bluuebunny/crossref_metadata_2025 huggingface dataset:
Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
Authors: Perez‐Riverol Yasset , Alpi Emanuele , Wang Rui , Hermjakob Henning , Vizcaíno Juan Antonio
Published: August 2014

Compared to other data‐intensive disciplines such as genomics, public deposition and storage of MS‐based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data.
Performances Enhancement of H‐Doped ZnO Nanorods by H2/Ar Plasma Treatment
Authors: Wang Ruey‐Chi , Cheng Chiao‐Fang
Published: August 2014

The thermal stability of H dopants in ZnO nanorod (NR) array is demonstrated to be greatly enhanced by a H2/Ar mixed plasma treatment compared to a H2 plasma treatment and hence their optoelectronic properties. For all the as‐treated samples with the plasma containing H2 plasma, ultraviolet emission and electrical conductivity are enhanced as well as sensitivity and photoresponsivity of UV sensing. Notably, only the H2/Ar‐treated samples show high thermal stability of H dopants and enhanced optoelectronic properties after annealing at 300 °C for 1 h, which is attributed to the assistance of Ar plasma.
Cancer Patients at Risk of Herb/Food Supplement–Drug Interactions: A Systematic Review
Authors: Alsanad Saud M. , Williamson Elizabeth M. , Howard Rachel L.
Published: August 2014

Herbal medicines and dietary supplements are commonly taken by patients with cancer, leading to concern over interactions with conventional medicines. A literature search was carried out to identify published studies exploring supplement use by patients with a cancer diagnosis. A total of 818 articles were retrieved using the key words, but only 41 are judged to be relevant based on title. Following the review of the abstracts, ten papers were considered to be potentially relevant, but of these, only two met the selection criteria, and three additional papers were identified from published reviews. Of 806 patients surveyed, 433 (53.7%) were reported to be taking combinations of supplements and drugs, and 167 incidents of risk were identified, affecting 60 patients (13.9%). The interactions identified were mainly theoretical and not supported by clinical data. No studies reported any adverse events associated with these combinations; most did not record the actual drug combinations taken, and the risk potential of some supplements appears to have been over‐estimated. More effort should be made to investigate supplement use in this vulnerable patient group, based on sound evidence of plausible interaction, not only to avoid harm but also to provide reassurance where appropriate if the patient wishes to take a particular supplement. Copyright © 2014 John Wiley & Sons, Ltd.
Dynamic Modelling of Soil Nitrogen Budget and Vegetation Colonization in Sediment Bars of a Regulated River
Authors: Asaeda T. , Rashid M. H. , Abu Bakar R.
Published: August 2014

Intensive forestation widely occurs in East Asian rivers. It deteriorates the ecosystem of gravelly or sandy bars, affects flood protection, and changes the landscape of the river. For the regulation of forestation and vegetative succession on the bars, a suitable tool, through either a numerical simulation model or through empirical knowledge that will predict the future process after treatment, is required. With this background, a dynamic model is developed based on the empirical knowledge obtained by field observations in order to simulate the vegetative growth process on the bars. Observations were conducted at several Japanese rivers in order to better understand tree growth and biomass, herbaceous plant biomass, and soil nitrogen content. The model is composed of four modules: a hydrological module, which provides for flood inundation, flushing and sedimentation processes, a tree module, which describes the recruitment, growth and thinning of tree densities, and a herbaceous plant module, which describes the biomass of herbs as a function of environmental conditions. Finally, there is a soil module, which mostly describes nitrogen budgets. The model was successfully applied to the Arakawa River in central Japan in order to simulate a 30‐year process after a major flood. Simulations were conducted for several cases related to the processes of two tree species: Robinia pseudoacacia and Salix spp. The model was then applied in order to elucidate the forestation mechanism of the bar, which indicated a possible reason for the effect of decreasing the supply of coarse sediment. The impact of the tree and herbaceous plants by different hydrological processes is also discussed. Copyright © 2014 John Wiley & Sons, Ltd.
Rain granularity effects on bandwidth demand for faded DVB‐RCS systems
Authors: Al‐Mosawi Mohamed , Khusainov Rinat , Gremont Boris
Published: August 2014

Broadband satellite communication networks, operating at Ka band and above, play a vital role in today's worldwide telecommunication infrastructure. The problem, however, is that rain can be the most dominant impairment factor for radio propagation above 10 GHz. This paper studies bandwidth and time slot allocation problem for rain faded DVB‐RCS satellite networks. We investigate how using finer rain granularity can improve bandwidth utilization in DVB‐RCS return links. The paper presents a mathematical model to calculate the bandwidth on demand. We formulate the radio resource allocation as an optimization problem and propose a novel algorithm for dynamic carrier bandwidth and time slots allocation, which works with constant bit rate type of traffic. We provide theoretical analysis for the time slot allocation problem and show that the proposed algorithm achieves optimal results. The algorithm is evaluated using a MATLAB simulation with historical rain data for the UK. Copyright © 2014 John Wiley & Sons, Ltd.
A model‐free estimation for the covariate‐adjusted Youden index and its associated cut‐point
Authors: Xu Tu , Wang Junhui , Fang Yixin
Published: August 2014

In medical research, continuous markers are widely employed in diagnostic tests to distinguish diseased and non‐diseased subjects. The accuracy of such diagnostic tests is commonly assessed using the receiver operating characteristic (ROC) curve. To summarize an ROC curve and determine its optimal cut‐point, the Youden index is popularly used. In literature, the estimation of the Youden index has been widely studied via various statistical modeling strategies on the conditional density. This paper proposes a new model‐free estimation method, which directly estimates the covariate‐adjusted cut‐point without estimating the conditional density. Consequently, covariate‐adjusted Youden index can be estimated based on the estimated cut‐point. The proposed method formulates the estimation problem in a large margin classification framework, which allows flexible modeling of the covariate‐adjusted Youden index through kernel machines. The advantage of the proposed method is demonstrated in a variety of simulated experiments as well as a real application to Pima Indians diabetes study. Copyright © 2014 John Wiley & Sons, Ltd.
Transcriptional profiles of glutathione‐S‐Transferase isoforms, Cyp, and AOE genes in atrazine‐exposed zebrafish embryos
Authors: Glisic Branka , Hrubik Jelena , Fa Svetlana , Dopudj Nela , Kovacevic Radmila , Andric Nebojsa
Published: August 2014

Glutathione‐S‐transferase (GST) superfamily consists of multiple members involved in xenobiotic metabolism. Expressional pattern of the GST isoforms in adult fish has been used as a biomarker of exposure to environmental chemicals. However, GST transcriptional responses vary across organs, thus requiring a cross‐tissue examination of multiple mRNAs for GST profiling in an animal after chemical exposure. Zebrafish embryos express all GST isoforms as adult fish and could therefore represent an alternative model for identification of biomarkers of exposure. To evaluate such a possibility, we studied a set of cytosolic and microsomal GST isoform‐specific expression profiles in the zebrafish embryos after exposure to atrazine, a widely used herbicide. Expression of the GST isoforms was compared with that of CYP genes involved in the phase I of xenobiotic metabolism and antioxidant enzyme (AOE) genes. Using quantitative real‐time PCR, we showed dynamic changes in the expressional pattern of twenty GST isoforms, cyp1a, cyp3a65, ahr2, and four AOEs in early development of zebrafish. Acute (48 and 72 h) exposure of 24 h‐old embryos to atrazine, from environmentally relevant (0.005 mg/L) to high (40 mg/L) concentrations, caused a variety of transient, albeit minor changes (<2.5‐fold) in the GST isoforms, ahr2 and AOE genes response. However, expression of cyp1a and cyp3a65 mRNA was markedly and consistently induced by high doses of atrazine (5 and 40 mg/L). In summary, an analysis of the response of multiple systems in the zebrafish embryos provided a comprehensive understanding of atrazine toxicity and its potential impact on biological processes. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 233–244, 2016.
Fetal intervention for severe lower urinary tract obstruction: a multicenter case–control study comparing fetal cystoscopy with vesicoamniotic shunting
Authors: Ruano R. , Sananes N. , Sangi‐Haghpeykar H. , Hernandez‐Ruano S. , Moog R. , Becmeur F. , Zaloszyc A. , Giron A. M. , Morin B. , Favre R.
Published: August 2014

Objective

To evaluate the efficacy of fetal intervention using fetal cystoscopy or vesicoamniotic shunting in the treatment of severe lower urinary obstruction (LUTO).

Methods

A cohort of 111 fetuses with severe LUTO attending two centers between January 1990 and August 2013 were included retrospectively. Fetuses were categorized into three groups based on the method of intervention: (1) fetal cystoscopy, (2) vesicoamniotic shunting or (3) no intervention. Multivariate analyses were performed to determine the probability of survival and normal renal function until 6 months of age by comparing fetal cystoscopy and vesicoamniotic shunting to no fetal intervention.

Results

Of the 111 fetuses with severe LUTO that were included in the analysis, fetal cystoscopy was performed in 34, vesicoamniotic shunting was performed in 16 and there was no fetal intervention in 61. Gestational age at diagnosis, method of fetal intervention and cause of bladder obstruction were associated with prognosis. In multivariate analysis and after adjustment for potential confounders (considering all causes of LUTO) the overall probability of survival was significantly higher with fetal cystoscopy and vesicoamniotic shunting when compared to no intervention (adjusted relative risk (ARR), 1.86 (95% CI, 1.01–3.42; P = 0.048) and ARR, 1.73 (95% CI, 1.01–3.08; P = 0.04) respectively). A clear trend for normal renal function was present in the fetal cystoscopy group (ARR, 1.73 (95% CI, 0.97–3.08; P = 0.06)) but was not observed in the vesicoamniotic shunt group (ARR, 1.16 (95% CI, 0.86–1.55; P = 0.33)). In cases in which there was a postnatal diagnosis of posterior urethral valves, fetal cystoscopy was effective in improving both the 6‐month survival rate and renal function (ARR, 4.10 (95% CI, 1.75–9.62; P < 0.01) and 2.66 (95% CI, 1.25–5.70; P = 0.01) respectively) while vesicoamniotic shunting was associated only with an improvement in the 6‐month survival rate (ARR, 3.76 (95% CI, 1.42–9.97; P < 0.01)) with no effect on renal function (ARR, 1.03 (95% CI, 0.49–2.17, P = 0.93)).

Conclusion

Fetal cystoscopy and vesicoamniotic shunting improve the 6‐month survival rate in cases of severe LUTO. However, only fetal cystoscopy may prevent impairment of renal function in fetuses with posterior urethral valves. Our data support the idea of performing a subsequent randomized controlled trial to compare the effectiveness of fetal cystoscopy vs vesicoamniotic shunting for severe fetal LUTO. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.
Continuing progress toward controlled intracellular delivery of semiconductor quantum dots
Authors: Breger Joyce , Delehanty James B. , Medintz Igor L.
Published: August 2014

The biological applications of luminescent semiconductor quantum dots (QDs) continue to grow at a nearly unabated pace. This growth is driven, in part, by their unique photophysical and physicochemical properties which have allowed them to be used in many different roles in cellular biology including: as superior fluorophores for a wide variety of cellular labeling applications; as active platforms for assembly of nanoscale sensors; and, more recently, as a powerful tool to understand the mechanisms of nanoparticle mediated drug delivery. Given that controlled cellular delivery is at the intersection of all these applications, the latest progress in delivering QDs to cells is examined here. A brief discussion of relevant considerations including the importance of materials preparation and bioconjugation along with the continuing issue of endosomal sequestration is initially provided for context. Methods for the cellular delivery of QDs are then highlighted including those based on passive exposure, facilitated strategies that utilize peptides or polymers and fully active modalities such as electroporation and other mechanically based methods. Following on this, the exciting advent of QD cellular delivery using multiple or combined mechanisms is then previewed. Several recent methods reporting endosomal escape of QD materials in cells are also examined in detail with a focus on the mechanisms by which access to the cytosol is achieved. The ongoing debate over QD cytotoxicity is also discussed along with a perspective on how this field will continue to evolve in the future. WIREs Nanomed Nanobiotechnol 2015, 7:131–151. doi: 10.1002/wnan.1281

This article is categorized under:

Diagnostic Tools > In Vitro Nanoparticle-Based Sensing

Implantable Materials and Surgical Technologies > Nanomaterials and Implants

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
A Serious Game Can Be a Valid Method to Train Clinical Decision‐Making in Surgery
Authors: Graafland Maurits , Vollebergh Maarten F. , Lagarde Sjoerd M. , van Haperen M. , Bemelman Willem A. , Schijven Marlies P.
Published: August 2014

Background

A serious game was developed to train surgical residents in clinical decision‐making regarding biliary tract disease. Serious or applied gaming is a novel educational approach to postgraduate training, combining training and assessment of clinical decision‐making in a fun and challenging way. Although interest for serious games in medicine is rising, evidence on its validity is lacking. This study investigates face, content, and construct validity of this serious game.

Methods

Experts structurally validated the game’s medical content. Subsequently, 41 participants played the game. Decision scores and decision speed were compared among surgeons, surgical residents, interns, and medical students, determining the game’s discriminatory ability between different levels of expertise. After playing, participants completed a questionnaire on the game’s perceived realism and teaching ability.

Results

Surgeons solved more cases correctly (mean 77 %) than surgical residents (67 %), interns (60 %), master‐degree students (50 %), and bachelor‐degree students (39 % (p < 0.01). Trainees performed significantly better in their second play session than in the first (median 72 vs. 48 %, p = 0.00). Questionnaire results showed that educators and surgical trainees found the game both realistic and useful for surgical training. The majority perceived the game as fun (91.2 %), challenging (85.3 %), and would recommend the game to educate their colleagues (81.8 %).

Conclusions

This serious game showed clear discriminatory ability between different levels of expertise in biliary tract disease management and clear teaching capability. It was perceived as appealing and realistic. Serious gaming has the potential to increase adherence to training programs in surgical residency training and medical school.
The paleoclimatic and geochronologic utility of coring red beds and evaporites: a case study from the RKB core (Permian, Kansas, USA)
Authors: Soreghan Gerilyn S. , Benison Kathleen C. , Foster Tyler M. , Zambito Jay , Soreghan Michael J.
Published: August 2014

Drill core is critical for robust and high-resolution reconstructions of Earth’s climate record, as well demonstrated from both marine successions and modern long-lived lake systems. Deep-time climate reconstructions increasingly require core-based data, but some facies, notably red beds and evaporites, have garnered less attention for both paleoclimatic and geochronologic analyses. Here, we highlight studies from the Rebecca K. Bounds (RKB) core, a nearly continuous, >1.6 km drill core extending from the Cretaceous to the Mississippian, recovered from the US Midcontinent by Amoco Production Company in 1988, and serendipitously made available for academic research. Recent research conducted on this core illustrates the potential to recover high-resolution data for geochronologic and climatic reconstructions from both the fine-grained red bed strata, which largely represent paleo-loess deposits, and associated evaporite strata. In this case, availability of core was instrumental for (1) accessing a continuous vertical section that establishes unambiguous superposition key to both magnetostratigraphic and paleoclimatic analyses, and (2) providing pristine sample material from friable, soluble, and/or lithofacies and mineralogical species otherwise poorly preserved in surface exposures. The potential for high-resolution paleoclimatic reconstruction from coring of deep-time loess strata in particular remains severely underutilized.
Effect of Head Groups, Temperature, and Polymer Concentration on Surfactant—Polymer Interactions
Authors: Banipal Tarlok Singh , Kaur Harjinder , Banipal Parampaul Kaur , Sood Ashwani Kumar
Published: August 2014

The micellization behaviour of sodium dodecyl sulphate, sodium dodecylbenzenesulfonate, hexadecyltrimethylammonium bromide, tetradecyltrimethylammonium bromide, and cetylpyridinium chloride in water and in aqueous solutions of polyethylene oxide (PEO, molecular weight = 100,000) having concentrations (0.005–0.04 %, w/v) has been studied at different temperatures (288.15–318.15 K) using conductivity, surface tension, and viscosity methods. From conductivity measurements various micellar parameters, like critical micellar concentration (CMC), critical aggregation concentration (CAC), polymer saturation point (PSP), degree of ionization (β), and standard free energy of transfer (), have been calculated. CAC values have been found to decrease with polymer concentration and increase with temperature. However, the PSP values increase with both polymer concentration and temperature for all surfactants. Similar parameters have also been calculated from surface tension data (CMCσ, CACσ, PSPσ) along with other parameters such as maximum surface excess concentration at the air/water interface (), minimum area per molecule (Amin), and packing parameter (p). The CMCσ, CACσ, and PSPσ values are smaller than the corresponding CMC, CAC, and PSP values, but both show similar behaviour with temperature and concentration of polymer. Various parameters indicate that the presence of the aromatic ring in the head group of surfactant decreases its interaction with PEO, whereas the increased hydrophobicity in the tail leads to stronger interactions with PEO. Viscosity studies further supplement the conclusions drawn from the above results.
Tsukushi is involved in the wound healing by regulating the expression of cytokines and growth factors
Authors: Niimori Daisuke , Kawano Rie , Niimori‐Kita Kanako , Ihn Hironobu , Ohta Kunimasa
Published: August 2014

During the wound‐healing process, macrophages, fibroblasts, and myofibroblasts play a leading role in shifting from the inflammation phase to the proliferation phase, although little is known about the cell differentiation and molecular control mechanisms underlying these processes. Previously, we reported that Tsukushi (TSK), a member of the small leucine‐rich repeat proteoglycan family, functions as a key extracellular coordinator of multiple signalling networks. In this study, we investigated the contribution of TSK to wound healing. Analysis of wound tissue in heterozygous TSK‐lacZ knock‐in mice revealed a pattern of sequential TSK expression from macrophages to myofibroblasts. Quantitative PCR and in vitro cell induction experiments showed that TSK controls macrophage function and myofibroblast differentiation by inhibiting TGF‐β1 secreted from macrophages. Our results suggest TSK facilitates wound healing by maintaining inflammatory cell quiescence.
Target specificity of the CRISPR‐Cas9 system
Authors: Wu Xuebing , Kriz Andrea J. , Sharp Phillip A.
Published: August 2014

The CRISPR‐Cas9 system, naturally a defense mechanism in prokaryotes, has been repurposed as an RNA‐guided DNA targeting platform. It has been widely used for genome editing and transcriptome modulation, and has shown great promise in correcting mutations in human genetic diseases. Off‐target effects are a critical issue for all of these applications. Here we review the current status on the target specificity of the CRISPR‐Cas9 system.
Tribological properties of platinum/ruthenium/nitrogen doped diamond-like carbon thin films deposited with different negative substrate biases
Authors: Khun Nay Win , Liu Erjia
Published: August 2014

The platinum/ruthenium/nitrogen doped diamond-like carbon (PtRuN-DLC) thin films were deposited on Si substrates via DC magnetron sputtering by varying negative substrate bias. The tribological performance of the PtRuN-DLC films was systematically investigated using ball-on-disc microtribological test. The Raman results showed that the increased negative substrate bias significantly increased the number of sp3 bonds in the PtRuN-DLC films as a result of the increased kinetic energies of impinging ions. The adhesion strength of the PtRuN-DLC films apparently decreased with increased negative substrate bias due to the promoted residual stress in the films. The tribological results clearly revealed that the increased negative substrate bias decreased the friction and wear of the PtRuN-DLC films by improving the sp3 bonded cross-linking structures of the films. It can be concluded that the PtRuN-DLC films could effectively prevent their underlying Si substrates from wear as the negative substrate bias had a significant influence on the tribological properties of the PtRuN-DLC films.
Implementing AORN Recommended Practices for a Safe Environment of Care, Part II
Authors: Kennedy Lynne
Published: August 2014

Construction in and around a working perioperative suite is a challenge beyond merely managing traffic patterns and maintaining the sterile field. The AORN “Recommended practices for a safe environment of care, part II” provides guidance on building design; movement of patients, personnel, supplies, and equipment; environmental controls; safety and security; and control of noise and distractions. Whether the OR suite evolves through construction, reconstruction, or remodeling, a multidisciplinary team of construction experts and health care professionals should create a functional plan and communicate at every stage of the project to maintain a safe environment and achieve a well‐designed outcome. Emergency preparedness, a facility‐wide security plan, and minimization of noise and distractions in the OR also help enhance the safety of the perioperative environment.
Prosopography of the Book and the Politics of Legal Language in Late Medieval England
Authors: Kennedy Kathleen E.
Published: August 2014

This article explores the intersection of book history and prosopography. It uses several case studies of copies of the medieval parliamentary statutes translated into English, together with later copies of English statutes translated into French, to argue for both thick prosopographical study of individual volumes and large, statistically based studies of books drawn from the largest possible data sets. Together, these methods amount to a new “prosopograhy of the book.” The case studies analyzed here reveal a complicated politicized relationship not only between script and print but also between French and English in the early Tudor era.
“The Only Man of Nature That Ever Appeared in the World”: “Walking” John Stewart and the Trajectories of Social Radicalism, 1790–1822
Authors: Claeys Gregory
Published: August 2014

This article explores the ideas of “Walking” John Stewart (1747–1822), a little-known adventurer and philosopher active in debates over social reformation during the French Revolutionary period. Renowned as a peripatetic who walked from India to Britain, Stewart befriended Thomas Paine and others during the early years of the Revolution. His main aim was to persuade them of the value of his philosophy, which was derived from French materialism as well as Hindu and Buddhist sources. But Stewart also came under the influence of the Shakers, Dunkers, Moravians, and other North American sectarian communities. As early as 1791 he commended small-scale “cohabitations” of no more than 100 men and 100 women as the ideal form of association. Here, and in his radical approaches to marriage and sexual relationships, he strikingly anticipated the ideas of Robert Owen and the early socialists.
The Making of a Translator: James Strachey and the Origins of British Psychoanalysis
Authors: Linstrum Erik
Published: August 2014

Both critics and defenders of James Strachey's translations of Sigmund Freud have tended to judge their worth by the standard of “accuracy”—in other words, their faithfulness to Freud's theories. This article takes a different approach, tracing Strachey's choices as a translator to his own experiences in Edwardian, wartime, and interwar Britain. Convinced that the ruling elite and the mass public alike were captive to dangerously irrational forces, Strachey saw the science of the unconscious as a vehicle for political and social criticism. As an attempt to mobilize expert knowledge against the status quo, Strachey's translation represents a divergence from two influential paradigms for interpreting the history of psychoanalysis: Carl Schorske's account of the Freudian “retreat from politics” and Michel Foucault's portrait of the “superstructural” state as an extension and ally of the human sciences. Strachey's translation also demonstrates that the political and social ambitions of British psychoanalysis were powerfully formed by the era of the First World War, and not only the Second, which historians have often identified as the crucial moment.
Calvinist Absolutism: Archbishop James Ussher and Royal Power
Authors: Campbell Ian W. S.
Published: August 2014

Archbishop James Ussher's manuscript notebooks allow us to observe the making of a Calvinist absolutist and to orientate the archbishop's beliefs about royal power within European Reformed thought as a whole. By 1643, Ussher was preaching a polished and complete theory of absolute royal power, and it is possible to track the development of this political theory forward from his undergraduate days in the 1590s. Throughout his life Ussher engaged anxiously with Reformed theologians abroad, who generally favored limited rather than absolute monarchy. Nevertheless, Ussher shared with these Reformed colleagues both an antipathy to aspects of Aristotelian politics and a commitment to the divine institution of royal power. Finally, despite Ussher's hostility to Laudian innovations in the Irish Church, his heartfelt political beliefs made him a firm supporter of Stuart absolutism throughout the Three Kingdoms.
Mutual inductance instability of the tip vortices behind a wind turbine
Authors: Sarmast Sasan , Dadfar Reza , Mikkelsen Robert F. , Schlatter Philipp , Ivanell Stefan , Sørensen Jens N. , Henningson Dan S.
Published: August 2014

Two modal decomposition techniques are employed to analyse the stability of wind turbine wakes. A numerical study on a single wind turbine wake is carried out focusing on the instability onset of the trailing tip vortices shed from the turbine blades. The numerical model is based on large-eddy simulations (LES) of the Navier–Stokes equations using the actuator line (ACL) method to simulate the wake behind the Tjæreborg wind turbine. The wake is perturbed by low-amplitude excitation sources located in the neighbourhood of the tip spirals. The amplification of the waves travelling along the spiral triggers instabilities, leading to breakdown of the wake. Based on the grid configurations and the type of excitations, two basic flow cases, symmetric and asymmetric, are identified. In the symmetric setup, we impose a 120° symmetry condition in the dynamics of the flow and in the asymmetric setup we calculate the full 360° wake. Different cases are subsequently analysed using dynamic mode decomposition (DMD) and proper orthogonal decomposition (POD). The results reveal that the main instability mechanism is dispersive and that the modal growth in the symmetric setup arises only for some specific frequencies and spatial structures, e.g. two dominant groups of modes with positive growth (spatial structures) are identified, while breaking the symmetry reveals that almost all the modes have positive growth rate. In both setups, the most unstable modes have a non-dimensional spatial growth rate close to$\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\pi /2$and they are characterized by an out-of-phase displacement of successive helix turns leading to local vortex pairing. The present results indicate that the asymmetric case is crucial to study, as the stability characteristics of the flow change significantly compared to the symmetric configurations. Based on the constant non-dimensional growth rate of disturbances, we derive a new analytical relationship between the length of the wake up to the turbulent breakdown and the operating conditions of a wind turbine.
A metabolomics approach used to profile plasma from portal–arterial pigs revealed differences between breads incurred by dietary fibre and protein contents
Authors: Nielsen Kirstine Lykke , Hedemann Mette Skou , Lærke Helle Nygaard , Jørgensen Henry , Bach Knudsen Knud Erik
Published: August 2014

A liquid chromatography–MS (LC-MS) metabolomics analysis of plasma from portal–arterial catheterised pigs fed breads prepared with whole-grain rye or wheat flour with added concentrated arabinoxylan (AX) or β-glucan (BG) was conducted. Comparison of the effects of concentrated fibres with whole grains has received little attention. Six female catheterised pigs were given two white wheat breads with wheat AX or oat BG, two rye breads with ground rye (GR) or intact rye kernels (RK), and a control white wheat bread (WF) on separate occasions in a randomised cross-over design. The amount of available carbohydrate was similar for the five breads but varied in the content of protein. Plasma was collected continuously for 4 h after feeding. Glucose levels in the portal vein were reduced postprandially in response to the AX, GR and RK breads that had high contents of AX compared with WF bread (P < 0·03). AX and RK breads further tended to decrease plasma levels of some lysophosphatidylcholine species (P ≤ 0·10). The abundance of amino acids in plasma correlated with the protein contents in the breads and leucine uptake significantly affected insulin secretion in the mesenteric artery. In conclusion, the present study revealed that concentrated AX in wheat bread had similar positive effects as whole-grain rye bread on glucose and lipid metabolism.
How Many Parents Can a Child Have? Philosophical Reflections on the 'Three Parent Case'
Authors: BRENNAN SAMANTHA , CAMERON BILL
Published: August 2014

In light of recent legal decisions affording more than two parents to Canadian children, we consider whether there is any moral reason for limiting the number of parents a child can have to two. We look at several traditional arguments for this position and find that they fail to justify it. We also consider an argument inspired by Brighouse and Swift’s work on the goods of parenting and find that while it brings up important points, it is not strong enough to support a limit of just two parents. We conclude with some thoughts about how else the notion of parenthood could be helpfully separated from traditional notions.
Irritable bowel syndrome: the problem and the problem of treating it – is there a role for probiotics?
Authors: Santos Antonieta R. , Whorwell P. J.
Published: August 2014

The aim of this review is to highlight the impact of irritable bowel syndrome (IBS) in those patients who consult the medical profession and examine the therapeutic potential of probiotics in this condition, where there is a strong need for new treatment options. Traditionally, IBS is frequently regarded as a trivial condition which is certainly not life threatening and mainly psychological in origin. However, these preconceptions are misplaced, as in some patients the condition can be devastating with the pain being as severe as that of childbirth coupled with incapacitating bowel dysfunction. In addition, patients suffer from a variety of non-colonic symptoms such as low backache, constant lethargy, nausea and genito-urinary problems, all of which lead to these patients having extremely poor quality of life. Unfortunately, the treatment of IBS is very unsatisfactory with only one new medication being developed for this condition in the last 25 years. It is now recognised that IBS is a multifactorial condition with symptoms being triggered by a variety of factors, some of which appear to be influenced by probiotics, resulting in speculation that they may have therapeutic potential in this condition. There have been over thirty controlled clinical trials of probiotics in IBS with approximately two-thirds of these studies showing evidence of an improvement in symptoms. However, not all probiotics appear to be effective with different symptoms being improved by different strains and some improving symptoms more than others. Consequently, the ideal probiotic for the treatment of IBS has yet to be defined, but the evidence is good enough to encourage further research with the aim of identifying an optimal strain or strains.
Population status of the Bornean orang-utanPongo pygmaeusin a vanishing forest in Indonesia: the former Mega Rice Project
Authors: Cattau Megan E. , Husson Simon , Cheyne Susan M.
Published: August 2014

As peat-swamp forests in Borneo become progressively more fragmented, the species that inhabit them are increasingly threatened, notably the Endangered Bornean orang-utanPongo pygmaeus. The area of a failed agricultural project known as the Mega Rice Project in Central Kalimantan, Indonesia, is composed of fragments of peat-swamp forest that are reported to contain orang-utans, although no comprehensive survey has previously been conducted. In a portion of this area we identified remaining forest fragments, using satellite imagery, and surveyed line transects for orang-utan sleeping nests to determine the density, abundance and distribution of the species. The total area of peat-swamp forest in the study area is 76,755 ha, 59,948 ha of which comprises patches at least as large as the home range of a female orang-utan (250 ha). We estimate a mean population density of 2.48 ± SE 0.32 individuals km−2and a population of 1,700 ± SE 220 or 1,507 ± SE 195 individuals, based on a 25 and 250 ha minimum patch size threshold, respectively. This is c. 40–45% of the original population, and the fragmented population is unlikely to be viable in terms of long-term demographic and genetic stability. To ensure persistence of this population of orang-utans, direct conservation action to connect forest fragments and prevent further loss of peat-swamp forest will be required, including re-establishing the hydrological regime, reforesting barren areas and fighting fires.
Developmental interplay between children's biobehavioral risk and the parenting environment from toddler to early school age: Prediction of socialization outcomes in preadolescence
Authors: Kochanska Grazyna , Boldt Lea J. , Kim Sanghag , Yoon Jeung Eun , Philibert Robert A.
Published: August 2014

We followed 100 community families from toddler age to preadolescence. Each mother– and father–child dyad was observed at 25, 38, 52, 67, and 80 months (10 hr/child) to assess positive and power-assertive parenting. At age 10 (N= 82), we obtained parent- and child-reported outcome measures of children's acceptance of parental socialization: cooperation with parental monitoring, negative attitude toward substance use, internalization of adult values, and callous–unemotional tendencies. Children who carried a short serotonin transporter linked polymorphic region gene (5-HTTLPR) allele and were highly anger prone, based on anger observed in laboratory from 25 to 80 months, were classified as high in biobehavioral risk. The remaining children were classified as low in biobehavioral risk. Biobehavioral risk moderated links between parenting history and outcomes. For low-risk children, parenting measures were unrelated to outcomes. For children high in biobehavioral risk, variations in positive parenting predicted cooperation with monitoring and negative attitude toward substance use, and variations in power-assertive parenting predicted internalization of adult values and callous–unemotional tendencies. Suboptimal parenting combined with high biobehavioral risk resulted in the poorest outcomes. The effect for attitude toward substance use supported differential susceptibility: children high in biobehavioral risk who received optimal parenting had a more adaptive outcome than their low-risk peers. The remaining effects were consistent with diathesis–stress.
On Statistics of Permutations Chosen From the Ewens Distribution
Authors: BAKSHAJEVA TATJANA , MANSTAVIČIUS EUGENIJUS
Published: August 2014

We explore the asymptotic distributions of sequences of integer-valued additive functions defined on the symmetric group endowed with the Ewens probability measure as the order of the group increases. Applying the method of factorial moments, we establish necessary and sufficient conditions for the weak convergence of distributions to discrete laws. More attention is paid to the Poisson limit distribution. The particular case of the number-of-cycles function is analysed in more detail. The results can be applied to statistics defined on random permutation matrices.
Reducing patient radiation exposure during paediatric SVT ablations: use of CARTO® 3 in concert with “ALARA” principles profoundly lowers total dose
Authors: Pass Robert H. , Gates Gregory G. , Gellis Laura A. , Nappo Lynn , Ceresnak Scott R.
Published: August 2014

Background: “ALARA – As Low As Reasonably Achievable” protocols reduce patient radiation dose. Addition of electroanatomical mapping may further reduce dose. Methods: From 6/11 to 4/12, a novel ALARA protocol was utilised for all patients undergoing supraventricular tachycardia ablation, including low frame rates (2–3 frames/second), low fluoro dose/frame (6–18 nGy/frame), and other techniques to reduce fluoroscopy (ALARA). From 6/12 to 3/13, use of CARTO® 3 (C3) with “fast anatomical mapping” (ALARA+C3) was added to the ALARA protocol. Intravascular echo was not utilised. Demographics, procedural, and radiation data were analysed and compared between the two protocols. Results: A total of 75 patients were included: 42 ALARA patients, and 33 ALARA+C3 patients. Patient demographics were similar between the two groups. The acute success rate in ALARA was 95%, and 100% in ALARA+C3; no catheterisation-related complications were observed. Procedural time was 125.7 minutes in the ALARA group versus 131.4 in ALARA+C3 (p=0.36). Radiation doses were significantly lower in the ALARA+C3 group with a mean air Kerma in ALARA+C3 of 13.1±28.3 mGy (SD) compared with 93.8±112 mGy in ALARA (p<0.001). Mean dose area product was 92.2±179 uGym2 in ALARA+C3 compared with 584±687 uGym2 in ALARA (p<0.001). Of the 33 subjects (42%) in the ALARA+C3 group, 14 received ⩽1 mGy exposure. The ALARA+C3 dosages are the lowest reported for a combined electroanatomical–fluoroscopy technique. Conclusions: Addition of CARTO® 3 to ALARA protocols markedly reduced radiation exposure to young people undergoing supraventricular tachycardia ablation while allowing for equivalent procedural efficacy and safety.
Role of speckle tracking echocardiography in the assessment of post-repair left ventricular function in patients with late presentation of anomalous origin of the left coronary artery from the pulmonary artery
Authors: Ajami Gholamhosein , Edraki Mohammad R. , Moarref Ali R. , Amirghofran Ahmad A. , Borzouee Mohammad , Amoozgar Hamid , Cheriki Sirous , Shakiba Ali M.
Published: August 2014

The aim of this study was to determine the left ventricular myocardial deformation and segmental myocardial dysfunction by speckle tracking echocardiography and tissue Doppler imaging among the operated patients with anomalous origin of the left coronary artery from the pulmonary artery. The study was conducted on 12 patients diagnosed with anomalous origin of the left coronary artery from the pulmonary artery, who had been operated upon between 2001 and 2013 at the medical centres of Shiraz University of Medical Sciences, Shiraz, Iran. The mean age of the patients at the time of surgical correction was 12.6 years ranging from 6 months to 43 years, and the duration of postoperative follow-up was between 1 and 12 years. Comparison of the strain rate between the patients with acceptable ejection fraction and the control group by tissue Doppler imaging showed significant differences between the two groups regarding the lateral wall (p<0.001), but not the septal wall of the left ventricle (p=0.65). Moreover, the strain values by the speckle tracking method revealed significant differences between the patient and the control group regarding the global strain (p=0.016) and anterior, lateral, and posterior segments of the left ventricle. Although postoperative conventional echocardiography revealed normal global left ventricular function with acceptable ejection fraction, abnormal myocardial deformation of the variable segments of the left ventricle with regional and global myocardial dysfunction were well defined by speckle tracking echocardiography.
Subjective Cognitive Complaints Contribute to Misdiagnosis of Mild Cognitive Impairment
Authors: Edmonds Emily C. , Delano-Wood Lisa , Galasko Douglas R. , Salmon David P. , Bondi Mark W.
Published: August 2014

Subjective cognitive complaints are a criterion for the diagnosis of mild cognitive impairment (MCI), despite their uncertain relationship to objective memory performance in MCI. We aimed to examine self-reported cognitive complaints in subgroups of the Alzheimer’s Disease Neuroimaging Initiative (ADNI) MCI cohort to determine whether they are a valuable inclusion in the diagnosis of MCI or, alternatively, if they contribute to misdiagnosis. Subgroups of MCI were derived using cluster analysis of baseline neuropsychological test data from 448 ADNI MCI participants. Cognitive complaints were assessedviathe Everyday Cognition (ECog) questionnaire, and discrepancy scores were calculated between self- and informant-report. Cluster analysis revealedAmnesticandMixedcognitive phenotypes as well as a thirdCluster-Derived Normalsubgroup (41.3%), whose neuropsychological and cerebrospinal fluid (CSF) Alzheimer’s disease (AD) biomarker profiles did not differ from a “robust” normal control group. This cognitively intact phenotype of MCI participants overestimated their cognitive problems relative to their informant, whereasAmnesticMCI participants with objective memory impairment underestimated their cognitive problems. Underestimation of cognitive problems was associated with positive CSF AD biomarkers and progression to dementia. Overall, there was no relationship between self-reported cognitive complaints and objective cognitive functioning, but significant correlations were observed with depressive symptoms. The inclusion of self-reported complaints in MCI diagnostic criteria may cloud rather than clarify diagnosis and result in high rates of misclassification of MCI. Discrepancies between self- and informant-report demonstrate that overestimation of cognitive problems is characteristic of normal aging while underestimation may reflect greater risk for cognitive decline. (JINS, 2014,20, 1–12)
Characterization of Functionalized Multiwalled Carbon Nanotubes for Use in an Enzymatic Sensor
Authors: Guadarrama-Fernández Leonor , Chanona-Pérez Jorge , Manzo-Robledo Arturo , Calderón-Domínguez Georgina , Martínez-Rivas Adrián , Ortiz-López Jaime , Vargas-García Jorge Roberto
Published: August 2014

Carbon nanotubes (CNT) have proven to be materials with great potential for the construction of biosensors. Development of fast, simple, and low cost biosensors to follow reactions in bioprocesses, or to detect food contaminants such as toxins, chemical compounds, and microorganisms, is presently an important research topic. This report includes microscopy and spectroscopy to characterize raw and chemically modified multiwall carbon nanotubes (MWCNTs) synthesized by chemical vapor deposition with the intention of using them as the active transducer in bioprocessing sensors. MWCNT were simultaneously purified and functionalized by an acid mixture involving HNO3–H2SO4and amyloglucosidase attached onto the chemically modified MWCNT surface. A 49.0% decrease in its enzymatic activity was observed. Raw, purified, and enzyme-modified MWCNTs were analyzed by scanning and transmission electron microscopy and Raman and X-ray photoelectron spectroscopy. These studies confirmed purification and functionalization of the CNTs. Finally, cyclic voltammetry electrochemistry was used for electrical characterization of CNTs, which showed promising results that can be useful for construction of electrochemical biosensors applied to biological areas.
Annuitisation and cross-subsidies in a two-tiered retirement saving system
Authors: Avanzi Benjamin , Purcal Sachi
Published: August 2014

We develop a generalisation of the World Bank (1994) model of forced saving for retirement. This broader model consists of two tiers of second pillar savings – mandated and non-mandated (voluntary). Furthermore, the government can set two types of guarantees on the first (mandated) tier – investment returns and annuity prices – leading to possible cross-subsidisation between the tiers. This has the potential to induce social redistribution, foster a liquid private market for life annuities, and obviate some of the investment risk and annuity price risk that retirees face.

We formulate a quantitative model of financial flows within such a system, which explains the mechanism by which cross-subsidisation occurs. Based on this analysis, a taxonomy of two-tiered retirement systems is presented, that is based on the choices that the government makes.