bluuebunny/crossref_metadata_2025 huggingface dataset:
Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics
Authors: Xue Yi , Skrynnikov Nikolai R.
Published: January 2014

Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free‐energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography‐based restraints into the MD protocol. Because these restraints are aimed at the ensemble‐average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native‐like fashion as dictated by the original force field. To validate this approach, we have used the data from solid‐state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well‐established model protein, ubiquitin. The ensemble‐restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid‐state chemical shifts, and backbone order parameters. The predictions for 15N
relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high‐resolution crystallographic data can be viewed as protein‐specific empirical corrections to the standard force fields.
Impact of sequence on the molecular assembly of short amyloid peptides
Authors: Wagoner Victoria A. , Cheon Mookyung , Chang Iksoo , Hall Carol K.
Published: January 2014

The goal of this work is to understand how the sequence of a protein affects the likelihood that it will form an amyloid fibril and the kinetics along the fibrillization pathway. The focus is on very short fragments of amyloid proteins since these play a role in the fibrillization of the parent protein and can form fibrils themselves. Discontinuous molecular dynamics simulations using the PRIME20 force field were performed of the aggregation of 48‐peptide systems containing SNQNNF (PrP (170–175)), SSTSAA (RNaseA(15–20)), MVGGVV (Aβ(35–40)), GGVVIA (Aβ(37–42)), and MVGGVVIA (Aβ(35–42)). In our simulations SNQQNF, SSTTSAA, and MVGGVV form large numbers of fibrillar structures spontaneously (as in experiment). GGVVIA forms β‐sheets that do not stack into fibrils (unlike experiment). The combination sequence MVGGVVIA forms less fibrils than MVGGVV, hindered by the presence of the hydrophobic residues at the C‐terminal. Analysis of the simulation kinetics and energetics reveals why MVGGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures. The latter helps explain why Aβ(1–42) assembles into more complex oligomers than Aβ(1–40), a consequence of which is that it is more strongly associated with Alzheimer's disease. Proteins 2014; 82:1469–1483. © 2014 Wiley Periodicals, Inc.
The rise of spin noise spectroscopy in semiconductors: From acoustic to GHz frequencies
Authors: Hübner Jens , Berski Fabian , Dahbashi Ramin , Oestreich Michael
Published: January 2014

This article gives an overview on the advance of spin noise spectroscopy (SNS) in semiconductors in the past 8 years from the first measurements in bulk n‐GaAs [Oestreich et al., Phys. Rev. Lett. 95, 216603 (2005)] up to the recent achievement of optical detection of the intrinsic spin fluctuations of a single hole confined in an individual self‐assembled quantum dot [Dahbashi et al., arXiv:1306.3183 (2013)]. We discuss the general technical implementation of optical SNS and the invaluable profit of the introduction of real‐time fast Fourier transform analysis into the data acquisition. By now, the full spin dynamic from the milli‐ to picosecond timescales can be addressed by SNS and the technique quickly strides ahead to enable real quantum non‐demolition measurements in semiconductors.

Spin noise spectra recorded in 2005 in bulk n‐GaAs with approximately 109 electron spins (Oestreich et al.) and 2013 (Dahbashi et al.) for a single hole spin. The integration time for the latter is more than a factor of 40 shorter due to the significant advances in the measurement technique.
Photoluminescence of m‐plane GaN grown on m‐plane sapphire by MOCVD
Authors: Paduano Qing S. , Weyburne David W. , Look David C.
Published: January 2014

The photoluminescence of m‐plane GaN grown on m‐plane sapphire substrate by MOCVD is reported. The defect related emissions with temperature and excitation power dependence are detailed. In addition to the near band‐edge emission (at ∼3.472 eV), two major defect‐related bands (D1∼3.43 eV and D2∼3.34 eV) are dominant in the low temperature spectra. The D1 emission exhibits thermal quenching with two activation energies (8 and 30 meV), similar to that of a‐plane GaN grown on r‐plane sapphire. The D2 band was found to consist of a complex overlap of multiple emissions. By fitting the asymmetric band using multiple Gaussian functions, the extracted emission at ∼3.34 eV was shown to have thermal activation energy ∼17–20 meV. This emission exhibits different behavior from that of D2 in a‐plane GaN in temperature and excitation power dependency, indicating the possible involvement of different defects due to the changes in growth characteristics. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Non‐polar GaN quantum dots integrated into high quality cubic AlN microdisks
Authors: Bürger M. , Callsen G. , Kure T. , Hoffmann A. , Pawlis A. , Reuter D. , As D. J.
Published: January 2014

We report on lasing of non‐polar GaN quantum dots which are integrated into novel cubic AlN microdisks. Optical spectroscopy of freestanding microdisks at low temperature (∼10 K) revealed distinct whispering gallery modes with quality factors up to Q ∼3000 in the high energy range around ∼4 eV of microdisks with a diameter of 4 µm. Furthermore, we obtained S‐shaped curves of the integral mode intensity, accompanied by a significant linewidth narrowing in power dependent micro‐photoluminescence experiments. The spontaneous emission coupling factors were determined to β = 0.26 and β = 0.58 with respect to the radial order of the resonator modes. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
MOVPE growth of AlxGa1‐xN with x ∼ 0.5 on epitaxial laterally overgrown AlN/sapphire templates for UV‐LEDs
Authors: Knauer A. , Zeimer U. , Kueller V. , Weyers M.
Published: January 2014

The crystalline perfection of AlxGa1‐xN layers with Al content of x ∼ 0.5 on epitaxial laterally overgrown (ELO) AlN with low defect density was investigated by spatially and spectrally resolved cathodoluminescence, scanning electron and atomic force microscopy. Cathodoluminescence mapping reveals compositional variations caused by different Ga incorporation during growth over macro‐steps resulting from step bunching on the ELO‐AlN. Introducing AlN interlayers as marker the influence of the macrosteps as well as of the growth rate on the development of Ga‐rich regions was studied. With increasing growth rate from 0.2 to 1 µm/h the spatial extension of the Ga‐rich regions is strongly reduced. At the same time the difference in Ga content is increased. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In Vitro Evaluation of Bacopa monniera Extract and Individual Constituents on Human Recombinant Monoamine Oxidase Enzymes
Authors: Singh Rajbir , Ramakrishna Rachumallu , Bhateria Manisha , Bhatta Rabi Sankar
Published: January 2014

Bacopa monniera is a traditional Ayurvedic medicinal plant that has been used worldwide for its nootropic action. Chemically standardized extract of B. monniera is now available as over the counter herbal remedy to enhance memory in children and adults. Considering the nootropic action of B. monniera, we evaluated the effect of clinically available B. monniera extract and six of B. monniera constituents (bacoside A3, bacopaside I, bacopaside II, bacosaponin C, bacosine, and bacoside A mixture) on recombinant human monoamine oxidase (MAO) enzymes. The effect of B. monniera extract and individual constituents on human recombinant MAO‐A and MAO‐B enzymes was evaluated using MAO‐GloTM assay kit (Promega Corporation, USA), following the instruction manual. IC50 and mode of inhibition were measured for MAO enzymes. Bacopaside I and bacoside A mixture inhibited the MAO‐A and MAO‐B enzymes. Bacopaside I exhibited mixed mode of inhibition with IC50 and Ki values of 17.08 ± 1.64 and 42.5 ± 3.53 µg/mL, respectively, for MAO‐A enzyme. Bacopaside I is the major constituent of B. monniera, which inhibited the MAO‐A enzyme selectively. Copyright © 2014 John Wiley & Sons, Ltd.
Well‐Being and Personal Growth in Mothers of Full‐Term and Pre‐Term Singletons and Twins
Authors: Noy Adi , Taubman – Ben‐Ari Orit , Kuint Jacob
Published: January 2014

The present study examined well‐being and personal growth in mothers (n = 414) 1 year after childbirth. We examined the contribution of the event characteristics (birth of singletons or twins, full‐ or pre‐term babies, first or non‐first child, spontaneous pregnancy or fertility treatments and infant temperament), internal resources (attachment anxiety and avoidance) and external resources (marital quality and maternal grandmother's support). Regressions indicated that having a first child, child's easier temperament, lower attachment anxiety and avoidance, grandmother's emotional support and some aspects of the spousal relationships contributed to well‐being. Personal growth was found to be related to the birth of a pre‐term baby or babies, positively associated with maternal grandmother's support, and the marital quality of parenthood, and negatively with mothers' education. Beyond the findings that well‐being and personal growth are related to the availability of certain resources, the current study demonstrates that the two outcomes are separate phenomena that reveal different patterns of associations with other variables. Several explanations for the findings are proposed, and practical implications are discussed. Copyright © 2014 John Wiley & Sons, Ltd.
Asymmetric Nitrene Transfer Reactions: Sulfimidation, Aziridination and C–H Amination Using Azide Compounds as Nitrene Precursors
Authors: Uchida Tatsuya , Katsuki Tsutomu
Published: January 2014

Nitrogen functional groups are found in many biologically active compounds and their stereochemistry has a profound effect on biological activity. Nitrene transfer reactions such as aziridination, C–H bond amination, and sulfimidation are useful methods for introducing nitrogen functional groups, and the enantiocontrol of the reactions has been extensively investigated. Although high enantioselectivity has been achieved, most of the reactions use (N‐arylsulfonylimino)phenyliodinane, which co‐produces iodobenzene, as a nitrene precursor and have a low atom economy. Azide compounds, which give nitrene species by releasing nitrogen, are ideal precursors but rather stable. Their decomposition needs UV irradiation, heating in the presence of a metal complex, or Lewis acid treatment. The examples of previous azide decomposition prompted us to examine Lewis acid and low‐valent transition‐metal complexes as catalysts for azide decomposition. Thus, we designed new ruthenium complexes that are composed of a low‐valent Ru(II) ion, apical CO ligand, and an asymmetry‐inducing salen ligand. With these ruthenium complexes and azides, we have achieved highly enantioselective nitrene transfer reactions under mild conditions. Recently, iridium–salen complexes were added to our toolbox.
The Origins of Homochirality Examined by Using Asymmetric Autocatalysis
Authors: Soai Kenso , Kawasaki Tsuneomi , Matsumoto Arimasa
Published: January 2014

Pyrimidyl alkanol was found to act as an asymmetric autocatalyst in the enantioselective addition of diisopropylzinc to pyrimidine‐5‐carbaldehyde. Asymmetric autocatalysis of 2‐alkynylpyrimidyl alkanol with an extremely low enantiomeric excess (ca. 0.00005% ee) exhibits enormous asymmetric amplification to afford the same compound with >99.5% ee. This asymmetric autocatalysis with amplification of ee has been employed to examine the validity of proposed theories of the origins of homochirality. Circularly polarized light, quartz, sodium chlorate, cinnabar, chiral organic crystals and spontaneous absolute asymmetric synthesis were considered as possible candidates for the origin of chirality; each could act as a chiral source in asymmetric autocatalysis. Asymmetric autocatalysis can discriminate the isotope chirality arising from the small difference between carbon (carbon‐13/carbon‐12) and hydrogen (D/H) isotopes. Cryptochiral compounds were also discriminated by asymmetric autocatalysis.
Organoplatinum‐Mediated Synthesis of Cyclic π‐Conjugated Molecules: Towards a New Era of Three‐Dimensional Aromatic Compounds
Authors: Yamago Shigeru , Kayahara Eiichi , Iwamoto Takahiro
Published: January 2014

This article describes the most recent developments in the synthesis of three‐dimensional π‐conjugated molecules and the elucidation of their properties made by our research group. Various cycloparaphenylenes (CPPs) of different sizes and a cage‐like 3D molecule were synthesized based on the platinum‐mediated assembly of π‐units and subsequent reductive elimination of platinum. The assembly of π‐units by this method mimics the self‐assembly process for the formation of supramolecular ligand–metal complexes with 3D cages and polyhedral structures. Furthermore, reductive elimination of platinum successfully took place with high efficiency, despite the high strain energy of the target molecule. Several size‐dependent physical properties of CPPs, namely the photophysical, redox, and host–guest chemistries, were also clarified. These results are of use for a molecular‐level understanding of CNT physical properties as well as fullerene peapods. Theoretical and electrochemical studies suggest that small CPPs and their derivatives should be excellent lead compounds for molecular electronics.
Development of Chiral Catalysts for Mukaiyama Aldol Reactions in Aqueous Media
Authors: Kitanosono Taku , Kobayashi Shū
Published: January 2014

Since the discovery of the Mukaiyama aldol reaction in 1973, tremendous efforts have been made to develop a definitive catalyst that catalyzes asymmetric Mukaiyama aldol reactions under mild conditions with broad substrate tolerance. Forty years later, an exhaustive search for a water‐compatible Lewis acid was able to uncover the hidden potential of iron(II) and bismuth(III), leading to the establishment of broadly applicable and versatile catalytic systems for asymmetric Mukaiyama aldol reactions in aqueous media. The ternary catalytic system was able to expand the substrate generality considerably as the most distinguished catalyst ever reported. The superiority of this methodology over conventional methods has also been demonstrated in terms of high catalytic activity, simplicity of experimental procedures, and a wide substrate range including aqueous aldehydes, for which the stereochemistry had been regarded as difficult to control. Furthermore, a facile synthesis of the chiral ligand underscores its versatility. The reaction did not proceed at all without use of water. In the postulated mechanism, water plays prominent roles in: (1) producing the active metal complexes with a high water‐exchange rate constant (3.2 × 106) to activate substrates effectively and to catalyze the reaction through a rapid proton transfer on the order of picoseconds; (2) facilitating the catalytic turnover with simultaneous desilylation as direct access to aldol adducts or facile recovery of active metal complexes; and (3) stabilizing rigid transition states composed of metal complexes and reactants through entropy‐driven aggregation derived from the highest cohesive energy density.
On providing wormhole‐attack‐resistant localization using conflicting sets
Authors: Chen Honglong , Lou Wei , Wang Zhi
Published: January 2014

Wormhole attack is a severe attack that can be easily mounted on a wide range of wireless networks without compromising any cryptographic entity or network node. In the wormhole attack, an attacker sniffs packets at one point in the network and tunnels them through the wormhole link to another point. Such kind of attack can deteriorate the localization procedure in wireless sensor networks. In this paper, we first analyze the impacts of the wormhole attack on the localization procedure. Then, we propose a secure localization scheme against the wormhole attacks called SLAW including three phases: wormhole attack detection, neighboring locators differentiation, and secure localization. The main idea of the SLAW is to build a so‐called conflicting set for each locator based on the abnormalities during the message exchanges, which can be used to differentiate the dubious locators to achieve secure localization. We first consider the simplified system model in which there is no packet loss and all the nodes have the same transmission range. We further consider the general system model where the packet loss exists and different types of nodes have different transmission radii. We conduct the simulations to illustrate the effectiveness of the proposed secure localization scheme and compare it with the existing schemes under different network parameters. Copyright © 2014 John Wiley & Sons, Ltd.
Incorporating foray behavior into models estimating contact risk between bighorn sheep and areas occupied by domestic sheep
Authors: O'brien Joshua M. , O'brien Chans S. , MCcarthy Clinton , Carpenter Tim E.
Published: January 2014

Respiratory disease epidemics are considered a primary factor limiting bighorn sheep (Ovis canadensis) populations in most of the western United States. Diverse sources of evidence indicate that domestic sheep harbor pathogens that cause fatal pneumonia in bighorn sheep, and that contact between the species often leads to respiratory disease and mortality in wild bighorn sheep populations. Managers have long argued that maintaining species separation is essential to conserving bighorn sheep. However, few studies have quantified probability of interspecies contact under different separation‐based management scenarios. We present an approach to estimating relative risk of interspecies contact that uses telemetry data to characterize bighorn sheep home ranges, habitat selection, and the occasional long‐distance exploratory movements (forays) characteristic of the species. We developed this approach to assess probability of bighorn sheep entering domestic sheep allotments on the Payette National Forest in central Idaho, USA, and we present that analysis as a case study. First, a large telemetry data set was used to identify bighorn sheep core herd home ranges and foray characteristics, including frequency, distance traveled, and habitat selection. Observed summer‐season foray probabilities for males and females were, respectively, 0.141 and 0.015 forays per animal per summer, with 50% of foraying males traveling at least 8.1 km and 10% of foraying males traveling at least 21.7 km beyond their core herd home range boundary. Risk of bighorn sheep contact with a domestic sheep allotment was then modeled by combining observed bighorn habitat preferences and movement patterns with geographic data, including habitat suitability and distance of core herd home ranges from domestic sheep allotments. For the domestic sheep grazing alternatives analyzed by the Payette National Forest, modeled contact rates between foraying bighorn sheep and domestic sheep allotments ranged from 0 to 1.33 contacts per year. Managers elsewhere can apply this methodology to estimate risk of interspecies contact based on bighorn sheep space use and habitat preferences. © 2014 The Wildlife Society.
Can the effect of tall structures on birds be isolated from other aspects of development?
Authors: Walters Kimberly , Kosciuch Karl , Jones Jason
Published: January 2014

As technology and energy development increase, undeveloped land and land traditionally used for agriculture now host structures not part of the historical landscape. These structures (e.g., communication towers, transmission lines) are taller than many objects in natural landscapes. Concerns have been raised regarding the effects of tall structures on birds, primarily functional habitat loss due to avoidance. Two hypotheses have been advanced to explain observed patterns of birds near tall structures: increased perceived predation risk and neophobia. We examined the literature (1969–2013) and used a vote‐counting methodology to document 1) the reported direction (positive or negative) of a potential tall‐structure effect, 2) whether the effect of tall structures can be isolated from other effects of development, 3) whether the study design lent itself to drawing a supportable conclusion, and 4) whether the authors suggested a causal mechanism for any observed pattern. We did not detect any consistent response to tall structures, nor did we find evidence to support the two hypotheses. In addition, a structure's “tallness” could not be isolated from other factors associated with development such as human activity. Understanding causal mechanisms is important for management and conservation because observed effects might not be related to the tallness of the structure but to other factors that could be managed, such as timing of construction. Our results suggest that the effect of tall structures on birds is not well understood, and focused studies that examine before‐and‐after effects and specific causal mechanisms are needed to support effective project siting and conservation planning. © 2014 The Wildlife Society.
Maximizing the ecological contribution of conservation banks
Authors: Bunn David A. , Moyle Peter B. , Johnson Christine K.
Published: January 2014

In 1995, California established the first conservation banking program in the United States to provide a new financial mechanism to conserve wildlife and natural communities in rapidly developing regions. Conservation banks are lands protected and managed for conservation of species of concern. Developers may purchase species credits from a conservation bank to offset adverse impacts of development at another site. Conservation banks facilitate pooling of mitigation resources from multiple development projects to protect planned habitat reserves of greater ecological value than can be achieved with project‐by‐project mitigation. In this study, we conducted the first ever assessment of the ecological performance of the California Conservation Banking Program. Specifically, we investigated to what extent conservation banks contribute to achieving regional conservation objectives. We hypothesized that conservation banks within a region should have similarly high ecological values if they are appropriately evaluated and prioritized based on principles of conservation planning. We created a new ecological value metric to evaluate and rank conservation banks and used it to compare potential conservation banks or reserves within a region. We found the ecological value of banks within regions varied and concluded that maximizing the ecological contribution of conservation banks requires prioritization of lands for potential bank sites and reserves. Our analysis identified circumstances where conservation banking is not an appropriate mitigation mechanism to protect rare species and natural communities. We concluded that limited funding for conservation planning should be directed toward regions where species of concern are wide‐ranging, biodiversity is highly variable, threats to species of concern are highly varied, and there are many potential conservation bank sites. © 2014 The Wildlife Society.
Thyroid Surgery without Antibiotic Prophylaxis: Experiences with 1,030 Patients from a Teaching Hospital in China
Authors: Qin Qian , Li Hong , Wang Li‐Bin , Li Ai‐Hui , Chen Li‐Ju , Lu Qiang
Published: January 2014

Objective

Our objective was to evaluate the outcome of thyroidectomy without the use of prophylactic antibiotics. This study was held from January 2005 to May 2012 in a teaching hospital in Dongguan, China.

Methods

A total of 1,030 thyroidectomy patients were retrospectively reviewed and basic data were recorded, including age, sex, peri‐operative antibiotic use, type of thyroid surgery done, and post‐operative complications. Either an open approach or an endoscopic approach was performed according to the doctor’s or patient’s preference following a strict aseptic technique. The drain was routinely placed. Any complications were analyzed.

Results

A total of 834 (81 %) females and 196 (19 %) males were included, giving a ratio of 4.2:1. The average age was 38.3 years. The mean operation time was 85.3 min. Pathological type included 818 (79.4 %) nodular goiter, 34 (3.3 %) Graves’ disease, 102 (9.9 %) nodular papillary hyperplasia, 12 (1.2 %) Hashimoto’s disease, 62 (6 %) papillary carcinoma, and 2 (0.2 %) medullary carcinoma. Four patients had postoperative bleeding, four had temporally recurrent nerve paralysis. Only one had wound infection (0.09 %).

Conclusion

Antibiotic prophylaxis in elective thyroidectomy is not an essential pre‐operation preparation for all patients, if guidelines for antibiotic prophylaxis in clean surgery are adhered to and surgeons have sophisticated skills in the procedure.
Kingella kingae septic arthritis in children: recognising an elusive pathogen
Authors: Williams Nicole , Cooper Celia , Cundy Peter
Published: January 2014

Purpose

Kingella kingae is an increasingly identified cause of musculoskeletal infections in young children. We report our experience with a recently developed polymerase chain reaction (PCR) method and review the clinical course of children diagnosed with K. kingae septic arthritis in a tertiary referral paediatric hospital.

Methods

All positive cases of K. kingae identified by PCR analysis of synovial fluid from August 2010 until July 2013 were included. A chart review was undertaken to determine history, presentation and management.

Results

27 Children (14 male, 13 female) had PCR positive synovial fluid samples for K. kingae with median age of 19 months (range 4 months to 5 years 3 months). The sites of infection were knee (17 cases), hip (2 cases), ankle (5 cases), shoulder (2 cases) and elbow. The median temperature on presentation was 37.1 °C, median peripheral white blood cell count 12.4 (9.9–13.8) × 109/L, erythrocyte sedimentation rate 55 (48–60) mm/h and C-reactive protein 24 (8–47) mg/L. The median synovial fluid white cell count was 21.8 (16.7–45.0) × 109/L. Routine cultures identified K. kingae in only two synovial fluid samples. Two samples were additionally positive for Staphylococcus aureus.

Conclusions

Kingella kingae is a significant cause of septic arthritis in young children. The authors recommend maintaining a high index of suspicion in young children presenting with joint inflammation, especially if indices of infection are mild. It appears likely that children historically treated with antibiotics for “culture negative” septic arthritis were infected with K. kingae. PCR techniques for detection of K. kingae should be encouraged.
Pathway-Based Analysis of the Hidden Genetic Heterogeneities in Cancers
Authors: Zhao Xiaolei , Zhong Shouqiang , Zuo Xiaoyu , Lin Meihua , Qin Jiheng , Luan Yizhao , Zhang Naizun , Liang Yan , Rao Shaoqi
Published: January 2014

Many cancers apparently showing similar phenotypes are actually distinct at the molecular level, leading to very different responses to the same treatment. It has been recently demonstrated that pathway-based approaches are robust and reliable for genetic analysis of cancers. Nevertheless, it remains unclear whether such function-based approaches are useful in deciphering molecular heterogeneities in cancers. Therefore, we aimed to test this possibility in the present study. First, we used a NCI60 dataset to validate the ability of pathways to correctly partition samples. Next, we applied the proposed method to identify the hidden subtypes in diffuse large B-cell lymphoma (DLBCL). Finally, the clinical significance of the identified subtypes was verified using survival analysis. For the NCI60 dataset, we achieved highly accurate partitions that best fit the clinical cancer phenotypes. Subsequently, for a DLBCL dataset, we identified three hidden subtypes that showed very different 10-year overall survival rates (90%, 46% and 20%) and were highly significantly (P  = 0.008) correlated with the clinical survival rate. This study demonstrated that the pathway-based approach is promising for unveiling genetic heterogeneities in complex human diseases.
Maternal micronutrient imbalance alters gene expression of BDNF, NGF, TrkB and CREB in the offspring brain at an adult age
Authors: Sable Pratiksha , Kale Anvita , Joshi Asmita , Joshi Sadhana
Published: January 2014

Micronutrients like folate, vitamin B12, and fatty acids which are interlinked in the one carbon cycle play a vital role in mediating epigenetic processes leading to an increased risk for neurodevelopmental disorders in the offspring. Our earlier study demonstrates that a micronutrient imbalanced diet adversely affects docosahexaenoic acid (DHA) and protein levels of neurotrophins like brain‐derived neurotrophic factor (BDNF) and nerve growth factor (NGF) in the brain and cognition in the offspring by 3 months of age. In this study we attempt to analyze if these effects are a consequence of a change in gene expression of these molecules. Further, we also examined the effect of either a postnatal control diet or a prenatal omega‐3 fatty acid supplementation on gene expression in the cortex of the offspring. Pregnant rats were divided into control and five treatment groups at two levels of folic acid (normal and excess folate) in the presence and absence of vitamin B12. Omega‐3 fatty acid (eicosapentaenoic acid – EPA + DHA) supplementation was given to vitamin B12 deficient groups. Following delivery, 8 dams from each group were shifted to control diet and remaining continued on the same treatment diet. Our results demonstrate that the imbalanced diet caused a marked reduction in the mRNA levels of BDNF, NGF, TrkB, and cAMP response element‐binding protein (CREB). Prenatal omega‐3 fatty acid supplementation to the maternal imbalanced diet was able to normalize the mRNA levels of all the above genes. This study demonstrates that a maternal diet imbalanced in micronutrients (folic acid, vitamin B12) influences gene expression of neurotrophins and their signalling molecules and thereby adversely affects the brain of the offspring.
Photoimmunotherapy: Comparative effectiveness of two monoclonal antibodies targeting the epidermal growth factor receptor
Authors: Sato Kazuhide , Watanabe Rira , Hanaoka Hirofumi , Harada Toshiko , Nakajima Takahito , Kim Insook , Paik Chang H. , Choyke Peter L. , Kobayashi Hisataka
Published: January 2014

Photoimmunotherapy (PIT) is a new cancer treatment that combines the specificity of antibodies for targeting tumors with the toxicity induced by photosensitizers after exposure to near infrared (NIR) light. Herein we compare two commonly available anti‐EGFR monoclonal antibodies, cetuximab and panitumumab, for their effectiveness as PIT agents in EGFR positive tumor models. A photosensitizer, IR‐700, conjugated to either cetuximab (cet‐IR700) or panitumumab (pan‐IR700), was evaluated using EGFR‐expressing A431 and MDAMB468‐luc cells in 2D‐ and 3D‐culture. PIT was conducted with irradiation of NIR light after exposure of the sample or animal to each conjugate. In vivo PIT was performed with fractionated exposure of NIR light after injection of each agent into A431 xenografts or a MDAMB468‐luc orthotopic tumor bearing model.

Cet‐IR700 and pan‐IR700 bound with equal affinity to the cells in 2D‐culture and penetrated equally into the 3D‐spheroid, resulting in identical PIT cytotoxic effects in vitro. In contrast, in vivo anti‐tumor effects of PIT with cet‐IR700 were inferior to that of pan‐IR700. Assessment of the biodistribution showed lower accumulation into the tumors and more rapid hepatic catabolism of cet‐IR700 compared to pan‐IR700. Although cet‐IR700 and pan‐IR700 showed identical in vitro characteristics, pan‐IR700 showed better therapeutic tumor responses than cet‐IR700 in in vivo mice models due to the prolonged retention of the conjugate in the circulation, suggesting that retention in the circulation is advantageous for tumor responses to PIT. These results suggest that the choice of monoclonal antibody in photosensitizer conjugates may influence the effectiveness of PIT.
Use of the Visual Range of Detection to Estimate Effective Sweep Width for Land Search and Rescue Based On 10 Detection Experiments in North America
Authors: Koester Robert J. , Chiacchia Kenneth B. , Twardy Charles R. , Cooper Donald C. , Frost John R. , Robe R. Quincy
Published: January 2014

Objective

Standard-of-practice search management requires that the probability of detection (POD) be determined for each search resource after a task. To calculate the POD, a detection index ( W) is obtained by field experiments. Because of the complexities of the land environment, search planners need a way to estimate the value of W without conducting formal experiments. We demonstrate a robust empirical correlation between detection range ( Rd) and W, and argue that Rd may reliably be used as a quick field estimate for W.

Methods

We obtained the average maximum detection range (AMDR), Rd, and W values from 10 detection experiments conducted throughout North America. We measured the correlation between Rd and W, and tested whether the apparent relationship between W and Rd was statistically significant.

Results

On average we found W ≈ 1.645 × Rd with a strong correlation ( R2 = .827). The high-visibility class had W ≈ 1.773 × Rd (also R2 = .867), the medium-visibility class had W ≈ 1.556 × Rd ( R2 = .560), and the low-visibility had a correction factor of 1.135 ( R2 = .319) for Rd to W. Using analysis of variance and post hoc testing, only the high- and low-visibility classes were significantly different from each other ( P < .01). We also found a high correlation between the AMDR and Rd ( R2 = .9974).

Conclusions

Although additional experiments are required for the medium- and low-visibility search objects and in the dry-domain ecoregion, we suggest search planners use the following correction factors to convert field-measured Rd to an estimate of the effective sweep width ( W): high-visibility W = 1.8 × Rd; medium-visibility W = 1.6 × Rd; and low-visibility W = 1.1 × Rd.
Too Soft for Economics, Too Rigid for Sociology, or Just Right? The Productive Ambiguities of Sen’s Capability Approach
Authors: Kremakova Milena I.
Published: January 2014

The capability approach has been developed by Amartya Sen, Martha Nussbaum and others as a human-centred normative framework for the evaluation of individual and group well-being, quality of life and social justice. Sen and Nussbaum’s ideas have influenced global, national and local policy and have been further developed in a number of academic disciplines, but so far have remained largely unnoticed in sociology. This article examines recent capability-informed theories and empirical applications in the sociology of human rights and other academic fields adjacent to sociology, focussing on examples of social policy studies in the fields of welfare, the labour market, health and disability, and education. The article outlines several potential areas in which capability-informed frameworks are relevant for critical social theory, public sociology and global sociology.
Compensation or Constraint? How Different Dimensions of Economic Globalization Affect Government Spending and Electoral Turnout
Authors: Marshall John , Fisher Stephen D.
Published: January 2014

This article extends theoretical arguments regarding the impact of economic globalization on policy making to electoral turnout and considers how distinct dimensions of globalization may produce different effects. It theorizes that constraints on government policy that reduce incentives to vote are more likely to be induced by foreign ownership of capital, while compensation through increased government spending is more likely (if at all) to be the product of structural shifts in production associated with international trade. Using data from twenty-three OECD countries from 1970–2007, the study finds strong support for the ownership-constraint hypothesis in which foreign ownership reduces turnout, both directly and – in strict opposition to the compensation hypothesis – indirectly by reducing government spending (and thus the importance of politics). The results suggest that increased foreign ownership, especially the most mobile capital flows, can explain up to two-thirds of the large declines in turnout over recent decades.
Multiple isotope analyses of the pike tapewormTriaenophorus nodulosusreveal peculiarities in consumer–diet discrimination patterns
Authors: Behrmann-Godel J. , Yohannes E.
Published: January 2014

Previous studies of dietary isotope discrimination have led to the general expectation that a consumer will exhibit enriched stable isotope levels relative to its diet. Parasite–host systems are specific consumer–diet pairs in which the consumer (parasite) feeds exclusively on one dietary source: host tissue. However, the small numbers of studies previously carried out on isotopic discrimination in parasite–host (ΔXP-HT) systems have yielded controversial results, showing some parasites to be isotopically depleted relative to their food source, while others are enriched or in equilibrium with their hosts. Although the mechanism for these deviations from expectations remains to be understood, possible influences of specific feeding niche or selection for only a few nutritional components by the parasite are discussed. ΔXP-HTfor multiple isotopes (δ13C, δ15N, δ34S) were measured in the pike tapewormTriaenophorus nodulosusand two of its life-cycle fish hosts, perchPerca fluviatilisand pikeEsox lucius, within whichT. nodulosusoccupies different feeding locations. Variability in the value of ΔXP-HTcalculated for the parasite and its different hosts indicates an influence of feeding location on isotopic discrimination. In perch liver ΔXP-HTwas relatively more negative for all three stable isotopes. In pike gut ΔXP-HTwas more positive for δ13C, as expected in conventional consumer–diet systems. For parasites feeding on pike gut, however, the δ15N and δ34S isotope values were comparable with those of the host. We discuss potential causes of these deviations from expectations, including the effect of specific parasite feeding niches, and conclude that ΔXP-HTshould be critically evaluated for trophic interactions between parasite and host before general patterns are assumed.
Pomegranate extract: a potential protector against aminoglycoside ototoxicity
Authors: Kahya V , Ozucer B , Dogan R , Meric A , Yuksel M , Gedikli O , Ozturan O
Published: January 2014

Objective:

To investigate the effectiveness of pomegranate extract as protection against aminoglycoside ototoxicity.

Design:

Prospective, randomised, controlled, experimental study.

Subjects:

Eighteen Wistar albino rats were randomly allocated to 5 days of either: saline injections; gentamicin injections; or pomegranate extract (100 µl/day via gavage) plus gentamicin injections. Distortion product otoacoustic emissions were tested before treatment and on day 3. After treatment, reactive oxygen species levels were measured in each rat's right cochlea and right kidney via chemiluminescence.

Results:

Baseline emission amplitudes were similar. Post-treatment emissions differed significantly in the two treatment groups (p < 0.001). Cochlear reactive oxygen species levels were significantly higher in the gentamicin group (mean ± standard deviation, 316.6 ± 36.5 relative light units per mg) than the gentamicin plus pomegranate extract group (240 ± 24.6 relative light units per mg) (p = 0.004); control group levels were 119.1 ± 10.3 relative light units per mg. Renal reactive oxygen species levels were similar for the control and gentamicin plus pomegranate extract groups (p = 0.59) but much higher in the gentamicin group (p = 0.004).

Conclusion:

Concurrent systemic pomegranate extract administration reduced reactive oxygen species level increases and otoacoustic emission changes, following aminoglycoside injection.
Effects of transitional bilingual education on Spanish-speaking preschoolers’ literacy and language development: Year 2 results
Authors: DURÁN LILLIAN , ROSETH CARY J. , HOFFMAN PATRICIA
Published: January 2014

Year 2 findings are reported from a longitudinal, experimental-control study involving 31 Spanish-speaking preschoolers (aged 38–48 months) randomly assigned to two Head Start classrooms. In Year 1, classrooms differed only in the language of instruction, with teachers using only Spanish in one classroom and only English in the other. In Year 2, an experimental transitional bilingual education (TBE) model was implemented, with English being gradually introduced in the TBE classroom until a ratio of 30:70 English-to-Spanish was achieved and Spanish being gradually introduced in the predominantly English (PE) classroom until a ratio of 70:30 English-to-Spanish was achieved. Year 2 results were consistent with Year 1, with the TBE classroom exceeding the PE classroom on all Spanish measures of language and literacy development and no significant differences favoring the PE classroom. Results also indicated that Year 2 trajectories were conditional on first-year effects, suggesting that sustained growth in dual language learner's early literacy may depend on early intervention among 3-year-old preschoolers.
Effect of laser irradiance on the surface morphology and laser induced plasma parameters of zinc
Authors: Akram Mahreen , Bashir Shazia , Hayat Asma , Mahmood Khaliq , Ahmad Riaz , Khaleeq-U-Rahaman M.
Published: January 2014

The effect of laser-irradiance on the surface morphology and laser induced breakdown spectroscopy of zinc has been investigated by employing Nd:YAG laser (wavelength λ = 1064 nm, pulse durationt ~ 10 ns, and repetition rate = 10 Hz) under ambient environment of argon at a pressure of 20 Torr. For this purpose, zinc targets were exposed to various laser irradiances ranging from 13 GW/cm2to 100 GW/cm2. Scanning electron microscope analysis has been performed to analyze the surface modification of irradiated zinc targets. Scanning electron microscope analysis revealed the formation of various kinds of structures such as ripples, cones, cavities, and wave like ridges at the center and peripheral regions of ablated zinc. In the central ablated region with increasing laser irradiance, the growth of distinct and well defined ripples is observed. Further increase in irradiance makes the appearance of these ripples diffusive and narrow. In order to correlate the plasma parameters with the surface modification, laser induced breakdown spectroscopy analysis has also been performed. The electron temperature and number density of zinc plasma have been evaluated at various laser irradiances. For both plasma parameters, an increasing trend up to a certain value of laser irradiance is observed which is due to enhanced energy deposition. Afterword a decreasing trend is achieved which is attributed to the shielding effect. With further increase in irradiance a saturation stage comes and almost no change in plasma parameters is observed. This saturation is explainable on the basis of the formation of a self-regulating regime near the target surface. A strong correlation between surface modification and plasma parameters is established.
RAPID REVIEW: AN EMERGING APPROACH TO EVIDENCE SYNTHESIS IN HEALTH TECHNOLOGY ASSESSMENT
Authors: Khangura Sara , Polisena Julie , Clifford Tammy J. , Farrah Kelly , Kamel Chris
Published: January 2014

Background: Increasingly, healthcare decision makers demand quality evidence in a short timeframe to support urgent and emergent decisions related to procurement, clinical practice, and policy. Health technology assessment (HTA) producers are responding by developing innovative approaches to evidence synthesis that can be executed more quickly than traditional systematic review. These approaches, and the broader implications they bring to bear on health decision making and policy development, however, are generally neither well-understood nor well-described. This study intends to contribute to an emerging literature around methodological approaches to rapid review in HTA by outlining those developed and implemented by the Canadian Agency for Drugs and Technologies in Health (CADTH).

Methods: Since 2005, CADTH has developed and implemented a rapid review approach that synthesizes evidence to support informed healthcare decisions and policy. Rapid Response reports are tailored to the identified needs of Canadian health decision makers, representing a range of options with regard to depth, breadth, and time-to-delivery.

Results: Preliminary observations indicate that CADTH's approach to rapid evidence review is generally well-received by Canadian health decision makers; real-world case studies provide pragmatic examples of how health decision makers have used Rapid Response reports to support evidence-informed health decisions across Canada.

Conclusions: Rapid review is becoming an increasingly important approach to evidence synthesis, both within and external to the field of HTA. Transparent reporting of the methods used to develop rapid review products will be critical to the assessment of their relevance, utility and effects in a range of contexts.
Multiscale variability of ambient conditions, fast ice dynamics and biogeochemistry in the coastal zone of Victoria Land, Ross Sea
Authors: Cozzi Stefano
Published: January 2014

Interannual and seasonal variability of the biogeochemical characteristics of fast ice were analysed in relation to ambient conditions, water column properties and ice biota. According to Zubov's Law, the annual atmospheric cooling should generate 2.5 m thick fast ice sheets in this coastal zone, but katabatic wind peaks in July–August often cause ice breakouts, resulting in highly variable growth periods (2–9 months) and thickness (1.0–2.5 m). In spring, atmospheric forcings significantly modulate brine content (5–20%) and drainage in fast ice, as well as salinity oscillations in bottom and platelet layers (15 psu). In the water column, the formation of nutrient-impoverished Summer Surface Waters is triggered by seawater warming (-1.9 to 0.7°C), ice melting (0.03 m d-1) and pelagic production. Negative NO3 and SiO2 balances and positive NH4 balances (-41, -153 and +173 kg km-2, respectively) were estimated in fast ice in spring, whereas nutrient budgets in the platelet layer are regulated by its variable level of isolation from seawater. The large accumulation of dissolved organic carbon (3890 kg km-2) in the ice system and its release in seawater in late spring are important features of the carbon cycle in these Antarctic coastal zones, with possible implications for the modulation of climate.