bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional and quality‐of‐life outcomes after reirradiation for head and neck cancer
Authors: Chen Allen M. , Vazquez Esther , Michaud Anthony L. , Farwell D. Gregory , Purdy James A.
Published: December 2013

Objectives/Hypothesis

To examine functional and quality‐of‐life outcomes for patients treated by reirradiation to the head and neck for recurrent or new primary cancers.

Study Design

Retrospective review.

Methods

The University of Washington Quality of Life Instrument (UW‐QOL) scores were reviewed with swallow evaluations for 17 patients with biopsy‐proven recurrent or new primary squamous cell carcinoma of the head and neck treated with reirradiation who were clinically without evidence of disease at a minimum follow‐up of 1 year. All patients had received their initial radiation therapy to a median dose of 66 Gy (range, 60–72 Gy). The median interval between radiation courses was 30 months (range, 6–132 months). The median reirradiation dose was 60 Gy (range, 54–70 Gy).

Results

At 1 year after reirradiation, the mean UW‐QOL composite score was 67.0 (range, 22.1–83.5), which did not differ significantly from baseline (P = .57). The proportion of patients who rated their global quality of life as “very good” or “outstanding” at 1 year after reirradiation was 35%. The percentage of patients who reported their global quality of life as “good/fair” and “poor/very poor” were 59% and 6%, respectively.

Conclusions

The majority of survivors in this highly selected series were devoid of new impairment after reirradiation and were satisfied with their functional status. Although nearly all patients had side effects from their prior radiation course prior to reirradiation, no patient reported a decline in global quality of life from before reirradiation to 1 year post‐treatment.

Level of Evidence

2c Laryngoscope, 124:1807–1812, 2014
Investigation of corrosion behavior of 6060 and 6082 aluminum alloys under simulated acid rain conditions
Authors: Gerengi H. , Slepski P. , Ozgan E. , Kurtay M.
Published: December 2013

Instantaneous impedance changes of 6060 and 6082 type aluminum alloys in pure water, and simulated acid rain poured into the pure water was investigated by dynamic electrochemical impedance spectroscopy (DEIS). In this way, the influence of aluminum content on the corrosion behavior of 6060 and 6082 type aluminum alloys immersed in simulated acid rain was determined. The corrosion rate of the alloy decreased with increasing Al content, which may be related to the distribution of the Al‐rich phase. The surface morphology of studied alloys was also examined with scanning electron microscopy.
The estimation of corrosion behavior of new TiNbTaZr alloys for biomedical applications
Authors: Bărbînţă A. C. , Mareci D. , Chelariu R. , Bolat G. , Munteanu C. , Cho K. , Niinomi M.
Published: December 2013

The corrosion behavior of two TiNbTaZr alloys (Ti25Nb8Ta10Zr and Ti21Nb15Ta6Zr) in Dulbecco's minimum essential medium (MEM) are evaluated and its protective ability is compared with that of Cp‐Ti, to ascertain their stability for biomedical application. All the samples were examined using electrochemical techniques: electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization curves. The electrochemical corrosion parameters obtained from the EIS and potentiodynamic polarization curves indicated a typical passive behavior for TiNbTaZr alloys. In addition, scanning electron microscopy was employed to observe the surface morphology after polarization test in MEM solution. Low anodic current density values were obtained from the polarization curves, indicating a typical passive behavior for TiNbTaZr alloys. EIS studies showed high impedance values for all samples, increasing with exposure time. The Ti21Nb15Ta6Zr alloy appears to possess superior corrosion resistance than the Ti25Nb8Ta10Zr alloy and Cp‐Ti in MEM solution.
Microstructure characterisation and reconstruction of intermetallic particles
Authors: Chen F. F. , Cole I. , Hughes A. E. , Glenn A.M. , Sapper E. , Osborne J.
Published: December 2013

Pitting corrosion is associated with the distribution and composition of intermetallic (IM) particles. However, quantitatively studying the relationship between alloy corrosion and IM particle property remains a challenging topic. In this paper, a computational method is presented for IM particle characterisation and reconstruction based on backscattered scanning electron micrographs of aluminium alloy AA2024‐T3. The reconstructed mapping of IM particles provides a 2D map of the intermetallic distribution that conforms to empirical statistical data but is generated randomly. This enables a range of statistically identical virtual microstructures which are generated in order to determine variability in pitting models as well as for systematic variation of input parameters in a sensitivity analysis (e.g., concentration of a given alloying element) used to deduce new microstructural maps for modified compositions. IM particle spatial distribution patterns are analysed based on the reconstruction maps to study the clustering properties of different types of IM particles. The presented approach provides a quantitative tool for studying the relationship between alloy corrosion and the distribution and composition of a range of IM particles.
Permeability determination of porous media using large‐scale finite elements and iterative solver
Authors: Karim M. R. , Krabbenhoft K. , Lyamin A. V.
Published: December 2013

The problem of finite element simulation of incompressible fluid flow in porous medium is considered. The porous medium is characterized by the X‐ray microtomography technique in three dimensions. The finite calculus‐based stabilization technique is reviewed to implement the equal order finite element interpolation functions for both velocity and pressure. A noble preconditioner, the nodal block diagonal preconditioner, is considered whose performance is thoroughly investigated. Combining this preconditioner with a standard iterative solver during the computational homogenization procedure, it is possible to carry out the large‐scale fluid flow simulation for estimating permeability of the porous medium with reasonable accuracy and reliability. Copyright © 2013 John Wiley & Sons, Ltd.
Using fuzzy comprehensive evaluation method to establish a credible spectrum sensing and allocation model
Authors: Zhang Guanghua , Zhang Yuqing , Liu Xuefeng
Published: December 2013

This study focuses on the false feedback of spectrum information and the malicious behavior that forcibly occupies spectrum resources in cognitive radio networks. A credible spectrum sensing and allocation model based on fuzzy theory is proposed. The spectrum sensing behavior and spectrum utilization behavior are taken as two evaluation factors. On the basis of subjectivity and uncertainty of trust, this study adopts the fuzzy comprehensive evaluation method to construct the trust evaluation of nodes. In cooperative spectrum sensing, comprehensive evaluation results can be used to identify malicious nodes and eliminate false feedback information. In spectrum allocation, the degree of lattice closeness among fuzzy sets is used to define and calculate the difference between the actual comprehensive evaluation set and the ideal comprehensive evaluation. The difference is calculated to quantify the credibility of non‐malicious nodes and to determine the allocation of spectrum resources to nodes using the multi‐objective optimization algorithm. These techniques can control the malicious behaviors of nodes and encourage cooperative behavior among nodes. Consequently, the joint design of spectrum sensing at the physical layer and spectrum allocation at the media access control layer is realized. Simulation results and analysis indicate that under malicious attacks, the proposed model has sound performance in terms of system sensing, throughput, and fair spectrum allocation compared with existing models. Copyright © 2013 John Wiley & Sons, Ltd.
Preserving identity privacy on multi‐owner cloud data during public verification
Authors: Wang Boyang , Li Hui , Liu Xuefeng , Li Xiaoqing , Li Fenghua
Published: December 2013

The low prices on cloud data storage and sharing services incentive users to outsource their data to the cloud. Because data stored in the cloud may be lost or corrupted, users are suggested to verify data integrity before the utilization of cloud data. A series of schemes have been proposed to enable a public verifier to efficiently check the correctness of cloud data without downloading the whole data from the cloud server. Unfortunately, few of them have considered about public verification on multi‐owner cloud data while still preserving identity privacy of owners from public verifiers, where each block in these cloud data should be signed by multiple owners. In this paper, we design a novel public verification scheme to audit the integrity of multi‐owner data stored in the cloud. With our scheme, a public verifier is able to efficiently check the integrity of multi‐owner data with a very small communication cost compared with the size of the entire data. Meanwhile, the private identities of these owners are protected and not revealed to any public verifier. In addition, our scheme can also efficiently support group dynamics for multiple owners and enable batch verification. Security analyses and experimental results indicate our scheme is correct, secure and efficient. Copyright © 2013 John Wiley & Sons, Ltd.
Use of empirical likelihood to calibrate auxiliary information in partly linear monotone regression models
Authors: Chen Baojiang , Qin Jing
Published: December 2013

In statistical analysis, a regression model is needed if one is interested in finding the relationship between a response variable and covariates. When the response depends on the covariate, then it may also depend on the function of this covariate. If one has no knowledge of this functional form but expect for monotonic increasing or decreasing, then the isotonic regression model is preferable. Estimation of parameters for isotonic regression models is based on the pool‐adjacent‐violators algorithm (PAVA), where the monotonicity constraints are built in. With missing data, people often employ the augmented estimating method to improve estimation efficiency by incorporating auxiliary information through a working regression model. However, under the framework of the isotonic regression model, the PAVA does not work as the monotonicity constraints are violated. In this paper, we develop an empirical likelihood‐based method for isotonic regression model to incorporate the auxiliary information. Because the monotonicity constraints still hold, the PAVA can be used for parameter estimation. Simulation studies demonstrate that the proposed method can yield more efficient estimates, and in some situations, the efficiency improvement is substantial. We apply this method to a dementia study. Copyright © 2013 John Wiley & Sons, Ltd.
Uncertainties of the 50‐year wind from short time series using generalized extreme value distribution and generalized Pareto distribution
Authors: Larsén Xiaoli Guo , Mann Jakob , Rathmann Ole , Jørgensen Hans E.
Published: December 2013

This study examines the various sources to the uncertainties in the application of two widely used extreme value distribution functions, the generalized extreme value distribution (GEVD) and the generalized Pareto distribution (GPD). The study is done through the analysis of measurements from several Danish sites, where the extreme winds are caused by the Atlantic lows. The simple extreme wind mechanism here helps us to focus on the issues mostly related to the use of limited wind measurements. Warnings are flagged and possible solutions are discussed. Thus, this paper can be used as a guideline for applying GEVD and GPD to wind time series of limited length. The data analysis shows that, with reasonable choice of relevant parameters, GEVD and GPD give consistent estimates of the return winds. For GEVD, the base period should be chosen in accordance with the occurrence of the extreme wind events of the same mechanism. For GPD, the choices of the threshold, the definition of independent samples and the shape factor are interrelated. It is demonstrated that the lack of climatological representativity is a major source of uncertainty to the use of both GEVD and GPD; the information of climatological variability is suggested to be extracted from global or mesoscale models. © 2013 The Authors.Wind Energypublished by John Wiley & Sons, Ltd.
Metaphysical analyticity and the epistemology of logic
Authors: Russell Gillian K.
Published: December 2013

Recent work on analyticity distinguishes two kinds, metaphysical and epistemic. This paper argues that the distinction allows for a new view in the philosophy of logic according to which the claims of logic are metaphysically analytic and have distinctive modal profiles, even though their epistemology is holist and in many ways rather Quinean. It is argued that such a view combines some of the more attractive aspects of the Carnapian and Quinean approaches to logic, whilst avoiding some famous problems.
Hierarchical Bayesian Modeling for Test Theory Without an Answer Key
Authors: Oravecz Zita , Anders Royce , Batchelder William H.
Published: December 2013

Cultural Consensus Theory (CCT) models have been applied extensively across research domains in the social and behavioral sciences in order to explore shared knowledge and beliefs. CCT models operate on response data, in which the answer key is latent. The current paper develops methods to enhance the application of these models by developing the appropriate specifications for hierarchical Bayesian inference. A primary contribution is the methodology for integrating the use of covariates into CCT models. More specifically, both person- and item-related parameters are introduced as random effects that can respectively account for patterns of inter-individual and inter-item variability.
Discussions of adolescent sexuality in news media coverage of the HPV vaccine
Authors: Casciotti Dana M. , Smith Katherine C. , Tsui Amy , Klassen Ann C.
Published: December 2013

Given the sexually transmitted nature of human papillomavirus (HPV), some worry the HPV vaccine will create a false sense of security and promote adolescent sexual activity. Media coverage of vaccines can influence social norms, parental attitudes, and vaccine acceptance; in this paper we examine U.S. news media messages related to sexuality and HPV vaccination. Drawing on a structured analysis of 447 articles published during 2005–2009, we qualitatively analyzed a purposive sample of 49 articles discussing adolescent health behaviors related to HPV vaccination. Commonly, articles discussed vaccination in the context of abstinence‐only versus comprehensive sexual health education; cited research findings to support vaccination or sex education; argued against connecting vaccination to promiscuous behavior; but included fear‐inducing messages. Media messages concerning health behaviors related to HPV vaccination tended to support government and parental involvement in sex education, and dismiss concerns linking vaccination to sexual activity, while also presenting the vaccine as lifesaving.
Jim Crow 2.0? Why States Consider and Adopt Restrictive Voter Access Policies
Authors: Bentele Keith G. , O'Brien Erin E.
Published: December 2013

Recent years have seen a dramatic increase in state legislation likely to reduce access for some voters, including photo identification and proof of citizenship requirements, registration restrictions, absentee ballot voting restrictions, and reductions in early voting. Political operatives often ascribe malicious motives when their opponents either endorse or oppose such legislation. In an effort to bring empirical clarity and epistemological standards to what has been a deeply-charged, partisan, and frequently anecdotal debate, we use multiple specialized regression approaches to examine factors associated with both the proposal and adoption of restrictive voter access legislation from 2006–2011. Our results indicate that proposal and passage are highly partisan, strategic, and racialized affairs. These findings are consistent with a scenario in which the targeted demobilization of minority voters and African Americans is a central driver of recent legislative developments. We discuss the implications of these results for current partisan and legal debates regarding voter restrictions and our understanding of the conditions incentivizing modern suppression efforts. Further, we situate these policies within developments in social welfare and criminal justice policy that collectively reduce electoral access among the socially marginalized.
Why Do We Report Suicides and How Can We Facilitate Suicide Prevention Efforts?
Authors: Cheng Qijin , Fu King-wa , Caine Eric , Yip Paul S. F.
Published: December 2013

Background: The Hong Kong news media report suicide-related events more frequently and sensationally than Western countries. Little is known about Hong Kong media professionals’ experiences and thoughts about such reporting. Aims: To understand Hong Kong media professionals’ experiences and perceptions of suicide reporting and whether the news media can be better engaged into suicide prevention. Method: We conducted three focus groups of journalists from both the Cantonese and English language news media. Data were analyzed using grounded theory methods. Results: We discerned three rationales from participants regarding their intense coverage of suicide-related events: (1) satisfying commercial competitiveness, (2) addressing social problems, and (3) responding to readers’ interests. The first rationale was a dominant and vigorous motivating factor, and often influenced suicide reporting among local Cantonese media. Media professionals recommended engagement strategies targeted at frontline journalists, media managers, and general media consumers. Conclusion: We see potential to involve news media professionals in Hong Kong as working partners in suicide prevention. To succeed, this effort requires engagement in a proactive, consistent, and sustained fashion.
Facing a Patient Who Seeks Help After a Suicide Attempt
Authors: Rothes Inês Areal , Henriques Margarida Rangel , Leal Joana Barreiros , Lemos Marina Serra
Published: December 2013

Background: Although intervention with suicidal patients is one of the hardest tasks in clinical practice, little is known about health professionals’ perceptions about the difficulties of working with suicidal patients. Aims: The aims of this study were to: (1) describe the difficulties of professionals facing a suicidal patient; (2) analyze the differences in difficulties according to the sociodemographic and professional characteristics of the health professionals; and (3) identify the health professionals’ perceived skills and thoughts on the need for training in suicide. Method: A self-report questionnaire developed for this purpose was filled out by 196 health professionals. Exploratory principal components analyses were used. Results: Four factors were found: technical difficulties; emotional difficulties; relational and communicational difficulties; and family-approaching and logistic difficulties. Differences were found between professionals who had or did not have training in suicide, between professional groups, and between the number of patient suicide attempts. Sixty percent of the participants reported a personal need for training and 85% thought it was fundamental to implement training plans targeted at health professionals. Conclusion: Specific training is fundamental. Experiential and active methodologies should be used and technical, relational, and emotional questions must be included in the training syllabus.
Culture‐differentiated CD8+ T cells acquire innate memory‐like traits and respond to a pathogen‐associated molecule
Authors: Biswas Ratna , Mukherjee Subhadeep , Sinha Debolina , Ghosh Amlan Kanti , Biswas Tapas
Published: December 2013

Selection of conventional CD4+ or CD8+ T cells is usually driven by the interaction of double‐positive CD4+CD8+ thymocytes with epithelial cells. Here, we demonstrate preferential selection of CD8+ thymocytes from in vitro differentiation of CD4+CD8+ double‐positive thymocytes exhibiting the characteristics of nonconventional innate memory CD8+ cells. In contrast to conventional CD8+ thymocytes, these culture‐differentiated CD8+ cells are eomesodermin positive and robustly express CXCR3, CD44, CD122 and TLR2. Interestingly, the pathogen‐associated molecule porin promotes preferential differentiation of the CD8+ single‐positive subset in association with promyelocytic leukemia zinc‐finger upregulation and interleukin (IL)‐4 production. On priming with anti‐CD3 antibody, porin augmented TLR2 and IFN‐γ indicating a role of the TLR ligand in acquisition of innate memory response of CD8+ thymocytes. In addition, porin has a cooperative role with IL‐15 on the expansion of memory‐phenotype CD8+ T cells along with its effector function. Thus, the study opens an avenue to unfold the cues for development of these cells and the strategies adopted for bolstering immunity during primary infection.
Integrated approach to evaluating the toxicity of novel cysteine-capped silver nanoparticles to Escherichia coli and Pseudomonas aeruginosa
Authors: Priester John H. , Singhal Aditi , Wu Binghui , Stucky Galen D. , Holden Patricia A.
Published: December 2013

The toxicity of cysteine capped Ag nanoparticles toE. coliandP. aeruginosawas evaluated using an integrated approach that measured particle dissolution, bacterial growth, and effects on cell membranes.
A handheld magnetic sensing platform for antigen and nucleic acid detection
Authors: Pai Alex , Khachaturian Aroutin , Chapman Stephen , Hu Alexander , Wang Hua , Hajimiri Ali
Published: December 2013

A portable magnetic-based biosensing platform is introduced for antigen and nucleic acid detection utilizing the “magnetic freezing” technique.
Self-promoted post-synthetic modification of metal–ligand M2L3 mesocates
Authors: Young Michael C. , Johnson Amber M. , Hooley Richard J.
Published: December 2013

Self-assembled FeII-iminopyridine mesocates can be post-synthetically modified upon treatment with suitable isocyanates. The self-assembled mesocates promote their own reaction via intramolecular hydrogen bonding.
Stepwise addition of difluorocarbene to a transition metal centre
Authors: Lee Graham M. , Harrison Daniel J. , Korobkov Ilia , Baker R. Tom
Published: December 2013

The Ruppert–Prakash reagent (Me3SiCF3) is used to introduce difluorocarbene (CF2) and tetrafluoroethylene (TFE) ligands to cobalt(i) metal centres, whereby the TFE ligand is generated via [2+1] cycloaddition between [Co]CF2 and CF2.
A spiroborate-based anionic bis-N-heterocyclic carbene
Authors: Su Jia-Hong , Lee Gene-Hsiang , Peng Shie-Ming , Chiu Ching-Wen
Published: December 2013

A twisted bis-benzimidazolium salt was isolated from the reaction of 5,6-dihydroxyl-benzimidazolium and benzenediboronic acid. Deprotonation of the azolium salt led to the formation of a spiroborate-linked bis-NHC, which was further transformed into the corresponding diborane adduct and the di-Rh complex.
Effect of the different synthetic parameters on the morphology and magnetic properties of nickel nanoparticles
Authors: Paredes-Garcia Veronica , Cruz Carlos , Toledo Nestor , Denardin Juliano , Venegas-Yazigi Diego , Castillo Carolina , Spodine Evgenia , Luo Zhiping
Published: December 2013

The morphology of stable spherical Ni(0) nanoparticles can be modified to obtain flower-like Ni(0) arrangements by reheating them, retaining their high crystallinity and without oxidation of the nanoparticles.
Plasmon-enhanced catalysis of photo-induced charge transfer from TCNQF4− to TCNQF42−
Authors: Wang Jing , Xu Weiqing , Wu Jinxia , Yu Guangtao , Zhou Xianghua , Xu Shuping
Published: December 2013

The transformation from Ag-TCNQF4 to Ag2-TCNQF4via photo-induced charge transfer under Au nanoparticles catalysis was monitored by Raman spectroscopy.
A purine nucleoside phosphorylase in Solanum tuberosum L. (potato) with specificity for cytokinins contributes to the duration of tuber endodormancy
Authors: Bromley Jennifer R. , Warnes Barbara J. , Newell Christine A. , Thomson Jamie C. P. , James Celia M. , Turnbull Colin G. N. , Hanke David E.
Published: December 2013

StCKP1 (Solanum tuberosum cytokinin riboside phosphorylase) catalyses the interconversion of the N9-riboside form of the plant hormone CK (cytokinin), a subset of purines, with its most active free base form. StCKP1 prefers CK to unsubstituted aminopurines. The protein was discovered as a CK-binding activity in extracts of tuberizing potato stolon tips, from which it was isolated by affinity chromatography. The N-terminal amino acid sequence matched the translation product of a set of ESTs, enabling a complete mRNA sequence to be obtained by RACE-PCR. The predicted polypeptide includes a cleavable signal peptide and motifs for purine nucleoside phosphorylase activity. The expressed protein was assayed for purine nucleoside phosphorylase activity against CKs and adenine/adenosine. Isopentenyladenine, trans-zeatin, dihydrozeatin and adenine were converted into ribosides in the presence of ribose 1-phosphate. In the opposite direction, isopentenyladenosine, trans-zeatin riboside, dihydrozeatin riboside and adenosine were converted into their free bases in the presence of Pi. StCKP1 had no detectable ribohydrolase activity. Evidence is presented that StCKP1 is active in tubers as a negative regulator of CKs, prolonging endodormancy by a chill-reversible mechanism.
Wide‐stopband Wilkinson power divider with bandpass response
Authors: Chau W.‐M. , Hsu K.‐W. , Tu W.‐H.
Published: December 2013

A wide‐stopband Wilkinson power divider with bandpass response and good isolation is presented. A 3‐terminal, 2‐pole bandpass filter and two 3‐pole lowpass filters are used to replace the two quarter‐wavelength transformer in a conventional Wilkinson power. The divider consists of two shorted‐circuited half‐wavelength stepped‐impedance resonators and two 3‐pole microstrip stepped‐impedance lowpass filters. Thus, the divider achieves not only a bandpass response but also a very wide stopband. For the upper stopband performance, the rejection level is >10 dB up to 22.2 times the centre frequency.
Identification and control of class of non‐linear systems with non‐symmetric deadzone using recurrent neural networks
Authors: Pérez‐Cruz José Humberto , Chairez Isaac , de Jesús Rubio Jose , Pacheco Jaime
Published: December 2013

In this study, a neuro‐controller with adaptive deadzone compensation for a class of unknown SISO non‐linear systems in a Brunovsky form with uncertain deadzone input is presented. Based on a proper smooth parameterisation of the deadzone, the unknown dynamics is identified by using a continuous time recurrent neural network whose weights are adjusted on‐line by stable differential learning laws. On the basis of this neural model so obtained, a feedback linearisation controller is developed in order to follow a bounded reference trajectory specified. By means of Lyapunov analysis, the boundedness of all the closed‐loop signals as well as the weights and deadzone parameter estimations is rigorously proven. Besides, the exponential convergence of the actual tracking error to a bounded zone is guaranteed. The effectiveness of this scheme is illustrated by a numerical simulation.
Distributed H∞ and H2 consensus control in directed networks
Authors: Wang Jingyao , Duan Zhisheng , Li Zhongkui , Wen Guanghui
Published: December 2013

In this study, the H∞ consensus problem of a group of linear multi‐agent systems with directed communication graph is addressed. To achieve H∞ consensus, a new class of distributed consensus protocols based only on the relative states of the neighbouring agents is proposed. Compared with the existing protocols, the one presented in this study focuses on solving the H∞ consensus problem in strongly connected directed networks. By using tools from algebraic graph theory and Lyapunov stability analysis, it is theoretically shown that distributed H∞ consensus in the closed‐loop multi‐agent systems with strongly connected topology can be achieved if the distributed consensus protocol is appropriately designed. A two‐step algorithm is then presented to construct such a protocol. The H2 consensus problem for networked systems is further investigated. Finally, the effectiveness of the theoretical analysis is verified via numerical simulations.
Genetically encoded fluorescent probe to visualize intracellular phosphatidylinositol 3,5-bisphosphate localization and dynamics
Authors: Li Xinran , Wang Xiang , Zhang Xiaoli , Zhao Mingkun , Tsang Wai Lok , Zhang Yanling , Yau Richard Gar Wai , Weisman Lois S. , Xu Haoxing
Published: December 2013

Significance

Phosphatidylinositol polyphosphates (PIPs) are transiently generated at specific membrane subdomains. Changes of PIP levels regulate the trafficking of vesicles and the activity of membrane transport proteins. To directly visualize the intracellular dynamics of phosphatidylinositol 3,5-bisphosphate [PI(3,5)P
2
], a key phosphoinositide in the endosome and lysosome, we have engineered a PI(3,5)P
2
probe by fusing fluorescent proteins directly to the lipid-binding domain of TRPML1, a lysosomal ion channel that is potently and specifically activated by PI(3,5)P
2
. This PI(3,5)P
2
probe binds to PI(3,5)P
2
with biochemical specificity in vitro and responds quickly to changes in the intracellular PI(3,5)P
2
level in living cells. With this biosensor, rapid changes of PI(3,5)P
2
on single vesicle membranes are captured prior to membrane fusion of two vesicles.
Awake reactivation predicts memory in humans
Authors: Staresina Bernhard P. , Alink Arjen , Kriegeskorte Nikolaus , Henson Richard N.
Published: December 2013

Significance

How is new information converted into a memory trace? Here, we used functional neuroimaging to assess what happens to representations of new events after we first experience them. We found that a particular part of the medial temporal lobe, a brain region known to be critical for intact memory, spontaneously reactivates these events even when we are engaged in unrelated activities. Indeed, the extent to which such automatic reactivation occurs seems directly related to later memory performance. This finding shows that we can now study the dynamics of memory processes for specific experiences during the “offline” periods that follow the initial learning phase.
Cultural assemblages show nested structure in humans and chimpanzees but not orangutans
Authors: Kamilar Jason M. , Atkinson Quentin D.
Published: December 2013

Significance

The evolution of culture is well-documented in the human archeological and fossil records, but equivalent data are absent for nonhuman primates. Here, we use modern variation to learn about processes of temporal evolution by measuring nestedness across human and great ape “cultural repertoires.” Cultural assemblages are nested if cultures with a small repertoire of traits tend to comprise a proper subset of traits present in more complex cultures. We find a significant degree of nestedness in human and chimpanzee cultural repertoires, but not for orangutans. Our findings are consistent with a sequential “layering” of culture in humans and chimpanzees only, suggesting that the traits required for sequential cultural evolution first appeared in the last common ancestor of these species.
Biologically derived melanin electrodes in aqueous sodium-ion energy storage devices
Authors: Kim Young Jo , Wu Wei , Chun Sang-Eun , Whitacre Jay F. , Bettinger Christopher J.
Published: December 2013

Significance

Here we present important findings related to biologically derived pigments for potential use as battery electrodes. Namely, we report the synthesis, fabrication, and characterization of melanins as materials for use in aqueous sodium-ion batteries. We demonstrate the use of naturally occurring melanins as active electrode materials in charge storage devices. Furthermore, the performance of melanin anodes is comparable to many commonly available synthetic organic electrode materials. The structure–property relationships that govern the storage capacity in melanin materials were also elucidated. These findings suggest that the unique chemistry and nanostructure in natural melanins increase the charge storage capacity compared with synthetic melanin analogues.
Genetic mapping of adaptation reveals fitness tradeoffs in
Arabidopsis thaliana
Authors: Ågren Jon , Oakley Christopher G. , McKay John K. , Lovell John T. , Schemske Douglas W.
Published: December 2013

Significance

Adaptation to local environmental conditions is common, but the genetic mechanisms of adaptation are poorly known. We produced recombinant inbred lines (RILs) of the model plant
Arabidopsis thaliana
by crossing populations that inhabit drastically different climates in Sweden and Italy, grew the RILs at the parental sites for 3 y, and genetically mapped quantitative trait loci (QTL) for fitness. The results demonstrate that surprisingly few QTL explain much of the adaptive divergence between the two plant populations. Moreover, we find strong evidence for tradeoffs (i.e., adaptation to one environment reduces performance elsewhere). The results shed light on processes governing the evolution of biological diversity and the potential for adaptive evolution in response to environmental change.
Restoration of function after brain damage using a neural prosthesis
Authors: Guggenmos David J. , Azin Meysam , Barbay Scott , Mahnken Jonathan D. , Dunham Caleb , Mohseni Pedram , Nudo Randolph J.
Published: December 2013

Significance

Closed-loop systems, or brain–machine–brain interfaces (BMBIs), have not been widely developed for brain repair. In this study, we targeted spared motor and somatosensory regions of the rat brain after traumatic brain injury for establishment of a functional bridge using a battery-powered microdevice. The results show that by using discriminated action potentials as a trigger for stimulating a distant cortical location, rapid recovery of fine motor skills is facilitated. This study provides strong evidence that BMBIs can be used to bridge damaged neural pathways functionally and promote recovery after brain injury. Although this study is restricted to a rodent model of TBI, it is likely that the approach will also be applicable to other types of acquired brain injuries.
Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors
Authors: Ma Hanhui , Reyes-Gutierrez Pablo , Pederson Thoru
Published: December 2013

Significance

Repetitive DNA sequences such as telomeres and centromeres are, like the chromosomes in which they reside, highly dynamic within the interphase nucleus, moving about by diffusion. Live cell imaging of these specific chromosomal sites has been limited and the approach presented in this study, based on expressed transcription activator-like effector (TALE)-fluorescent proteins, offers new opportunities in basic research on chromosome dynamics. In parallel, the described use of fluorescent TALEs as probes with fixed cells presents advantages over fluorescent in situ hybridization and may find particular applications in clinical and diagnostic settings.
Venting and Reef Fish Survival: Perceptions and Participation Rates among Recreational Anglers in the Northern Gulf of Mexico
Authors: Scyphers Steven B. , Fodrie F. Joel , Hernandez Frank J. , Powers Sean P. , Shipp Robert L.
Published: December 2013

Fisheries scientists, managers, and industry have developed innovative tools and techniques to improve the survival of fishes captured and released in deepwater settings. Venting involves the insertion of a hollow needle to deflate a fish's swim bladder and is among the most widely promoted barotrauma mitigation techniques. However, its efficacy has been the subject of intense debate. In the northern Gulf of Mexico, venting tools are mandatory tackle for offshore reef anglers, but current mandates on usage are being reconsidered. We surveyed recreational and tournament anglers to understand the popularity and perceived effectiveness of venting and identify factors that affect these measures. Our survey results indicate that approximately two-thirds of anglers vent the fish they release offshore and most perceive it to be effective for improving survival rates. Among recreational anglers, we found that primary fishing locale (inshore, offshore) and experience were powerful predictors of perceptions and utilization rates. However, fishing experience did not appear to influence knowledge of proper venting techniques. While further ecological and physiological experimentation is needed to resolve many uncertainties that surround venting, our study demonstrates that angler perceptions and behaviors must also be considered and that aggressive education and outreach programs would be necessary to alter or improve current venting practices.

Received October 12, 2012; accepted July 4, 2013
MHC class II–dependent B cell APC function is required for induction of CNS autoimmunity independent of myelin-specific antibodies
Authors: Molnarfi Nicolas , Schulze-Topphoff Ulf , Weber Martin S. , Patarroyo Juan C. , Prod’homme Thomas , Varrin-Doyer Michel , Shetty Aparna , Linington Christopher , Slavin Anthony J. , Hidalgo Juan , Jenne Dieter E. , Wekerle Hartmut , Sobel Raymond A. , Bernard Claude C.A. , Shlomchik Mark J. , Zamvil Scott S.
Published: December 2013

Whether B cells serve as antigen-presenting cells (APCs) for activation of pathogenic T cells in the multiple sclerosis model experimental autoimmune encephalomyelitis (EAE) is unclear. To evaluate their role as APCs, we engineered mice selectively deficient in MHC II on B cells (B–MHC II−/−), and to distinguish this function from antibody production, we created transgenic (Tg) mice that express the myelin oligodendrocyte glycoprotein (MOG)–specific B cell receptor (BCR; IgHMOG-mem) but cannot secrete antibodies. B–MHC II−/− mice were resistant to EAE induced by recombinant human MOG (rhMOG), a T cell– and B cell–dependent autoantigen, and exhibited diminished Th1 and Th17 responses, suggesting a role for B cell APC function. In comparison, selective B cell IL-6 deficiency reduced EAE susceptibility and Th17 responses alone. Administration of MOG-specific antibodies only partially restored EAE susceptibility in B–MHC II−/− mice. In the absence of antibodies, IgHMOG-mem mice, but not mice expressing a BCR of irrelevant specificity, were fully susceptible to acute rhMOG-induced EAE, also demonstrating the importance of BCR specificity. Spontaneous opticospinal EAE and meningeal follicle–like structures were observed in IgHMOG-mem mice crossed with MOG-specific TCR Tg mice. Thus, B cells provide a critical cellular function in pathogenesis of central nervous system autoimmunity independent of their humoral involvement, findings which may be relevant to B cell–targeted therapies.
Characterization of two different Asf1 histone chaperones with distinct cellular localizations and functions in Trypanosoma brucei
Authors: Pascoalino Bruno , Dindar Gülcin , Vieira-da-Rocha João P. , Machado Carlos Renato , Janzen Christian J. , Schenkman Sergio
Published: December 2013

The anti-silencing function protein 1 (Asf1) is a chaperone that forms a complex with histones H3 and H4 facilitating dimer deposition and removal from chromatin. Most eukaryotes possess two different Asf1 chaperones but their specific functions are still unknown. Trypanosomes, a group of early-diverged eukaryotes, also have two, but more divergent Asf1 paralogs than Asf1 of higher eukaryotes. To unravel possible different functions, we characterized the two Asf1 proteins in Trypanosoma brucei. Asf1A is mainly localized in the cytosol but translocates to the nucleus in S phase. In contrast, Asf1B is predominantly localized in the nucleus, as described for other organisms. Cytosolic Asf1 knockdown results in accumulation of cells in early S phase of the cell cycle, whereas nuclear Asf1 knockdown arrests cells in S/G2 phase. Overexpression of cytosolic Asf1 increases the levels of histone H3 and H4 acetylation. In contrast to cytosolic Asf1, overexpression of nuclear Asf1 causes less pronounced growth defects in parasites exposed to genotoxic agents, prompting a function in chromatin remodeling in response to DNA damage. Only the cytosolic Asf1 interacts with recombinant H3/H4 dimers in vitro. These findings denote the early appearance in evolution of distinguishable functions for the two Asf1 chaperons in trypanosomes.
Causal inference of gene regulation with subnetwork assembly from genetical genomics data
Authors: Peng Chien-Hua , Jiang Yi-Zhi , Tai An-Shun , Liu Chun-Bin , Peng Shih-Chi , Liao Chun-Ta , Yen Tzu-Chen , Hsieh Wen-Ping
Published: December 2013

Deciphering the causal networks of gene interactions is critical for identifying disease pathways and disease-causing genes. We introduce a method to reconstruct causal networks based on exploring phenotype-specific modules in the human interactome and including the expression quantitative trait loci (eQTLs) that underlie the joint expression variation of each module. Closely associated eQTLs help anchor the orientation of the network. To overcome the inherent computational complexity of causal network reconstruction, we first deduce the local causality of individual subnetworks using the selected eQTLs and module transcripts. These subnetworks are then integrated to infer a global causal network using a random-field ranking method, which was motivated by animal sociology. We demonstrate how effectively the inferred causality restores the regulatory structure of the networks that mediate lymph node metastasis in oral cancer. Network rewiring clearly characterizes the dynamic regulatory systems of distinct disease states. This study is the first to associate an RXRB-causal network with increased risks of nodal metastasis, tumor relapse, distant metastases and poor survival for oral cancer. Thus, identifying crucial upstream drivers of a signal cascade can facilitate the discovery of potential biomarkers and effective therapeutic targets.
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data
Authors: Ding Jun , Hu Haiyan , Li Xiaoman
Published: December 2013

The identification of transcription factor binding motifs is important for the study of gene transcriptional regulation. The chromatin immunoprecipitation (ChIP), followed by massive parallel sequencing (ChIP-seq) experiments, provides an unprecedented opportunity to discover binding motifs. Computational methods have been developed to identify motifs from ChIP-seq data, while at the same time encountering several problems. For example, existing methods are often not scalable to the large number of sequences obtained from ChIP-seq peak regions. Some methods heavily rely on well-annotated motifs even though the number of known motifs is limited. To simplify the problem, de novo motif discovery methods often neglect underrepresented motifs in ChIP-seq peak regions. To address these issues, we developed a novel approach called SIOMICS to de novo discover motifs from ChIP-seq data. Tested on 13 ChIP-seq data sets, SIOMICS identified motifs of many known and new cofactors. Tested on 13 simulated random data sets, SIOMICS discovered no motif in any data set. Compared with two recently developed methods for motif discovery, SIOMICS shows advantages in terms of speed, the number of known cofactor motifs predicted in experimental data sets and the number of false motifs predicted in random data sets. The SIOMICS software is freely available at http://eecs.ucf.edu/∼xiaoman/SIOMICS/SIOMICS.html.
Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates
Authors: Walia Jeewan Jyot , Willemsen Anouk , Elci Eminur , Caglayan Kadriye , Falk Bryce W. , Rubio Luis
Published: December 2013

Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.
Mechanisms of Acupuncture–Electroacupuncture on Persistent Pain
Authors: Zhang Ruixin , Lao Lixing , Ren Ke , Berman Brian M.
Published: December 2013

In the last decade, preclinical investigations of electroacupuncture mechanisms on persistent tissue injury (inflammatory), nerve injury (neuropathic), cancer, and visceral pain have increased. These studies show that electroacupuncture activates the nervous system differently in health than in pain conditions, alleviates both sensory and affective inflammatory pain, and inhibits inflammatory and neuropathic pain more effectively at 2 to 10 Hz than at 100 Hz. Electroacupuncture blocks pain by activating a variety of bioactive chemicals through peripheral, spinal, and supraspinal mechanisms. These include opioids, which desensitize peripheral nociceptors and reduce proinflammatory cytokines peripherally and in the spinal cord, and serotonin and norepinephrine, which decrease spinal N-methyl-d-aspartate receptor subunit GluN1 phosphorylation. Additional studies suggest that electroacupuncture, when combined with low dosages of conventional analgesics, provides effective pain management which can forestall the side effects of often-debilitating pharmaceuticals.
Modelling reading development through phonological decoding and self-teaching: implications for dyslexia
Authors: Ziegler Johannes C. , Perry Conrad , Zorzi Marco
Published: December 2013

The most influential theory of learning to read is based on the idea that children rely on phonological decoding skills to learn novel words. According to the self-teaching hypothesis, each successful decoding encounter with an unfamiliar word provides an opportunity to acquire word-specific orthographic information that is the foundation of skilled word recognition. Therefore, phonological decoding acts as a self-teaching mechanism or ‘built-in teacher’. However, all previous connectionist models have learned the task of reading aloud through exposure to a very large corpus of spelling–sound pairs, where an ‘external’ teacher supplies the pronunciation of all words that should be learnt. Such a supervised training regimen is highly implausible. Here, we implement and test the developmentally plausible phonological decoding self-teaching hypothesis in the context of the connectionist dual process model. In a series of simulations, we provide a proof of concept that this mechanism works. The model was able to acquire word-specific orthographic representations for more than 25 000 words even though it started with only a small number of grapheme–phoneme correspondences. We then show how visual and phoneme deficits that are present at the outset of reading development can cause dyslexia in the course of reading development.