bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of preoperative positron emission tomography/computed tomography (PET/CT) in patients with high‐risk melanoma
Authors: Barsky Maya , Cherkassky Leonid , Vezeridis Michael , Miner Thomas J.
Published: December 2013

Background

Positron emission tomography/computed tomography (PET/CT) scanning is commonly used for the preoperative staging of patients with at least intermediate thickness (>1 mm) melanomas. Its role in staging at initial diagnosis for clinically asymptomatic patients is not yet established.

Methods

We examined records of all patients receiving an operation for at least an intermediate thickness melanoma from June 2005 to June 2011. Results of preoperative PET/CT scans were evaluated in asymptomatic patients with a negative physical exam. Outcome measures included changes in clinical management, as well as incidence of true‐ and false‐positives.

Results

PET/CT scans were performed for 149 patients with at least an intermediate thickness melanoma. Positive scans were identified in 28% (41/149) of patients. An invasive procedure to further aid in diagnosis was performed in 44% (18), yet only 6 (15%) patients were diagnosed with metastatic cancer (85% false positive rate). Each of these patients had regional disease subsequently diagnosed by a sentinel lymph node biopsy. No distant metastatic disease was identified.

Conclusions

Preoperative PET/CT in asymptomatic patients is of limited benefit in staging asymptomatic melanoma patients with at least an intermediate thickness melanoma and may lead to unnecessary invasive procedures. J. Surg. Oncol 2014; 109:726–729. © 2013 Wiley Periodicals, Inc.
A century of citation classics in otolaryngology–head and neck surgery journals revisited
Authors: Coelho Daniel H. , Edelmayer Luke W. , Fenton John E.
Published: December 2013

Objectives/Hypothesis

Citation classics have traditionally been defined in the smaller medical specialties as any article published in a peer‐reviewed journal that has received 100 or more citations from other articles also published in peer‐reviewed journals. This study aimed to determine patterns of citation classics changes in the medical field otorhinolaryngology and head and neck surgery (OHNS) over the past decade and serves as a follow‐up to an original study published in 2002, “A Century of Citation Classics in Otolaryngology–Head & Neck Surgery.”

Study Design

Bibliometric analysis.

Methods

Using the Journal Citation Reports and Web of Science, OHNS journals were selected and assessed for the content of citation classics.

Results

Nine‐hundred five citation classics were found, over 11‐fold more than 1 decade prior. Other significant changes were seen in country of origin, decade of publication, number of authors per article, subspecialty of article, and most frequently discussed topics.

Conclusions

The dramatic rise in quantity and nature of citation classics in the past decade may be due to unprecedented advancements in information technology and communication, allowing studies and experiments to be performed, written, reviewed, published, and cited at rapid rates.

Level of Evidence

NA Laryngoscope, 124:1358–1362, 2014
Temporal bone pneumatization in cystic fibrosis: A correlation with genotype?
Authors: Berkhout Maaike C. , van Rooden Cornelis J. , Aalbers Ralph C. , el Bouazzaoui Lahssan H. , Fokkens Wytske J. , Rijntjes Evert , Heijerman Harry G. M.
Published: December 2013

Objectives/Hypothesis

Paranasal sinus pneumatization in patients with cystic fibrosis (CF) is less extensive compared to the general population and seems to be correlated to CF genotype. Interestingly, in CF patients temporal bone pneumatization (TBP) is more extensive compared to the general population, and middle ear pathology is generally uncommon in CF. It is debated whether TBP is influenced environmentally or genetically. The aim of the present study was to investigate pneumatization of the temporal bone in patients with CF and to correlate this with genotype and paranasal sinus volume.

Study Design

Prospective collection of data.

Methods

In 104 adult CF patients, computed tomography of the temporal bone and the paranasal sinuses was performed. TBP was graded using a validated scoring system. Patients were divided into two groups, mild and severe CF, based on their mutations in the CF transmembrane conductance regulator gene.

Results

Of the 31 patients with mild CF, 71% had extensive TBP, and of the 73 patients with severe CF, 82% had extensive pneumatization of the temporal bone. TBP did not differ significantly for CF genotype, and TBP was not correlated to paranasal sinus volume.

Conclusions

Whereas paranasal sinus pneumatization in CF patients seems to be related to CF genotype among other influencing factors, this study showed no correlation between TBP and CF genotype. TBP was not correlated to paranasal sinus volume. Hypothetically, in CF, pneumatization of the temporal bone is under a different influence than paranasal sinus pneumatization.

Level of Evidence

4 Laryngoscope, 124:1682–1686, 2014
Small nerve fiber involvement in patients referred for fibromyalgia
Authors: Giannoccaro Maria Pia , Donadio Vincenzo , Incensi Alex , Avoni Patrizia , Liguori Rocco
Published: December 2013

Introduction: Fibromyalgia (FM) is a chronic syndrome characterized by widespread pain often accompanied by other symptoms suggestive of neuropathic pain. We evaluated patients for small fiber neuropathy (SFN) who were referred for fibromyalgia (FM). Methods: We studied 20 consecutive subjects with primary FM. Patients underwent neurological examination, nerve conduction studies, and skin biopsies from distal leg and thigh. Results: Electrodiagnostic studies were normal in all patients. SFN was diagnosed in 6 patients by reduced epidermal nerve fiber density. These patients also showed abnormalities of both adrenergic and cholinergic fibers. Conclusions: A subset of FM subjects have SFN, which may contribute to their sensory and autonomic symptoms. Skin biopsy should be considered in the diagnostic work‐up of FM. Muscle Nerve 49: 757–759, 2014
Neuroblastoma and pediatric delirium: A case series
Authors: Traube Chani , Augenstein Julie , Greenwald Bruce , LaQuaglia Michael , Silver Gabrielle
Published: December 2013

Delirium occurs frequently in critically ill children, and children with neuroblastoma may be at particular risk. Early diagnosis and treatment may improve short‐ and long‐term outcomes. In this case series, we present four critically ill children with neuroblastoma who were diagnosed with delirium in the post‐operative period. In all four patients, the diagnosis of delirium facilitated targeted intervention and improvement. Heightened awareness by pediatric oncologists, surgeons, and intensivists may lead to earlier diagnosis and improvement in clinical outcomes. Pediatr Blood Cancer 2014;61:1121–1123. © 2013 Wiley Periodicals, Inc.
Optical and colorimetric studies of thorium nitrate‐doped poly(vinyl alcohol) films
Authors: Mahmoud Khaled H. , Atef Karam
Published: December 2013

In this study, poly(vinyl alcohol) (PVA) films doped with thorium nitrate hydrate [Th(NO3)4] have been prepared using casting technique. The optical absorption spectra were recorded at room temperature in the wavelength range 200–800 nm. From the absorption edge studies, the values of the Urbach energy (Eu) have been evaluated. These energy values vary slightly with composition, indicating that the model based on electronic transitions between localized states is not preferable. Optical parameters such as refractive index and complex dielectric constant have been determined. The dispersion of the refractive index is discussed in terms of the single‐oscillator Wemple‐DiDomenico model. Color properties of the prepared samples were discussed in the framework of CIE L*u*v* color space. POLYM. COMPOS., 35:1786–1791, 2014. © 2013 Society of Plastics Engineers
Use of acoustics to deter bark beetles from entering tree material
Authors: Aflitto Nicholas C , Hofstetter Richard W
Published: December 2013

BACKGROUND

Acoustic technology is a potential tool to protect wood materials and eventually live trees from colonization by bark beetles. Bark beetles such as the southern pine beetle Dendroctonus frontalis, western pine beetle D. brevicomis and pine engraver Ips pini (Coleoptera: Curculionidae) use chemical and acoustic cues to communicate and to locate potential mates and host trees. In this study, the efficacy of sound treatments on D. frontalis, D. brevicomis and I. pini entry into tree materials was tested.

RESULTS

Acoustic treatments significantly influenced whether beetles entered pine logs in the laboratory. Playback of artificial sounds reduced D. brevicomis entry into logs, and playback of stress call sounds reduced D. frontalis entry into logs. Sound treatments had no effect on I. pini entry into logs.

CONCLUSION

The reduction in bark beetle entry into logs using particular acoustic treatments indicates that sound could be used as a viable management tool. © 2013 Society of Chemical Industry
Boldness towards novelty and translocation success in captive‐raised, orphaned Tasmanian devils
Authors: Sinn David L. , Cawthen Lisa , Jones Susan M. , Pukk Chrissy , Jones Menna E.
Published: December 2013

Translocation of endangered animals is common, but success is often variable and/or poor. Despite its intuitive appeal, little is known with regards to how individual differences amongst translocated animals influence their post‐release survival, growth, and reproduction. We measured consistent pre‐release responses to novelty in a familiar environment (boldness; repeatability = 0.55) and cortisol response in a group of captive‐reared Tasmanian devils, currently listed as “Endangered” by the IUCN. The devils were then released at either a hard‐ or soft‐release site within their mothers' population of origin, and individual growth, movement, reproduction (females only), and survival across 2–8 months post‐release was measured. Sex, release method, cohort, behavior, and cortisol response did not affect post‐release growth, nor did these factors influence the home range size of orphan devils. Final linear distances moved from the release site were impacted heavily by the release cohort, but translocated devils' movement overall was not different from that in the same‐age wild devils. All orphan females of reproductive age were subsequently captured with offspring. Overall survival rates in translocated devils were moderate (∼42%), and were not affected by devil sex, release method, cohort, release weight, or pre‐release cortisol response. Devils that survived during the study period were, however, 3.5 times more bold than those that did not (effect size r = 0.76). Our results suggest that conservation managers may need to provide developmental conditions in captivity that promote a wide range of behaviors across individuals slated for wild release. Zoo Biol. 33:36–48, 2014. © 2013 Wiley Periodicals Inc.
Is a Pejorative View of Power Assertion in the Socialization Process Justified?
Authors: Baumrind Diana
Published: December 2013

Power assertion is foundational to the authoritative parenting style and the authoritative parenting style is consistently acknowledged to be optimal so that a pejorative view of power assertion per se is unwarranted. In contrast to the “child-centered” presumption that power assertion by parents is detrimental to the well-being of children and bears an antinomian relation to reasoning, I argue that reasoning and confrontive power assertion are independent processes that, when synthesized, account for the benefits of authoritative parenting relative to the other primary parenting styles (authoritarian, permissive, disengaged) in which either or both confrontive power assertion and reasoning are minimal. Directive parenting, a newly identified power-assertive parenting style that is as demanding as the authoritarian style, but is not arbitrary, hostile, or punitive, has also been found to be beneficial.
Mind the Gap in Mindfulness Research: A Comparative Account of the Leading Schools of Thought
Authors: Hart Rona , Ivtzan Itai , Hart Dan
Published: December 2013

The literature on mindfulness has been dominated by the two leading schools of thought: one advanced by Langer and her colleagues; the other developed by Kabat-Zinn and his associates. Curiously, the two strands of research have been running in parallel lines for more than 30 years, scarcely addressing each others’ work, and with almost no attempt to clarify the relationship between them. In view of this gap, this article sought to systematically compare and contrast the two lines of research. The comparison between the two schools of thought suggests that although there are some similarities in their definitions of mindfulness, they differ in several core aspects: their philosophies, the components of their constructs, their goals, their theoretical scope, their measurement tools, their conceptual focus, their target audiences, the interventions they employ, the mechanisms underlying these interventions, and the outcomes of their interventions. However, the analysis also revealed that self-regulation is a core mechanism in both perspectives, which seems to mediate the impact of their interventions. In view of the differences between the two strands of research, we propose that they be given different titles that capture their prime features. We suggest “creative mindfulness” for Langer and her colleagues’ scholarship, and “meditative mindfulness” for Kabat-Zinn and his associates’ scholarly work.
Time Series Analysis in Pediatric Psychology
Authors: Rohan Jennifer M.
Published: December 2013

Single-subject research designs and relevant statistical methods have been neglected in the field of pediatric psychology, specifically in research investigating changes in clinical outcomes over time. This commentary provides a brief, nontechnical description and illustration of the use of time series analyses in pediatric psychology research. This commentary focuses on Auto-Regressive Integrated Moving Average (ARIMA), which is a type of time series analysis that models changes in clinical outcomes over time. A brief overview of single subject research designs and alternative time series analyses is described. Although time series analysis has been used infrequently in the field of pediatric research, this analytic approach could be applicable for investigating changes in clinical outcomes over time.
Laser Doppler vibrometry measurement of the mechanical myogram
Authors: Rohrbaugh John W. , Sirevaag Erik J. , Richter Edward J.
Published: December 2013

Contracting muscles show complex dimensional changes that include lateral expansion. Because this expansion process is intrinsically vibrational, driven by repetitive actions of multiple motor units, it can be sensed and quantified using the method of Laser Doppler Vibrometry (LDV). LDV has a number of advantages over more traditional mechanical methods based on microphones and accelerometers. The LDV mechanical myogram from a small hand muscle (the first dorsal interosseous) was studied under conditions of elastic loading applied to the tip of the abducted index finger. The LDV signal was shown to be related systematically to the level of force production, and to compare favorably with conventional methods for sensing the mechanical and electrical aspects of muscle contraction.
Elastic constants and critical thicknesses of ScGaN and ScAlN
Authors: Zhang S. , Fu W. Y. , Holec D. , Humphreys C. J. , Moram M. A.
Published: December 2013

Elastic constants of hexagonal ScxGa1−xN and ScxAl1−xN up to x = 0.375 were calculated using a stress-strain approach. C11, C33, C44, and C66 decreased while C12 and C13 increased slightly with increasing x. The biaxial [0001] Poisson ratios increased from 0.21 for GaN to 0.38 for Sc0.375Ga0.625 N and from 0.22 for AlN to 0.40 for Sc0.375Al0.625N, due to greater u values, in-plane bond lengths and bond ionicities. Subsequently, critical thicknesses for stress relaxation were calculated for ScxAl1−xN/AlN, ScxGa1−xN/GaN, and ScxAl1−xN/GaN heterostructures using an energy balance model. These range from 2 nm for Sc0.375Al0.625N/AlN and Sc0.375Ga0.625N/GaN to infinity for lattice-matched Sc0.18Al0.82N/GaN.
The operation principle of the well in quantum dot stack infrared photodetector
Authors: Lee Jheng-Han , Wu Zong-Ming , Liao Yu-Min , Wu Yuh-Renn , Lin Shih-Yen , Lee Si-Chen
Published: December 2013

The well in the quantum dot stack infrared photodetector (WD-QDIP) is proposed which can be operated at high temperature ∼230 K. The operation principle of this device is investigated, including the carrier transport and the enhancement in the photocurrent. The WD-QDIPs with different well numbers are fabricated to study the mechanisms. It is realized that the carrier transport from the emitter to the collector in traditional quantum dot infrared photodetectors consists of two channels deduced from current-voltage characteristics and dark current activation energy at different temperatures. At temperatures below 77 K, the current transports through the InAs quantum dot channel, whereas at temperatures higher than 77 K, the current is dominated by the GaAs leakage channel. In addition, the non-equilibrium situation at low temperatures is also observed owing to the presence of photovoltaic phenomenon. The carrier distribution inside the QDs is simulated to investigate the reasons for the increase of photocurrent. Based on the simulation and the photocurrent response, the hot carrier (electron) scattering effect by the insertion of a quantum well layer is inferred as the most probable reason that lead to the enhancement of the response and regarded as the key factor to achieve high- temperature operation.
Analysis of plasma distribution near the extraction region in surface produced negative ion sources
Authors: Fukano A. , Hatayama A.
Published: December 2013

In study of a negative ion source, it is important to understand the plasma characteristics near the extraction region. A recent experiment in the NIFS-R&D ion source has suggested that a “double ion plasma layer” which is a region consisting of hydrogen positive and negative ions exists near the plasma grid (PG). Density distribution of plasma near the extraction region is studied analytically. It is shown that the density distribution depends on an amount of the surface produced negative ions and the double ion plasma layer is formed near the PG surface for the case of strong surface production.
A quantum Cherry theorem for perturbations of the plane rotator
Authors: Barone Fiorella , Graffi Sandro
Published: December 2013

We consider on \documentclass[12pt]{minimal}\begin{document}$L^2(\mathbb {T}^2)$\end{document}L2(T2) the Schrödinger operator family \documentclass[12pt]{minimal}\begin{document}$L_\varepsilon : \varepsilon \in \mathbb {R}$\end{document}Lɛ:ɛ∈R with domain and action defined as \documentclass[12pt]{minimal}\begin{document}$\displaystyle D(L_\varepsilon )=H^2(\mathbb {T}^2),\; L_\varepsilon u=-\frac{1}{2}\hbar ^2(\alpha _1\partial _{\phi _1}^2+\alpha _2\partial _{\phi _2}^2)u-i\hbar (\gamma _1\partial _{\phi _1}+\gamma _2\partial _{\phi _2})u+\varepsilon Vu.$\end{document}D(Lɛ)=H2(T2),Lɛu=−12ℏ2(α1∂ϕ12+α2∂ϕ22)u−iℏ(γ1∂ϕ1+γ2∂ϕ2)u+ɛVu. Here \documentclass[12pt]{minimal}\begin{document}$\varepsilon \in \mathbb {R}$\end{document}ɛ∈R, α = (α1, α2), γ = (γ1, γ2) are vectors of complex non-real frequencies, and V a pseudodifferential operator of order zero. Lɛ represents the Weyl quantization of the Hamiltonian family \documentclass[12pt]{minimal}\begin{document}${\mathcal {L}}_\varepsilon (\xi ,x)=\frac{1}{2}(\alpha _1\xi _1^2+\alpha _2\xi _2^2)+\gamma _1\xi _1+\gamma _2\xi _2+\varepsilon {\mathcal {V}}(\xi ,x)$\end{document}Lɛ(ξ,x)=12(α1ξ12+α2ξ22)+γ1ξ1+γ2ξ2+ɛV(ξ,x) defined on the phase space \documentclass[12pt]{minimal}\begin{document}$\mathbb {R}^2\times \mathbb {T}^2$\end{document}R2×T2, where \documentclass[12pt]{minimal}\begin{document}${\mathcal {V}}(\xi ,x)\in C^2(\mathbb {R}^2\times \mathbb {T}^2;\mathbb {R})$\end{document}V(ξ,x)∈C2(R2×T2;R). We prove the uniform convergence with respect to ℏ ∈ [0, 1] of the quantum normal form, which reduces to the classical one for ℏ = 0. This result simultaneously entails an exact quantization formula for the quantum spectrum as well as a convergence criterion for the classical Birkhoff normal form generalizing a well known theorem of Cherry.
Regularized orbital-optimized second-order perturbation theory
Authors: Stück David , Head-Gordon Martin
Published: December 2013

Orbital-optimized second-order perturbation theory (OOMP2) optimizes the zeroth order wave function in the presence of correlations, removing the dependence of the method on Hartree–Fock orbitals. This is particularly important for systems where mean field orbitals spin contaminate to artificially lower the zeroth order energy such as open shell molecules, highly conjugated systems, and organometallic compounds. Unfortunately, the promise of OOMP2 is hampered by the possibility of solutions being drawn into divergences, which can occur during the optimization procedure if HOMO and LUMO energies approach degeneracy. In this work, we regularize these divergences through the simple addition of a level shift parameter to the denominator of the MP2 amplitudes. We find that a large level shift parameter of 400 mEh removes divergent behavior while also improving the overall accuracy of the method for atomization energies, barrier heights, intermolecular interactions, radical stabilization energies, and metal binding energies.
Nonlocal magnetoresistance due to Lorentz force in linear transport region in bulk silicon
Authors: Wan C. H. , Yuan Z. H. , Liu P. , Wu H. , Guo P. , Li D. L. , Ali S. S.
Published: December 2013

Magnetoresistance (MR) of lightly doped bulk silicon has been studied in linear transport region. Both nonlocal and local MR results from deflection of in-plane transport of carriers by Lorentz force. However, nonlocal MR is nearly one order of magnitude larger than local one. We ascribe the enhanced nonlocal MR to polarity-conserved charges accumulated on boundaries near anode and cathode, which alters potential distribution and meanwhile increases current flowing in nonlocal region. This mechanism of nonlocal MR can be generalized to other materials with high or moderate mobility.
Lusztig symmetries and Poincare-Birkhoff-Witt basis for $\mathfrak {wU}_{r, s}^{\mathrm{d}}({\rm osp}(1|2n))$wUr,sd( osp (1|2n))
Authors: Liu Junli , Yang Shilin
Published: December 2013

We investigate a new kind of two-parameter weak quantized superalgebra \documentclass[12pt]{minimal}\begin{document}$\mathfrak {wU}_{r, s}^{\mathrm{d}}({\rm osp}(1|2n))$\end{document}wUr,sd( osp (1|2n)), which is a weak Hopf superalgebra. It has a homomorphic image which is isomorphic to the usual two-parameter quantum superalgebra \documentclass[12pt]{minimal}\begin{document}$\textrm {U}_{r,s}(\textrm {osp}(1|2n))$\end{document}Ur,s( osp (1|2n)) of \documentclass[12pt]{minimal}\begin{document}$\textrm {osp}(1|2n)$\end{document} osp (1|2n). We also discuss the basis of \documentclass[12pt]{minimal}\begin{document}$\mathfrak {wU}_{r, s}^{\mathrm{d}}({\rm osp}(1|2n))$\end{document}wUr,sd( osp (1|2n)) by Lusztig's symmetries.
Energetics of vacancy segregation to symmetric tilt grain boundaries in hexagonal closed pack materials
Authors: Bhatia M. A. , Solanki K. N.
Published: December 2013

Molecular static simulations of 190 symmetric tilt grain boundaries in hexagonal closed pack metals were used to understand the energetics of vacancy segregation, which is important for designing stable interfaces in harsh environments. Simulation results show that the local arrangements of grain boundaries and the resulting structural units have a significant influence on the magnitude of vacancy binding energies, and the site-to-site variation within each boundary is substantial. Comparing the vacancy binding energies for each site in different c/a ratio materials shows that the binding energy increases significantly with an increase in c/a ratio. For example, in the [12¯10] tilt axis, Ti and Zr with c/a = 1.5811 have a lower vacancy binding energy than the Mg with c/a = 1.6299. Furthermore, when the grain boundary energies of all 190 boundaries in all three elements are plotted against the vacancy binding energies of the same boundaries, a highly negative correlation (r = −0.7144) is revealed that has a linear fit with a proportionality constant of −25 Å2. This is significant for applications where extreme environmental damage generates lattice defects and grain boundaries act as sinks for both vacancies and interstitial atoms.
Effective dopant activation by susceptor-assisted microwave annealing of low energy boron implanted and phosphorus implanted silicon
Authors: Zhao Zhao , David Theodore N. , Vemuri Rajitha N. P. , Lu Wei , Lau S. S. , Lanz A. , Alford T. L.
Published: December 2013

Rapid processing and reduced end-of-range diffusion result from susceptor-assisted microwave (MW) annealing, making this technique an efficient processing alternative for electrically activating dopants within ion-implanted semiconductors. Sheet resistance and Hall measurements provide evidence of electrical activation. Susceptor-assisted MW annealing, of ion-implanted Si, enables more effective dopant activation and at lower temperatures than required for rapid thermal annealing (RTA). Raman spectroscopy and ion channeling analyses are used to monitor the extent of ion implantation damage and recrystallization. The presence and behavior of extended defects are monitored by cross-section transmission electron microscopy. Phosphorus implanted Si samples experience effective electrical activation upon MW annealing. On the other hand, when boron implanted Si is MW annealed, the growth of extended defects results in reduced crystalline quality that hinders the electrical activation process. Further comparison of dopant diffusion resulting from MW annealing and rapid thermal annealing is performed using secondary ion mass spectroscopy. MW annealed ion implanted samples show less end-of-range diffusion when compared to RTA samples. In particular, MW annealed P+ implanted samples achieve no visible diffusion and equivalent electrical activation at a lower temperature and with a shorter time-duration of annealing compared to RTA. In this study, the peak temperature attained during annealing does not depend on the dopant species or dose, for susceptor-assisted MW annealing of ion-implanted Si.
Tunable dielectric liquid lens on flexible substrate
Authors: Lu Yen-Sheng , Tu Hongen , Xu Yong , Jiang Hongrui
Published: December 2013

We demonstrate the fabrication of a tunable-focus dielectric liquid lens (DLL) on a flexible substrate made of polydimethylsiloxane, which was wrapped onto a goggle surface to show its functionality. As a positive meniscus converging lens, the DLL has the focal length variable from 14.2 to 6.3 mm in 1.3 s when the driving voltage increases to 125 Vrms. The resolving power of the DLL is 17.95 line pairs per mm. The DLL on a flexible, curvilinear surface is promising for expanded field of view covered as well as in reconfigurable optical systems.
Properties of threading screw dislocation core in wurtzite GaN studied by Heyd-Scuseria-Ernzerhof hybrid functional
Authors: Matsubara M. , Godet J. , Pizzagalli L. , Bellotti E.
Published: December 2013

We propose another structure as the most stable configuration for threading screw dislocation core of wurtzite GaN in N-rich conditions by first-principles calculations using Heyd-Scuseria-Ernzerhof hybrid functional. This configuration is fully consistent with recent experimental results observing electrical inactivity of GaN samples grown in N-rich conditions, in contrast with previously suggested dislocation core structures.
Temperature dependence of the band gap of GaSb1−xBix alloys with 0 < x ≤ 0.042 determined by photoreflectance
Authors: Kopaczek J. , Kudrawiec R. , Linhart W. M. , Rajpalke M. K. , Yu K. M. , Jones T. S. , Ashwin M. J. , Misiewicz J. , Veal T. D.
Published: December 2013

GaSb1−xBix layers with 0 < x ≤ 0.042 have been studied by photoreflectance in 15–290 K temperature range. We found that due to the incorporation of Bi atoms into the GaSb host, the E0 band gap-related transition redshifts (∼30 meV per 1% Bi) and significantly broadens. The shift of the E0 transition in the temperature range 10–270 K has been found to be ∼70 meV, very similar to the energy shift in GaSb over the same temperature range. We analyzed the energy and broadening of the E0 transition using the Varshni and Bose-Einstein formulas and found that the Varshni and Bose-Einstein parameters of GaSb1−xBix are similar to those of GaSb. Moreover we concluded that the inhomogeneities in GaSb1−xBix alloys is less important than in dilute bismide arsenides since Bi atoms are more similar to Sb atoms (in electronegativities and ionic sizes).
Resistive switching properties of Ce and Mn co-doped BiFeO3 thin films for nonvolatile memory application
Authors: Tang Zhenhua , Zeng Jia , Xiong Ying , Tang Minghua , Xu Dinglin , Cheng Chuanpin , Xiao Yongguang , Zhou Yichun
Published: December 2013

The Ce and Mn co-doped BiFeO3 (BCFMO) thin films were synthesized on Pt/Ti/SiO2/Si substrates using a sol-gel method. The unipolar resistive switching (URS) and bipolar resistive switching (BRS) behaviors were observed in the Pt/BCFMO/Pt device structure, which was attributed to the formation/rupture of metal filaments. The fabricated device exhibits a large ROFF/RON ratio (>80), long retention time (>105 s) and low programming voltages (<1.5 V). Analysis of linear fitting current-voltage curves suggests that the space charge limited leakage current (SCLC) and Schottky emission were observed as the conduction mechanisms of the devices.
Interaction of magnetic resonators studied by the magnetic field enhancement
Authors: Hou Yumin
Published: December 2013

It is the first time that the magnetic field enhancement (MFE) is used to study the interaction of magnetic resonators (MRs), which is more sensitive than previous parameters–shift and damping of resonance frequency. To avoid the coherence of lattice and the effect of Bloch wave, the interaction is simulated between two MRs with same primary phase when the distance is changed in the range of several resonance wavelengths, which is also compared with periodic structure. The calculated MFE oscillating and decaying with distance with the period equal to resonance wavelength directly shows the retardation effect. Simulation also shows that the interaction at normal incidence is sensitive to the phase correlation which is related with retardation effect and is ultra-long-distance interaction when the two MRs are strongly localized. When the distance is very short, the amplitude of magnetic resonance is oppressed by the strong interaction and thus the MFE can be much lower than that of single MR. This study provides the design rules of metamaterials for engineering resonant properties of MRs.
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data
Authors: Hu Xihao , Wong Thomas K. F. , Lu Zhi John , Chan Ting Fung , Lau Terrence Chi Kong , Yiu Siu Ming , Yip Kevin Y.
Published: December 2013

Motivation: High-throughput sequencing has been used to probe RNA structures, by treating RNAs with reagents that preferentially cleave or mark certain nucleotides according to their local structures, followed by sequencing of the resulting fragments. The data produced contain valuable information for studying various RNA properties.

Results: We developed methods for statistically modeling these structure-probing data and extracting structural features from them. We show that the extracted features can be used to predict RNA ‘zipcodes’ in yeast, regions bound by the She complex in asymmetric localization. The prediction accuracy was better than using raw RNA probing data or sequence features. We further demonstrate the use of the extracted features in identifying binding sites of RNA binding proteins from whole-transcriptome global photoactivatable-ribonucleoside-enhanced cross-linking and immunopurification (gPAR-CLIP) data.

Availability: The source code of our implemented methods is available at http://yiplab.cse.cuhk.edu.hk/probrna/.

Contact:  kevinyip@cse.cuhk.edu.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The β clamp targets DNA polymerase IV to DNA and strongly increases its processivity
Authors: Wagner Jérôme , Fujii Shingo , Gruz Petr , Nohmi Takehiko , Fuchs Robert P P
Published: December 2013

The recent discovery of a new family of ubiquitous DNA polymerases involved in translesion synthesis has shed new light onto the biochemical basis of mutagenesis. Among these polymerases, the dinB gene product (Pol IV) is involved in mutagenesis in Escherichia coli. We show here that the activity of native Pol IV is drastically modified upon interaction with the β subunit, the processivity factor of DNA Pol III. In the absence of the β subunit Pol IV is strictly distributive and no stable complex between Pol IV and DNA could be detected. In contrast, the β clamp allows Pol IV to form a stable initiation complex (t1/2 ≈ 2.3 min), which leads to a dramatic increase in the processivity of Pol IV reaching an average of 300–400 nucleotides. In vivo, the β processivity subunit may target DNA Pol IV to its substrate, generating synthesis tracks much longer than previously thought.
Limiting DNA replication to once and only once
Authors: Boye Erik , Løbner‐Olesen Anders , Skarstad Kirsten
Published: December 2013

In Escherichia coli cells, the origin of chromosomal replication is temporarily inactivated after initiation has occurred. Origin sequestration is the first line of defence against over‐initiation, providing a time window during which the initiation potential can be reduced by: (i) titration of DnaA proteins to newly replicated chromosomal elements; (ii) regulation of the activity of the DnaA initiator protein; and (iii) sequestration of the dnaA gene promoter. This review represents the first attempt to consider together older and more recent data on such inactivation mechanisms in order to analyze their contributions to the overall tight replication control observed in vivo. All cells have developed mechanisms for origin inactivation, but those of other bacteria and eukaryotic cells are clearly distinct from those of E. coli. Possible differences and similarities are discussed.
Reconstitution of Sec‐dependent membrane protein insertion: nascent FtsQ interacts with YidC in a SecYEG‐dependent manner
Authors: van der Laan Martin , Houben Edith N G , Nouwen Nico , Luirink Joen , Driessen Arnold J M
Published: December 2013

The inner membrane protein YidC is associated with the preprotein translocase of Escherichia coli and contacts transmembrane segments of nascent inner membrane proteins during membrane insertion. YidC was purified to homogeneity and co‐reconstituted with the SecYEG complex. YidC had no effect on the SecA/SecYEG‐mediated translocation of the secretory protein proOmpA; however, using a crosslinking approach, the transmembrane segment of nascent FtsQ was found to gain access to YidC via SecY. These data indicate the functional reconstitution of the initial stages of YidC‐dependent membrane protein insertion via the SecYEG complex.
Secured cutting: controlling separase at the metaphase to anaphase transition
Authors: Uhlmann Frank
Published: December 2013

The final irreversible step in the duplication and distribution of genomes to daughter cells takes place at the metaphase to anaphase transition. At this point aligned sister chromatid pairs split and separate. During metaphase, cohesion between sister chromatids is maintained by the chromosomal multi‐subunit cohesin complex. Here, I review recent findings as to how anaphase is initiated by proteolytic cleavage of the Scc1 subunit of cohesin. Scc1 is cleaved by a site‐specific protease that is conserved in all eukaryotes, and is now called ‘separase’. As a result of this cleavage, the cohesin complex is destroyed, allowing the spindle to pull sister chromatids into opposite halves of the cell. Because of the final and irreversible nature of Scc1 cleavage, this reaction is tightly controlled. Several independent mechanisms seem to impose regulation on Scc1 cleavage, acting on both the activity of separase and the susceptibility of the substrate.
Manipulation of EAT-2 expression promotes induction of multiple beneficial regulatory and effector functions of the human innate immune system as a novel immunomodulatory strategy
Authors: Aldhamen Yasser A. , Seregin Sergey S. , Aylsworth Charles F. , Godbehere Sarah , Amalfitano Andrea
Published: December 2013

The signaling lymphocytic activation molecule (SLAM) receptor-associated adaptor Ewing’s sarcoma-associated transcript-2 (EAT-2) is primarily expressed in innate immune cells including dendritic cells (DCs), macrophages and NK cells. A recent human HIV vaccine study confirmed that EAT-2 expression was associated with the enhanced immunogenicity induced by the MRKAd5/HIV vaccine. We previously harnessed the capability of EAT-2 to modulate signaling mediated by SLAM receptors and demonstrated that by incorporating EAT-2 expression into vaccines, one could enhance innate and adaptive immune responses in mice, even in the face of pre-existing immunity to the vaccine vectors. Herein, we investigated the innate immune responses of human cells exposed to EAT-2-over-expressing vaccines. Our results demonstrate that EAT-2 over-expression can significantly alter the kinetics of critical pro-inflammatory cytokine and chemokine responses elaborated by human PBMCs. In addition, enhanced DC maturation and increased monocyte phagocytosis were observed in EAT-2-transduced human cells. We also found that EAT-2 over-expression improved antigen presentation by human cells. Moreover, EAT-2 over-expression increased the anti-tumor activity of human NK cells against K562 tumor cell targets. Many of these responses were extinguished with use of an EAT-2 variant carrying a mutant SH2 domain (R31Q), suggesting a critical role for the interaction between EAT-2 and SLAM receptors in mediating these responses. In conclusion, these results provide evidence that EAT-2 interacts with key components of multiple arms of the human innate immune system, and that this role highlights the potential for targeting EAT-2 functions so as to improve a number of human immunotherapeutic approaches, including vaccine development.
Single‐Center Experience With 1‐Step Low‐Profile Percutaneous Endoscopic Gastrostomy in Children
Authors: Pattamanuch Nicole , Novak Inna , Loizides Anthony , Montalvo Andrea , Thompson John , Rivas Yolanda , Pan Debra
Published: December 2013

Objectives:

The 1‐step low‐profile percutaneous endoscopic gastrostomy (1‐step PEG) uses a single procedure that allows immediate use of a low‐profile device. The aim of the present study was to provide our experience with this device and to analyze complications and outcomes after the initial placement.

Methods:

We performed a retrospective chart review of pediatric patients with 1‐step PEG placement done by our pediatric gastroenterologists between 2006 and June 2011. Patients were studied for a minimum period of 6 months.

Results:

A total of 121 patients were included in our study, with 23% infants. The most common indication for 1‐step PEG placement was swallowing dysfunction in children with neurological impairment (49%). Postplacement complications included granulation tissue (52%), cellulitis (23%), leakage (21%), vomiting (17%), tissue breakdown (8%), failed placement (6%), embedded bolster (5%), perforation (0.8%), and bowel obstruction (0.8%). One‐step PEG was maintained in 46 patients (38%). In the remaining 75 patients (62%), PEGs were changed to a balloon device in 66 patients and were completely removed in 9 patients. The most common indications for change were damaged PEG (19/75) and issues with size (11/75). The time to change ranged from <1 month to >4 years (14 ± 1.3 months). Sixty‐eight percent of 1‐step PEG changes/removal was performed with an obturator under brief inhalated anesthesia.

Conclusions:

The 1‐step PEG has complication rates and outcomes comparable with standard PEGs.
Low Temperature-Responsive Changes in the Anther Transcriptome’s Repeat Sequences Are Indicative of Stress Sensitivity and Pollen Sterility in Rice Strains
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Authors: Ishiguro Seiya , Ogasawara Kei , Fujino Kaien , Sato Yutaka , Kishima Yuji
Published: December 2013

Genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine responses to low temperatures in rice (Oryza sativa). We focused particularly on the rice anther at the booting stage, because a low temperature at this stage can result in pollen abortion. The five rice strains examined in this study showed different pollen fertilities due to a low-temperature treatment during the booting stage. The microarray analyses demonstrated that the low-temperature stress caused genome-wide changes in the transcriptional activities not only of genes but also of repeat sequences in the rice anther. The degree of the temperature-responsive changes varied among the five rice strains. Interestingly, the low-temperature-sensitive strains revealed more changes in the transcriptome when compared with the tolerant strains. The expression patterns of the repeat sequences, including miniature inverted-repeat transposable elements, transposons, and retrotransposons, were correlated with the pollen fertilities of the five strains, with the highest correlation coefficient being 0.979. Even in the low-temperature-sensitive strains, the transcriptomes displayed distinct expression patterns. The elements responding to the low temperatures were evenly distributed throughout the genome, and the major cis-motifs involved in temperature-responsive changes were undetectable from the upstream sequences in the corresponding repeats. The genome-wide responses of transcription to the temperature shift may be associated with chromatin dynamics, which facilitates environmental plasticity. A genome-wide analysis using repeat sequences suggested that stress tolerance could be conferred by insensitivity to the stimuli.
Control of the toxic plantColchicum autumnalein semi‐natural grasslands: effects of cutting treatments on demography and diversity
Authors: Winter Silvia , Jung Linda S. , Eckstein R. Lutz , Otte Annette , Donath Tobias W. , Kriechbaum Monika
Published: December 2013

Semi‐natural grasslands are important habitats for the conservation of biodiversity in Europe. High population densities of toxicColchicum autumnalein these grasslands may cause problems for livestock and the marketing of hay. Consequently, farmers may either intensify grassland management to reduceC. autumnalein the fodder or abandon the land; both practices will lead to a loss of biodiversity. Previous studies suggesting early cutting to controlC. autumnaledid not consider population dynamics and the effects on plant diversity.

We conducted a four‐year experiment in six regions within Austria and Germany, applying five cutting treatments in 16C. autumnalepopulations to test the effects of cutting date and frequency onC. autumnaleand co‐occurring vegetation. Demographic data were evaluated with matrix population models, life‐table response experiment (LTRE),anovaandmanova. Vegetation data were analysed with multiresponse permutation procedures (MRPP),anovaandmanova.

Population growth rate was significantly reduced in plots cut in early and late May compared to plots cut in June (control).

Plants cut in late April or early May showed the lowest survival probability. Significantly fewer large vegetative plants developed capsules in the following year when cut in early or late May.LTREanalysis showed that differences in the population growth rate between the control and early cut treatments were mainly the result of a reduced survival and growth and an increased retrogression to smaller stages.

Multiresponse permutation procedures revealed no differences in vegetation composition between treatments except for one site in 2011. There were no differences in Shannon index, evenness or species turnover rate within any year.

Synthesis and applications. The greatest reduction in vitality ofColchicum autumnalewas observed in grasslands cut in late April or early May. After three years of early cutting, no reduction in plant species diversity was observed. The second cut should be postponed to July to enable seed shed of plants. Grassland management decisions to control toxicC. autumnalemust be made in close cooperation with nature conservation authorities to consider site characteristics and requirements of endangered species.
Land‐use intensity and the effects of organic farming on biodiversity: a hierarchical meta‐analysis
Authors: Tuck Sean L. , Winqvist Camilla , Mota Flávia , Ahnström Johan , Turnbull Lindsay A. , Bengtsson Janne
Published: December 2013

The benefits of organic farming to biodiversity in agricultural landscapes continue to be hotly debated, emphasizing the importance of precisely quantifying the effect of organic vs. conventional farming.

We conducted an updated hierarchical meta‐analysis of studies that compared biodiversity under organic and conventional farming methods, measured as species richness. We calculated effect sizes for 184 observations garnered from 94 studies, and for each study, we obtained three standardized measures reflecting land‐use intensity. We investigated the stability of effect sizes through time, publication bias due to the ‘file drawer’ problem, and consider whether the current literature is representative of global organic farming patterns.

On average, organic farming increased species richness by about 30%. This result has been robust over the last 30 years of published studies and shows no sign of diminishing.

Organic farming had a greater effect on biodiversity as the percentage of the landscape consisting of arable fields increased, that is, it is higher in intensively farmed regions. The average effect size and the response to agricultural intensification depend on taxonomic group, functional group and crop type.

There is some evidence for publication bias in the literature; however, our results are robust to its impact. Current studies are heavily biased towards northern and western Europe and North America, while other regions with large areas of organic farming remain poorly investigated.

Synthesis and applications. Our analysis affirms that organic farming has large positive effects on biodiversity compared with conventional farming, but that the effect size varies with the organism group and crop studied, and is greater in landscapes with higher land‐use intensity. Decisions about where to site organic farms to maximize biodiversity will, however, depend on the costs as well as the potential benefits. Current studies have been heavily biased towards agricultural systems in the developed world. We recommend that future studies pay greater attention to other regions, in particular, areas with tropical, subtropical and Mediterranean climates, in which very few studies have been conducted.
Water utilisation, energy utilisation and waste water management in the dairy industry: A review
Authors: Rad Salimeh Jabbari , Lewis Michael John
Published: December 2013

Energy consumption, water utilisation and waste production are now important environmental issues. However, compilations of data are not readily available, making it difficult for companies to assess how they are performing. This review aims to summarise the data that are available, including some benchmarking values. Also discussed are techniques for reducing water and energy consumption and waste production, tools for monitoring this and assistance that is available to improve efficiency ratios and reduce costs associated with these issues. Using information in this review, an individual company should be able to compare its performance against others producing similar products, nationally or globally in order to set and maintain rational benchmarking values to improve its performance and deal with environmental concerns.