for internal plane waves
Authors: Bourget Baptiste , Dauxois Thierry , Joubaud Sylvain , Odier Philippe
Published: April 2013

Internal waves are believed to be of primary importance as they affect ocean mixing and energy transport. Several processes can lead to the breaking of internal waves and they usually involve nonlinear interactions between waves. In this work, we study experimentally the parametric subharmonic instability (PSI), which provides an efficient mechanism to transfer energy from large to smaller scales. It corresponds to the destabilization of a primary plane wave and the spontaneous emission of two secondary waves, of lower frequencies and different wave vectors. Using a time-frequency analysis, we observe the time evolution of the secondary waves, thus measuring the growth rate of the instability. In addition, a Hilbert transform method allows the measurement of the different wave vectors. We compare these measurements with theoretical predictions, and study the dependence of the instability with primary wave frequency and amplitude, revealing a possible effect of the confinement due to the finite size of the beam, on the selection of the unstable mode.
Applied Practices: Perspectives from the Field
Authors: COLMAR SUSAN
Published: April 2013

This is our second publication with this section in our journal which encourages and welcomes applied practice contributions from colleagues. These papers have an applied focus with scope for colleagues to offer work such as:

Evaluations of practice, even if these are not methodologically at the standard required for contributions to the main journal (e.g., no control group),

Conceptual reviews with implications for practice,

Linked case studies in therapeutic and learning and behaviour areas of intervention,

Reports from presentations and adapted student assignments,

Research work put forward for psychologists' registration requirements.

Fuller details are noted below. Please contact Dr Susan Colmar, who edits this section of the journal if you wish to discuss your ideas, possibilities, probabilities or even the germ of an idea. Papers will be refereed; however criteria, particularly methodological, will be less restrictive than aiming for a full journal article. If you need some encouragement and assistance in preparing your paper, I am happy to guide you with my red pen.
Induced resistance against the Asian citrus psyllid, Diaphorina citri, by β-aminobutyric acid in citrus
Authors: Tiwari Siddharth , Meyer Wendy L. , Stelinski Lukasz L.
Published: April 2013

β-Aminobutyric acid (BABA) is known to induce resistance to microbial pathogens, nematodes and insects in several host plant/pest systems. The present study was undertaken to determine whether a similar effect of BABA occurred against the Asian citrus psyllid, Diaphorina citri Kuwayama, in citrus. A 25 mM drench application of BABA significantly reduced the number of eggs/plant as compared with a water control, whereas 200 and 100 mM applications of BABA reduced the numbers of nymphs/plant and adults/plants, respectively. A 5 mM foliar application of BABA significantly reduced the number of adults but not eggs or nymphs when compared with a water control treatment. In addition, leaf-dip bioassays using various concentrations (25–500 mM) of BABA indicated no direct toxic effect on 2nd and 5th instar nymphs or adult D. citri. BABA-treated plants were characterized by significantly lower levels of iron, magnesium, phosphorus, sodium, sulfur and zinc as compared with control plants. The expression level of the PR-2 gene (β-1,3-glucanase) in BABA-treated plants that were also damaged by D. citri adult feeding was significantly higher than in plants exposed to BABA, D. citri feeding alone or control plants. Our results indicate the potential for using BABA as a systemic acquired resistance management tool for D. citri.
Conflicting management policies for the Arabian wolfCanis lupus arabsin the Negev Desert: is this justified?
Authors: Cohen Orly , Barocas Adi , Geffen Eli
Published: April 2013

Conservation plans may conflict when both predator and prey in the same ecological system are threatened species. In this study we present a problematic case of conflicting conservation policies involving the Arabian wolfCanis lupus arabsand two species of gazelles (Gazella gazella acaciaeandGazella dorcas), all of which are threatened in Israel. By studying genetic subdivision using faecal DNA we evaluated the policy of treating the Arabian wolves in the Negev Desert as two separate populations. We analysed 95 wolf faecal samples from 12 feeding sites c. 20 km apart. Network analysis and Bayesian clustering were used for separating populations. Mark–recapture design, rarefaction and an urn model were applied to estimate wolf population size. We found that wolves in the central and southern Negev cannot be genetically separated, and their density is similar in both regions. Our results provide a better baseline for a unified management of wolves in the Negev. We call for the consideration of other factors influencing gazelle population size before adopting drastic measures such as wolf removal.
The harvest of freshwater turtles (Chelidae) from Papua, Indonesia, for the international pet trade
Authors: Lyons Jessica Ann , Natusch Daniel James Deans , Shepherd Chris R.
Published: April 2013

The international trade in wildlife is currently one of the greatest threats to biodiversity. One group, the turtles, has experienced far-reaching population declines and extinctions because the majority of animals are sourced from the wild. The island of New Guinea has the highest diversity of freshwater turtles (Chelidae) in the Australasian region and large numbers are harvested from the Indonesian province of Papua to supply the international pet trade. A total of 264 of these turtles representing six species were recorded between December 2010 and March 2011 while gathering information about wildlife trade in the Indonesian province of Papua. Most were juveniles, although a substantial number of large adults were also harvested. None of the species recorded are CITES-listed. Despite one species not being allocated an annual harvest quota, it was observed being traded. Illegal and unregulated trade coupled with a lack of basic ecological data for these species can have a severe impact on wild populations. We present recommendations for law enforcement and conservation of these species.
Regional variability in eukaryotic protist communities in the Amundsen Sea
Authors: Wolf Christian , Frickenhaus Stephan , Kilias Estelle S. , Peeken Ilka , Metfies Katja
Published: April 2013

We determined the composition and structure of late summer eukaryotic protist assemblages along a west–east transect in the Amundsen Sea. We used state-of-the-art molecular approaches, such as automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing, combined with pigment measurements via high performance liquid chromatography (HPLC) to study the protist assemblage. We found characteristic offshore and inshore communities. In general, total chlorophyll a and microeukaryotic contribution were higher in inshore samples. Diatoms were the dominant group across the entire area, of which Eucampia sp. and Pseudo-nitzschia sp. were dominant inshore and Chaetoceros sp. was dominant offshore. At the most eastern station, the assemblage was dominated by Phaeocystis sp. Under the ice, ciliates showed their highest and haptophytes their lowest abundance. This study delivers a taxon detailed overview of the eukaryotic protist composition in the Amundsen Sea during the summer 2010.
Regular functors and relative realisability categories
Authors: STEKELENBURG WOUTER PIETER
Published: April 2013

The relative realisability toposes introduced by Awodey, Birkedal and Scott in Awodey et al. (2002) satisfy a universal property involving regular functors to other categories. We use this universal property to define what relative realisability categories are when they are based on categories other than the topos of sets. This paper explains the property and gives a construction for relative realisability categories that works for arbitrary base Heyting categories. The universal property also provides some new geometric morphisms to relative realisability toposes.
Ethical Issues in DNA Identification of Human Biological Material from Mass Disasters
Authors: Caenazzo Luciana , Tozzo Pamela , Rodriguez Daniele
Published: April 2013

Each mass disaster has its own characteristics and will involve a different approach, so the safeguarding and collection of forensic evidence have to be considered as part of the field response procedure. DNA typing has played a more prominent role in the identification of human remains, and particularly so for highly decomposed and fragmented remains. Although the ultimate goal is to obtain the identification, the specific context of each application of human identity testing has its specific problems, ranging from technical approach, through statistical interpretation, to ethical issues. The preparedness plan of the forensic genetics laboratory needs to include policies for family notification, long-term sample storage, and data archiving. For this reason, DNA sample collection and a strategy for DNA-based victim identification needs to be part of the preparedness plan. In this paper, the authors seek to define three of these ethical aspects: (1) the humanitarian importance of identification; (2) resource allocation in the victims’ DNA identification; and (3) the secondary use for research of the samples initially collected for identification purposes. DNA analysis for the purpose of identifying victims of mass disasters has complex implications that demand much more rigorous examination than they have received until now.

CaenazzoL,TozzoP,RodriguezD.Ethical issues in DNA identification of human biological material from mass disasters.Prehosp Disaster Med.2013;28(4):1-4.
Glucocorticoid receptors in the prefrontal cortex regulate dopamine efflux to stress via descending glutamatergic feedback to the ventral tegmental area
Authors: Butts Kelly A. , Phillips Anthony G.
Published: April 2013

Enhanced dopamine (DA) efflux in the medial prefrontal cortex (mPFC) is a well-documented response to acute stress. We have previously shown that glucocorticoid receptors in the mPFC regulate stress-evoked DA efflux but the underlying mechanism is unknown. DA neurons in the ventral tegmental area (VTA) receive excitatory input from and send reciprocal projections to the mPFC. We hypothesize that blockade of prefrontal glucocorticoid receptors can reduce activity of descending glutamatergic input to the VTA, thereby attenuating stress-evoked DA efflux in the mPFC. Using in vivo microdialysis, we demonstrate that acute tail-pinch stress leads to a significant increase in glutamate efflux in the VTA. Blockade of prefrontal glucocorticoid receptors with the selective antagonist CORT 108297 attenuates stress-evoked glutamate efflux in the VTA together with DA efflux in the mPFC. Furthermore, blockade of ionotrophic glutamate receptors in the VTA attenuates stress-evoked DA efflux in the mPFC. We also examine the possible role of glucocorticoid-induced synthesis and release of endocannabinoids acting presynaptically via cannabinoid CB1 receptors to inhibit GABA release onto prefrontal pyramidal cells, thus enhancing descending glutamatergic input to the VTA leading to an increase in mPFC DA efflux during stress. However, administration of the cannabinoid CB1 receptor antagonist into the mPFC does not attenuate stress-evoked DA efflux in the mPFC. Taken together, our data indicate that glucocorticoids act locally within the mPFC to modulate mesocortical DA efflux by potentiation of glutamatergic drive onto DA neurons in the VTA.
The minimum pension as an instrument of poverty protection in the defined contribution pension system – an example of Poland*
Authors: CHŁOŃ-DOMIŃCZAK AGNIESZKA , STRZELECKI PAWEŁ
Published: April 2013

Pension systems' reforms are often related to a shift towards (fully or partially) defined contribution (DC) systems, in which the pension distribution reflects to a larger extent the wage distribution. In addition, relatively shorter working lives of those who have lower earnings increase the risk of receiving lower benefits. The aim of the paper is to present the changing role of a minimum pension as a tool of redistribution in the country that replaced a defined benefit (DB) pension system with a DC pension system. The old system in Poland had a significant income redistribution in the pension formula and the minimum pension was only a tool supporting this redistribution. After the introduction of the new mandatory pension system the main mechanism of redistribution (and a tool of social policy preventing poverty) is the minimum pension, financed from general taxes. According to the current rule of indexation, the minimum pension is expected to fall relative to the average wage in the economy. According to our simulations, the lack of changes of the current indexation method means that the minimum pension will fall below the International Labour Organisation (ILO) standard of the poverty protection of elderly by mid 2020s and in practice the last instrument of the poverty protection of elderly is going to disappear. However, the sole decision to change the indexation mechanism to the one based on full wage can create a significant pressure on public finance and distort incentives for prolonging work as 45% of women would be probably covered by the minimum pension guarantee (MPG). Results of simulations show that a raise and equalization of the retirement age for men and women combined with keeping a constant ratio of the minimum pension to the average (and also minimum) wage in the economy can be considered as a balanced solution that assures no further reduction of poverty protection and effective maintaining of this redistribution instrument.
Analysis of capacitive force acting on a cantilever tip at solid/liquid interfaces
Authors: Umeda Ken-ichi , Kobayashi Kei , Oyabu Noriaki , Hirata Yoshiki , Matsushige Kazumi , Yamada Hirofumi
Published: April 2013

Dielectric properties of biomolecules or biomembranes are directly related to their structures and biological activities. Capacitance force microscopy based on the cantilever deflection detection is a useful scanning probe technique that can map local dielectric constant. Here we report measurements and analysis of the capacitive force acting on a cantilever tip at solid/liquid interfaces induced by application of an alternating voltage to explore the feasibility of the measurements of local dielectric constant by the voltage modulation technique in aqueous solutions. The results presented here suggest that the local dielectric constant measurements by the conventional voltage modulation technique are basically possible even in polar liquid media. However, the cantilever deflection is not only induced by the electrostatic force, but also by the surface stress, which does not include the local dielectric information. Moreover, since the voltage applied between the tip and sample are divided by the electric double layer and the bulk polar liquid, the capacitive force acting on the apex of the tip are strongly attenuated. For these reasons, the lateral resolution in the local dielectric constant measurements is expected to be deteriorated in polar liquid media depending on the magnitude of dielectric response. Finally, we present the criteria for local dielectric constant measurements with a high lateral resolution in polar liquid media.
Alternating current-dielectrophoresis driven on-chip collection and chaining of green microalgae in freshwaters
Authors: Suscillon Coralie , Velev Orlin D. , Slaveykova Vera I.
Published: April 2013

The capability of the AC dielectrophoresis (DEP) for on-chip capture and chaining of microalgae suspended in freshwaters was evaluated. The effects of freshwater composition as well as the electric field voltage, frequency, and duration, on the dielectrophoretic response of microalga Chlamydomonas reinhardtii were characterized systematically. Highest efficiency of cell alignment in one-dimensional arrays, determined by the percentage of cells in chain and the chain length, was obtained at AC-field of 20 V mm−1 and 1 kHz applied for 600 s. The DEP response and cell alignment of C. reinhardtii in water sampled from lake, pond, and river, as well as model media were affected by the chemical composition of the media. In the model media, the efficiency of DEP chaining was negatively correlated to the conductivity of the cell suspensions, being higher in suspensions with low conductivity. The cells suspended in freshwaters, however, showed anomalously high chaining at long exposure times. High concentrations of nitrate and dissolved organic matter decrease cell chaining efficiency, while phosphate and citrate concentrations increase it and favor formation of longer chains. Importantly, the application of AC-field had no effect on algal autofluorescence, cell membrane damage, or oxidative stress damages in C. reinhardtii.
Dual radio frequency plasma source: Understanding via electrical asymmetry effect
Authors: Bora B. , Bhuyan H. , Favre M. , Wyndham E. , Wong C. S.
Published: April 2013

On the basis of the global model, the influences of driving voltage and frequency on electron heating in geometrically symmetrical dual capacitively coupled radio frequency plasma have been investigated. Consistent with the experimental and simulation results, non-monotonic behavior of dc self bias and plasma heating with increasing high frequency is observed. In addition to the local maxima of plasma parameters for the integer values of the ratio between the frequencies (ξ), ourstudies also predict local maxima for odd integer values of 2ξ as a consequence of the electrical asymmetry effect produced by dual frequency voltage sources.
Thermoelectric properties of epitaxial ScN films deposited by reactive magnetron sputtering onto MgO(001) substrates
Authors: Burmistrova Polina V. , Maassen Jesse , Favaloro Tela , Saha Bivas , Salamat Shuaib , Rui Koh Yee , Lundstrom Mark S. , Shakouri Ali , Sands Timothy D.
Published: April 2013

Epitaxial ScN(001) thin films were grown on MgO(001) substrates by dc reactive magnetron sputtering. The deposition was performed in an Ar/N2 atmosphere at 2 × 10−3 Torr at a substrate temperature of 850 °C in a high vacuum chamber with a base pressure of 10−8 Torr. In spite of oxygen contamination of 1.6 ± 1 at. %, the electrical resistivity, electron mobility, and carrier concentration obtained from a typical film grown under these conditions by room temperature Hall measurements are 0.22 mΩ cm, 106 cm2 V−1 s−1, and 2.5 × 1020 cm−3, respectively. These films exhibit remarkable thermoelectric power factors of 3.3–3.5 × 10−3 W/mK2 in the temperature range of 600 K to 840 K. The cross-plane thermal conductivity is 8.3 W/mK at 800 K yielding an estimated ZT of 0.3. Theoretical modeling of the thermoelectric properties of ScN calculated using a mean-free-path of 23 nm at 300 K is in very good agreement with the experiment. These results also demonstrate that further optimization of the power factor of ScN is possible. First-principles density functional theory combined with the site occupancy disorder technique was used to investigate the effect of oxygen contamination on the electronic structure and thermoelectric properties of ScN. The computational results suggest that oxygen atoms in ScN mix uniformly on the N site forming a homogeneous solid solution alloy. Behaving as an n-type donor, oxygen causes a shift of the Fermi level in ScN into the conduction band without altering the band structure and the density of states.
Influence of silver nanoparticles on the infrared-to-visible frequency upconversion in Tm3+/Er3+/Yb3+ doped GeO2-PbO glass
Authors: Camilo Mauricio E. , Assumpção Thiago A. A. , da Silva Davinson M. , da Silva Diego S. , Kassab Luciana R. P. , de Araújo Cid B.
Published: April 2013

We investigated the influence of silver nanoparticles (NPs) on the infrared-to-visible frequency upconversion (UC) in GeO2-PbO glass triply doped with thulium (Tm3+), erbium (Er3+), and ytterbium (Yb3+) ions. The NPs were nucleated inside the samples by heat-treatment of the germanate glass that included small amount of AgNO3 in the starting composition. When excited at 980 nm, in resonance with the Yb3+ transition 2F7/2 → 2F5/2, the samples emit blue light at ≈477 nm due to the Tm3+ ions, green light at ≈530 nm and ≈550 nm due to the Er3+ ions, and red light at ≈652 nm due to Tm3+ and at ≈660 nm due to the Er3+ ions. Due to the silver NPs, the photoluminescence intensity grows by ≈60% in comparison with a sample having the same composition but without silver NPs. This is the first time that UC enhancement due to metallic NPs is investigated for a triply rare-earth (RE) doped glass. The results indicate the possibility of development of more efficient three-dimensional RE based color displays by nucleation of metallic particles in the glass host.
Equivalence of Kröner and weighted Voigt-Reuss models for x-ray stress determination
Authors: Murray Conal E.
Published: April 2013

The determination of stress in polycrystalline aggregates by diffraction-based methods relies on the proper choice of grain interaction model that links the observed strain to the elastic stress state in the ensemble. It is shown that for single-phase, polycrystalline samples composed of crystals with cubic symmetry, x-ray elastic constants (XEC) calculated under the Kröner model are equal to those from a weighted combination of Reuss and Voigt XEC, where the weighting factor is only a function of the single crystal elastic tensor coefficients. This weighting factor, xKr, generally scales with elastic anisotropy factor, A, with a value close to the Neerfeld limit for elastically isotropic materials (A = 1). Materials that possess large values of A, and correspondingly small xKr, exhibit a greater deviation between the Neerfeld and Kröner limit XEC. A dimensionless parameter, Q, based on a different combination of elastic coefficients than A, demonstrates a monotonic trend with respect to xKr and may serve as a better metric for describing the elastic response of a polycrystalline ensemble as interrogated by x-ray diffraction. For crystals possessing lower symmetry, a similar analysis reveals that Kröner XEC are not a unique combination of Voigt and Reuss limits. In the case of hexagonal crystal symmetry, xKr for a particular material varies as a function of the orientation parameter of the crystal, indicating that the degree of elastic anisotropy of the constituent crystals may impact the determination of stress depending on the choice of x-ray reflection.
High detection efficiency micro-structured solid-state neutron detector with extremely low leakage current fabricated with continuous p-n junction
Authors: Huang Kuan-Chih , Dahal Rajendra , Lu James J.-Q. , Danon Yaron , Bhat Ishwara B.
Published: April 2013

We report the continuous p-n junction formation in honeycomb structured Si diode by in situ boron deposition and diffusion process using low pressure chemical vapor deposition for solid-state thermal neutron detection applications. Optimized diffusion temperature of 800 °C was obtained by current density-voltage characteristics for fabricated p+-n diodes. A very low leakage current density of ∼2 × 10−8 A/cm2 at −1 V was measured for enriched boron filled honeycomb structured neutron detector with a continuous p+-n junction. The neutron detection efficiency for a Maxwellian spectrum incident on the face of the detector was measured under zero bias voltage to be ∼26%. These results are very encouraging for fabrication of large area solid-state neutron detector that could be a viable alternative to 3He tube based technology.
Large magnon band gaps created by introducing additional lattice scatterers
Authors: Wang Qi , Zhong Zhiyong , Jin Lichuan , Tang Xiaoli , Bai Feimin , Zhang Huaiwu
Published: April 2013

Magnon band gaps (MBGs) in 2D square and honeycomb lattices of circular cross-section rods can be increased by introducing a smaller diameter rod into the center of each lattice unit cell. The additional lattice scatterers reduce the structure symmetry to create significantly larger band gaps for original lattice. Magnon band structures are numerically calculated using the plane-wave method. The results show that the normalized width of band gaps in square-hybrid-rods and honeycomb-hybrid-rods structure are 167% and 285% sizes of those in the corresponding square-single-rods and honeycomb-single-rods structure. Crystal symmetry reduction by introducing additional scatterers opens up a new way for engineering MBGs of 2D magnonic crystals.
Reversible post-breakdown conduction in aluminum oxide-polymer capacitors
Authors: Chen Qian , Gomes Henrique L. , Rocha Paulo R. F. , de Leeuw Dago M. , Meskers Stefan C. J.
Published: April 2013

Aluminum/Al2O3/polymer/metal capacitors submitted to a low-power constant current stress undergo dielectric breakdown. The post-breakdown conduction is metastable, and over time the capacitors recover their original insulating properties. The decay of the conduction with time follows a power law (1/t)α. The magnitude of the exponent α can be raised by application of an electric field and lowered to practically zero by optical excitation of the polyspirofluorene polymer. The metastable conduction is attributed to formation of metastable pairs of oppositely charged defects across the oxide-polymer interface, and the self-healing is related to resistive switching.
A theory for structural phase transitions in BaTiO3 single crystal and PbZrO3 -xPbTiO3 solid solution
Authors: Zhang Hui
Published: April 2013

A phenomenological theory has been proposed for the diffusionless structuralphase transitions in BaTiO3single crystal and PbZrO3 -xPbTiO3 solid solution here. It has been found that for BaTiO3single crystal, both the phase transitionsand the crystal structurescan be predicted with the crystalline anisotropy constants and strain constants that depend on the temperature. For PbZrO3 -xPbTiO3 solution, the morphotropic phase boundaries arise from the strong dependence of the crystalline anisotropy constants on the composition. The good agreement between the numerical results and experimental observations has shown that our theory is effective for the diffusionless structuralphase transitions.
Failure of classical elasticity in auxetic foams
Authors: Roh J. H. , Giller C. B. , Mott P. H. , Roland C. M.
Published: April 2013

Poisson's ratio, ν, was measured for four materials, a rubbery polymer, a conventional soft foam, and two auxetic foams. We find that for the first two materials, having ν ≥ 0.2, the experimental determinations of Poisson's ratio are in good agreement with values calculated from the shear and tensile moduli using the equations of classical elasticity. However, for the two auxetic materials (ν < 0), the equations of classical elasticity give values significantly different from the measured ν. We offer an interpretation of these results based on a recently published analysis of the bounds on Poisson's ratio for classical elasticity to be applicable.
When Virtual and Material Worlds Collide: Democratic Fashion in the Digital Age
Authors: Crewe Louise
Published: April 2013

This paper explores the impact of digitally mediated communications technologies on the fashion sector. It argues that material and virtual fashion worlds are perpetually intersecting social realities that coexist relationally, simultaneously, and in mutual connection. The paper explores these shifting fashion landscapes in three particular ways in order to understand how fashion worlds are being transformed, enhanced, and reproduced in space and time. Firstly, it is argued that emergent digital technologies are remediating and refashioning existing cultural forms of signification such as fashion magazines and photography. Secondly, the potential disintermediatory effects that the Internet is having on fashion markets and consumption are explored, questioning to what extent digital technologies are enabling the devolution of fashion authority from traditional power brokers such as magazine editors and designers towards a more diversified assemblage of participants, including fashion bloggers and consumers. Thirdly, the transformative effects that digital technology is having on fashion consumption are explored. The Internet has opened up new spaces of fashion consumption that are unprecedented in their levels of ubiquity, immersion, fluidity, and interactivity. Fashion spaces are increasingly portable, must follow us around, travel with us through time and space. The network effects made possible by the Internet are enabling the creation of always-on, always-connected consumer communities. Increasingly we are adrift without the Internet, not with it. This is generating new ways of being in space where the absence of physical presence becomes second nature. Taken together, the collision between virtual and material fashion spaces requires a fundamental rethink about the role of fashion production, consumption, knowledge, and the laws of markets.
Myc-induced AMPK-phospho p53 pathway activates Bak to sensitize mitochondrial apoptosis
Authors: Nieminen Anni I. , Eskelinen Vilja M. , Haikala Heidi M. , Tervonen Topi A. , Yan Yan , Partanen Johanna I. , Klefström Juha
Published: April 2013

Oncogenic transcription factor Myc deregulates the cell cycle and simultaneously reprograms cellular metabolism to meet the biosynthetic and bioenergetic needs of proliferation. Myc also sensitizes cells to mitochondria-dependent apoptosis. Although metabolic reprogramming has been circumstantially connected to vulnerability to apoptosis, the connecting molecular pathways have remained poorly defined. Here, we show that Myc-induced altered glutamine metabolism involves ATP depletion and activation of the energy sensor AMP-activated protein kinase (AMPK), which induces stabilizing phosphorylation of p53 at Ser15. Under influence of Myc, AMPK-stabilized tumor suppressor protein p53 accumulates in the mitochondria and interacts with the protein complex comprised of B-cell lymphoma 2 (Bcl-2) antagonist/killer (BAK) and Bcl2-like 1 (Bcl-xL). Mitochondrial p53 induces conformational activation of proapoptotic Bak without disrupting the Bak–Bcl-x
L
interaction. Further liberation of Bak specifically from the p53-activated Bak–Bcl-x
L
complex leads to spontaneous oligomerization of Bak and apoptosis. Thus, Myc-induced metabolic changes are coupled via AMPK and phospho-p53 to the mitochondrial apoptosis effector Bak, demonstrating a cell-intrinsic mechanism to counteract uncontrolled proliferation.
SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals
Authors: Oosterveen Tony , Kurdija Sanja , Ensterö Mats , Uhde Christopher W. , Bergsland Maria , Sandberg Magnus , Sandberg Rickard , Muhr Jonas , Ericson Johan
Published: April 2013

The reiterative deployment of a small cadre of morphogen signals underlies patterning and growth of most tissues during embyogenesis, but how such inductive events result in tissue-specific responses remains poorly understood. By characterizing
cis
-regulatory modules (CRMs) associated with genes regulated by Sonic hedgehog (Shh), retinoids, or bone morphogenetic proteins in the CNS, we provide evidence that the neural-specific interpretation of morphogen signaling reflects a direct integration of these pathways with SoxB1 proteins at the CRM level. Moreover, expression of SoxB1 proteins in the limb bud confers on mesodermal cells the potential to activate neural-specific target genes upon Shh, retinoid, or bone morphogenetic protein signaling, and the collocation of binding sites for SoxB1 and morphogen-mediatory transcription factors in CRMs faithfully predicts neural-specific gene activity. Thus, an unexpectedly simple transcriptional paradigm appears to conceptually explain the neural-specific interpretation of pleiotropic signaling during vertebrate development. Importantly, genes induced in a SoxB1-dependent manner appear to constitute repressive gene regulatory networks that are directly interlinked at the CRM level to constrain the regional expression of patterning genes. Accordingly, not only does the topology of SoxB1-driven gene regulatory networks provide a tissue-specific mode of gene activation, but it also determines the spatial expression pattern of target genes within the developing neural tube.
Phosphoregulation promotes release of kinetochores from dynamic microtubules via multiple mechanisms
Authors: Sarangapani Krishna K. , Akiyoshi Bungo , Duggan Nicole M. , Biggins Sue , Asbury Charles L.
Published: April 2013

During mitosis, multiprotein complexes called kinetochores orchestrate chromosome segregation by forming load-bearing attachments to dynamic microtubule tips, and by participating in phosphoregulatory error correction. The conserved kinase Aurora B phosphorylates the major microtubule-binding kinetochore subcomplexes, Ndc80 and (in yeast) Dam1, to promote release of erroneous attachments, giving another chance for proper attachments to form. It is unknown whether Aurora B phosphorylation promotes release directly, by increasing the rate of kinetochore detachment, or indirectly, by destabilizing the microtubule tip. Moreover, the relative importance of phosphorylation of Ndc80 vs. Dam1 in the context of whole kinetochores is unclear. To address these uncertainties, we isolated native yeast kinetochore particles carrying phosphomimetic mutations on Ndc80 and Dam1, and applied advanced laser-trapping techniques to measure the strength and stability of their attachments to individual dynamic microtubule tips. Rupture forces were reduced by phosphomimetic mutations on both subcomplexes, in an additive manner, indicating that both subcomplexes make independent contributions to attachment strength. Phosphomimetics on either subcomplex reduced attachment lifetimes under constant force, primarily by accelerating detachment during microtubule growth. Phosphomimetics on Dam1 also increased the likelihood of switches from microtubule growth into shortening, further promoting release in an indirect manner. Taken together, our results suggest that, in vivo, Aurora B releases kinetochores via at least two mechanisms: by weakening the kinetochore-microtubule interface and also by destabilizing the kinetochore-attached microtubule tip.
SK4 Ca
2+
activated K
+
channel is a critical player in cardiac pacemaker derived from human embryonic stem cells
Authors: Weisbrod David , Peretz Asher , Ziskind Anna , Menaker Nataly , Oz Shimrit , Barad Lili , Eliyahu Sivan , Itskovitz-Eldor Joseph , Dascal Nathan , Khananshvili Daniel , Binah Ofer , Attali Bernard
Published: April 2013

Significance

The contractions of the heart are initiated and coordinated by pacemaker tissues, responsible for cardiac automaticity. Although the cardiac pacemaker was discovered more than a hundred years ago, the pacemaker mechanisms remain controversial. We used human embryonic stem cell-derived cardiomyocytes to study the embryonic cardiac automaticity of the human heart. We identified a previously unrecognized Ca
2+
-activated K
+
channel (SK4), which appears to play a pivotal role in cardiac automaticity. Our results suggest that SK4 Ca
2+
-activated K
+
channels represent an important target for the management of cardiac rhythm disorders and open challenging horizons for developing biological pacemakers.
A thin polymer membrane, nano-suit, enhancing survival across the continuum between air and high vacuum
Authors: Takaku Yasuharu , Suzuki Hiroshi , Ohta Isao , Ishii Daisuke , Muranaka Yoshinori , Shimomura Masatsugu , Hariyama Takahiko
Published: April 2013

Most multicellular organisms can only survive under atmospheric pressure. The reduced pressure of a high vacuum usually leads to rapid dehydration and death. Here we show that a simple surface modification can render multicellular organisms strongly tolerant to high vacuum. Animals that collapsed under high vacuum continued to move following exposure of their natural extracellular surface layer (or that of an artificial coat-like polysorbitan monolaurate) to an electron beam or plasma ionization (i.e., conditions known to enhance polymer formation). Transmission electron microscopic observations revealed the existence of a thin polymerized extra layer on the surface of the animal. The layer acts as a flexible “nano-suit” barrier to the passage of gases and liquids and thus protects the organism. Furthermore, the biocompatible molecule, the component of the nano-suit, was fabricated into a “biomimetic” free-standing membrane. This concept will allow biology-related fields especially to use these membranes for several applications.
Ocean acidification alters the otoliths of a pantropical fish species with implications for sensory function
Authors: Bignami Sean , Enochs Ian C. , Manzello Derek P. , Sponaugle Su , Cowen Robert K.
Published: April 2013

Ocean acidification affects a wide diversity of marine organisms and is of particular concern for vulnerable larval stages critical to population replenishment and connectivity. Whereas it is well known that ocean acidification will negatively affect a range of calcareous taxa, the study of fishes is more limited in both depth of understanding and diversity of study species. We used new 3D microcomputed tomography to conduct in situ analysis of the impact of ocean acidification on otolith (ear stone) size and density of larval cobia (
Rachycentron canadum
), a large, economically important, pantropical fish species that shares many life history traits with a diversity of high-value, tropical pelagic fishes. We show that 2,100 μatm partial pressure of carbon dioxide (
p
CO
2
) significantly increased not only otolith size (up to 49% greater volume and 58% greater relative mass) but also otolith density (6% higher). Estimated relative mass in 800 μatm
p
CO
2
treatments was 14% greater, and there was a similar but nonsignificant trend for otolith size. Using a modeling approach, we demonstrate that these changes could affect auditory sensitivity including a ∼50% increase in hearing range at 2,100 μatm
p
CO
2
, which may alter the perception of auditory information by larval cobia in a high-CO
2
ocean. Our results indicate that ocean acidification has a graded effect on cobia otoliths, with the potential to substantially influence the dispersal, survival, and recruitment of a pelagic fish species. These results have important implications for population maintenance/replenishment, connectivity, and conservation efforts for other valuable fish stocks that are already being deleteriously impacted by overfishing.