bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strand-Exchange Nucleic Acid Circuitry with Enhanced Thermo-and Structure- Buffering Abilities Turns Gene Diagnostics Ultra-Reliable and Environmental Compatible
Authors: Zhu Zhentong , Tang Yidan , Jiang Yu Sherry , Bhadra Sanchita , Du Yan , Ellington Andrew D. , Li Bingling 
Published: November 2016

AbstractCatalytic hairpin assembly (CHA) is one of the most promising nucleic acid amplification circuits based on toehold-mediated strand exchange reactions. But its performance is usually ruined by fluctuated environmental temperatures or unexpected self-structures existing in most real-world targets. Here we present an amide-assistant mechanism that successfully reduces the prevalence of these problems for CHA and maximizes its thermo- and structure- buffering abilities. Such an organic amide-promoted CHA (shortened as OHT-CHA) can unprecedentedly amplify through 4 °C to 60 °C without rebuilding sequences or concerning target complexity. We are then for the first time able to employ it as a direct and universal signal booster for loop mediated isothermal reaction (LAMP). LAMP is one of the most promising point-of-care (POC) gene amplifiers, but has been hard to detect precisely due to structured products and haunted off-target amplicons. OHT-CHA guarantees a significant and reliable signal for LAMP reaction amplified from as little as 10−19 M virus gene. And one single set of OHT-CHA is qualified to any detection requirement, either in real-time at LAMP running temperature (~60 °C), or at end-point on a POC photon counter only holding environmental temperatures fluctuating between 4 °C to 42 °C.
Retargeted Foamy Virus Vectors Integrate Less Frequently Near Proto-oncogenes
Authors: Hocum Jonah D. , Linde Ian , Rae Dustin T. , Collins Casey P. , Matern Lindsay K. , Trobridge Grant D. 
Published: November 2016

AbstractRetroviral gene therapy offers immense potential to treat many genetic diseases and has already shown efficacy in clinical trials. However, retroviral vector mediated genotoxicity remains a major challenge and clinically relevant approaches to reduce integration near genes and proto-oncogenes are needed. Foamy retroviral vectors have several advantages over gammaretroviral and lentiviral vectors including a potentially safer integration profile and a lower propensity to activate nearby genes. Here we successfully retargeted foamy retroviral vectors away from genes and into satellite regions enriched for trimethylated histone H3 at lysine 9 by modifying the foamy virus Gag and Pol proteins. Retargeted foamy retroviral vectors integrated near genes and proto-oncogenes less often (p < 0.001) than controls. Importantly, retargeted foamy retroviral vectors can be produced at high, clinically relevant titers (>107 transducing units/ml), and unlike other reported retargeting approaches engineered target cells are not needed to achieve retargeting. As proof of principle for use in the clinic we show efficient transduction and retargeting in human cord blood CD34+ cells. The modified Gag and Pol helper constructs we describe will allow any investigator to simply use these helper plasmids during vector production to retarget therapeutic foamy retroviral vectors.
Preliminary Investigation of the Passively Evoked N400 as a Tool for Estimating Speech-in-Noise Thresholds
Authors: Jamison Caroline , Aiken Steve J. , Kiefte Michael , Newman Aaron J. , Bance Manohar , Sculthorpe-Petley Lauren 
Published: November 2016

PurposeSpeech-in-noise testing relies on a number of factors beyond the auditory system, such as cognitive function, compliance, and motor function. It may be possible to avoid these limitations by using electroencephalography. The present study explored this possibility using the N400.MethodEleven adults with typical hearing heard high-constraint sentences with congruent and incongruent terminal words in the presence of speech-shaped noise. Participants ignored all auditory stimulation and watched a video. The signal-to-noise ratio (SNR) was varied around each participant's behavioral threshold during electroencephalography recording. Speech was also heard in quiet.ResultsThe amplitude of the N400 effect exhibited a nonlinear relationship with SNR. In the presence of background noise, amplitude decreased from high (+4 dB) to low (+1 dB) SNR but increased dramatically at threshold before decreasing again at subthreshold SNR (−2 dB).ConclusionsThe SNR of speech in noise modulates the amplitude of the N400 effect to semantic anomalies in a nonlinear fashion. These results are the first to demonstrate modulation of the passively evoked N400 by SNR in speech-shaped noise and represent a first step toward the end goal of developing an N400-based physiological metric for speech-in-noise testing.
Robust parameter estimation for dynamical systems from outlier-corrupted data
Authors: Maier Corinna , Loos Carolin , Hasenauer Jan 
Published: November 2016

Abstract

Motivation
Dynamics of cellular processes are often studied using mechanistic mathematical models. These models possess unknown parameters which are generally estimated from experimental data assuming normally distributed measurement noise. Outlier corruption of datasets often cannot be avoided. These outliers may distort the parameter estimates, resulting in incorrect model predictions. Robust parameter estimation methods are required which provide reliable parameter estimates in the presence of outliers.

Results
In this manuscript, we propose and evaluate methods for estimating the parameters of ordinary differential equation models from outlier-corrupted data. As alternatives to the normal distribution as noise distribution, we consider the Laplace, the Huber, the Cauchy and the Student’s t distribution. We assess accuracy, robustness and computational efficiency of estimators using these different distribution assumptions. To this end, we consider artificial data of a conversion process, as well as published experimental data for Epo-induced JAK/STAT signaling. We study how well the methods can compensate and discover artificially introduced outliers. Our evaluation reveals that using alternative distributions improves the robustness of parameter estimates.

Availability and Implementation
The MATLAB implementation of the likelihood functions using the distribution assumptions is available at Bioinformatics online.

Supplementary information
Supplementary material are available at Bioinformatics online.
Timing of Occurrence of Claviceps purpurea Ascospores in Northeast Oregon
Authors: Alderman Stephen C. , Walenta Darrin L. , Hamm Philip B. 
Published: November 2016

Ergot, caused by Claviceps purpurea, is an important floral disease of grasses, characterized by sclerotium formation within the host flowers. To determine whether annual variation in ergot severity in Kentucky bluegrass is a result of ascospore density and/or timing of ascospore occurrence, Burkard 7-day volumetric spores traps were used to monitor ascospores of C. purpurea in each of two Kentucky bluegrass fields in the Grand Ronde Valley in northeastern Oregon between mid-May and late June, 2008-2010. Ascospores were typically trapped between midnight and 6:00 a.m. In 2008 and 2010, most ascospores were released prior to flowering in Kentucky bluegrass, corresponding to no observed ergot in 2008 and a low level of ergot in 2010. In 2009, ascospore release and pollination coincided, but few airborne ascospores were present, resulting in a low level of ergot. Similar ergot levels were observed in fungicide trials, suggesting that fungicides for ergot control were unnecessary. In years when there are few ascospores during flowering in Kentucky bluegrass, a reduction of up to two fungicide applications may be possible. Accepted for publication 2 November 2010. Published 23 November 2010.
Evaluating the Precision of Auditory Sensory Memory as an Index of Intrusion in Tinnitus
Authors: Barrett Doug J. K. , Pilling Michael 
Published: November 2016

Objectives:
The purpose of this study was to investigate the potential of measures of auditory short-term memory (ASTM) to provide a clinical measure of intrusion in tinnitus.

Design:
Response functions for six normal listeners on a delayed pitch discrimination task were contrasted in three conditions designed to manipulate attention in the presence and absence of simulated tinnitus: (1) no-tinnitus, (2) ignore-tinnitus, and (3) attend-tinnitus.

Results:
Delayed pitch discrimination functions were more variable in the presence of simulated tinnitus when listeners were asked to divide attention between the primary task and the amplitude of the tinnitus tone.

Conclusions:
Changes in the variability of auditory short-term memory may provide a novel means of quantifying the level of intrusion associated with the tinnitus percept during listening.
RETINAL VASCULITIS ASSOCIATED WITH NEUROMYELITIS OPTICA
Authors: Mikhail Mikel , Khan Ayesha 
Published: November 2016

Purpose:To report a case of retinal vasculitis in a patient with neuromyelitis optica.Methods:Clinical case report, imaging was obtained with photographs, fluorescein angiography, spectral domain optical coherence tomography, and magnetic resonance imaging.Results:The aforementioned patient presented with urinary incontinence and spastic paraparesis. She was found to have a transverse myelitis on magnetic resonance imaging and positive anti–aquaporin-4 (AQP4-Ab) testing. She had no associated visual symptoms. Examination revealed a retinal vasculitis. There have been no previous reports of retinal vasculitis associated with neuromyelitis optica or neuromyelitis optica spectrum disorder.Conclusion:Retinal vasculitis can be associated with neuromyelitis optica.
ELECTRONEGATIVE ELECTRORETINOGRAM IN ACHROMATOPSIA
Authors: Schallhorn Craig S. , Granet David B. , Ferreyra Henry A. 
Published: November 2016

Purpose:
To report novel electroretinographic findings in a genetically confirmed case of achromatopsia.

Methods:
A patient with a history of childhood nystagmus, photoaversion, and absent color vision was examined. Electroretinography and fundus examination were performed under anesthesia at the time of corrective surgery for nystagmus. Genomic DNA isolated from peripheral blood was directly sequenced for variations in the CNGA3 and CNGB3 genes.

Results:
Ophthalmoscopic examination revealed no distinct abnormalities. Electroretinography obtained under anesthesia at age three years revealed absent photopic responses. The dark-adapted combined responses had reduced b-wave amplitudes resulting in an electronegative configuration. Genetic testing revealed two heterozygous sequence variations present in the coding sequence of the CNGA3 gene (Arg223Trp and Pro372Ser), which have been previously described in the setting of achromatopsia. Sequencing of the patient's parents confirmed that these two variations lie on separate alleles.

Conclusion:
Novel electroretinography findings in a patient with genetically confirmed achromatopsia are reported. The electronegative configuration in this clinical setting is of unclear etiology; however, it may suggest some component of inner retinal dysfunction.
Clinical Study of an Online Tool for Standardizing Hospital Care
Authors: Burgess Mary J. , Enzler Mark J. , Kashiwagi Deanne T. , Selby Andi J. , Sohail M. Rizwan , Daniels Paul R. , Lahr Brian D. , Lloyd Farrell , Baddour Larry D. 
Published: November 2016

Abstract:
We assessed if use of an online clinical decision support tool improved standardization and quality of care in hospitalized patients with lower extremity cellulitis (LEC). This was a 14-month preintervention and postintervention study of 85 LEC admissions. There was significantly higher usage of the online LEC care process model (CPM) in the postintervention phase (p < .001). There was a trend toward higher rates of appropriate antibiotic regimen in the postintervention group both initially and at discharge (p = .063 for both). A sensitivity analysis of CPM users versus nonusers demonstrated a significantly higher rate of appropriate initial antibiotics prescribed when the CPM was used (p < .001). Use of this online CPM was associated with improved standardization, as demonstrated by increased ordering of an appropriate initial antibiotic regimen for hospitalized patients with LEC.
Tissue specificity ofin vitrodrug sensitivity
Authors: Yao Fupan , Tonekaboni Seyed Ali Madani , Safikhani Zhaleh , Smirnov Petr , El-Hachem Nehme , Freeman Mark , Manem Venkata Satya Kumar , Haibe-Kains Benjamin 
Published: November 2016

ABSTRACTResearch in oncology traditionally focuses on specific tissue type from which the cancer develops. However, advances in high-throughput molecular profiling technologies have enabled the comprehensive characterization of molecular aberrations in multiple cancer types. It was hoped that these large-scale datasets would provide the foundation for a paradigm shift in oncology which would see tumors being classified by their molecular profiles rather than tissue types, but tumors with similar genomic aberrations may respond differently to targeted therapies depending on their tissue of origin. There is therefore a need to reassess the potential association between pharmacological response and tissue of origin for therapeutic drugs, and to test how these associations translate from preclinical to clinical settings.In this paper, we investigate the tissue specificity of drug sensitivities in large-scale pharmacological studies and compare these associations to those found in clinical trial descriptions. Our meta-analysis of the four largestin vitrodrug screening datasets indicates that tissue of origin is strongly associated with drug response. We identify novel tissue-drug associations, which may present exciting new avenues for drug repurposing. One caveat is that the vast majority of the significant associations found in preclinical settings do not concur with clinical observations. Accordingly, our results call for more testing to find the root cause of the discrepancies between preclinical and clinical observations.
Robustness of firm-specific and macroeconomic determinants of exploration investments
Authors: Eldomiaty Tarek , Lotfy Ibrahim Safwat , Rashwan Mohamed , Bahaa El Din Mohamed 
Published: November 2016

PurposeThe uncertainty that surrounds oil and gas exploration environments call for an examination at different angles. In terms of robustness, the purpose of this paper is to focus on three performance measurements: the amount of exploration investments, the growth rate of exploration investments, and the value at risk (VaR) of exploration investments.Design/methodology/approachThe study utilizes the properties of discriminant analysis for deriving Z-score models that can be used for monitoring firms’ performance. A cointegration analysis is utilized as well in order to examine the level of cointegration between predictors of each performance measure. The sample includes annual data for 41 firms (local and multinational) working in the oil and gas industry in Egypt for the period 2009-2014.FindingsThe results show that amount and growth of exploration investment are quite robust performance measures in the oil and gas industry; VaR of exploration investment is sporadic as it firm-specific; and GDP, capital expenditure and operating expenditure are quite relevant for managing and monitoring growth of exploration investments.Originality/valueThe study offers robust evidence that amount and growth of exploration investment are quiet relevant for measuring firm performance in the oil and gas industry.
Job resources, engagement, and proactivity: a moderated mediation model
Authors: Maden-Eyiusta Ceyda 
Published: November 2016

PurposeThe purpose of this paper is to investigate the mediating impact of work engagement on the relationship between three developmental job resources (i.e. autonomy, task variety, and feedback) and proactive work behaviors. It also attempted to explore the moderating role of job fit (demands-abilities (D-A) fit and needs-supplies (N-S) fit) in the proposed model.Design/methodology/approachData were collected from 225 employees in 20 small and medium-size enterprises in Istanbul, Turkey. Hypotheses were tested using hierarchical multiple regressions and hierarchical moderated regressions.FindingsIt was found that engagement mediated the relationships between job autonomy, task variety, and proactive behaviors. Results also revealed that the relationships between autonomy, task variety, and engagement were positive and significant only for the employees with low D-A fit while the positive impact of engagement on proactive behaviors existed only for those employees with high N-S fit. The conditional indirect impact of job resources on proactive behaviors was strongest when the D-A fit was low and the N-S fit was high while this effect was non-significant when the D-A fit was high and the N-S fit was (either) low or high.Research limitations/implicationsThe generalizability of the findings is limited. Moreover, as the data are cross-sectional, it is not possible to derive causal inferences about the hypothesized relationships.Practical implicationsOrganizations should provide their employees with more autonomy and task variety to enhance their engagement and proactivity. Moreover, organizations need to consider their employees’ level of job fit when they provide certain job resources.Originality/valueThis study tests the mediating role of engagement on the relationships between three developmental job resources and proactive behaviors. It also sheds light on the moderating role of job fit in the proposed mediation model.
Silence as a mediator between organizational factors and stress
Authors: Dedahanov Alisher Tohirovich , Lee Do Hyung , Rhee Jaehoon 
Published: November 2016

PurposeThe purpose of this paper is to investigate the mediating role of silence as a link between punishment, communication opportunities and stress.Design/methodology/approachThe authors conducted a survey among 1,015 highly skilled employees of South Korean companies using a self-administered instrument. In total, 748 questionnaires were received from the 1,015 participants. Of these, 61 questionnaires were incomplete and were discarded; the remaining 687 questionnaires were used in the analysis.FindingsThe results revealed that punishment and communication opportunities are significantly associated with silence. Silence showed a positive relationship with stress, and it mediates the relationship between punishment and stress. Meanwhile, findings indicate that silence does not mediate the link between communication opportunities and stress.Research limitations/implicationsThis study investigates the unitary construct of silence. Therefore, the authors suggest future researchers examine the other forms of silence such as multidimensional construct of silence that focuses on the motives of individuals to be silent.Practical implicationsThe study highlights the importance of establishing organizational ombudsman system, grievance procedures and employee management meetings to mitigate silence behavior. Moreover, the authors recommended management demonstrates their interest in shared information to avoid employee silence.Originality/valueThis study is the first to explore the mediating role of silence on the relationship between punishment and stress.
Conceptualizing task affordance in online crowdsourcing context
Authors: Zhao Yuxiang (Chris) , Zhu Qinghua 
Published: November 2016

PurposeThe purpose of this paper is to present a new concept – task affordance in crowdsourcing context, and build it as a theoretical lens to help the authors reconfigure the artifacts and process in task-oriented crowdsourcing projects. The paper differs from previous studies by focusing on the relationships between the task artifacts, systems and goal-directed actors in crowdsourcing process rather than on the pure examination of task properties.Design/methodology/approachAn operational definition of task affordance was proposed and a pseudo-entity-relationship model based approach was employed to portrait the task affordance in online crowdsourcing context. Furthermore, the authors developed a typology of task affordance and decomposed the concept into five dimensions, namely, design affordance, presentation affordance, assignment affordance, task-platform fit affordance, and task-worker fit affordance. A preliminary analysis of task affordances across various crowdsourcing categories was also conducted to validate the proposed typological framework.FindingsThe findings show that the task affordances have varying degree and extend among the diverse crowdsourcing categories. For instance, task design affordances seem to be low in the crowd processing and crowd rating cases compared with that in the crowd solving and crowd creation cases. For another example, in terms of the task presentation affordance, crowd rating cases need the lowest affordance while the crowd creation cases need the highest affordance. Therefore, the authors would like to emphasize that the successful adoption, implementation, and design of the task-oriented crowdsourcing owes to the careful examination of the relationships among the actors, artifacts, and environment of the crowdsourcing projects.Originality/valueTo the authors’ best knowledge, this paper is the first study on conceptualizing the task affordance in online crowdsourcing context. The study contributes to the academic literature on a comprehensive overview of task-related studies in crowdsourcing, which are scattered in several information related fields. Furthermore, this research contributes directly to the area of information science and technology due to a common interest in studying the environments and contexts in which people, information and technology interact and interplay. Practically, this study may yield some implications for the requester and platform operator when designing the relevant tasks or developing the specific crowdsourcing platform.
Computational modeling of Weibo user influence based on information interactive network
Authors: Yu Dingguo , Chen Nan , Ran Xu 
Published: November 2016

Purpose
With the development and application of mobile internet access, social media represented by Weibo, WeChat, etc. has become the main channel for information release and sharing. High-impact users in social networks are key factors stimulating the large-scale propagation of information within social networks. User influence is usually related to the user’s attention rate, activity level, and message content. The paper aims to discuss these issues.

Design/methodology/approach
In this paper, the authors focused on Sina Weibo users, centered on users’ behavior and interactive information, and formulated a weighted interactive information network model, then present a novel computational model for Weibo user influence, which combined multiple indexes such as the user’s attention rate, activity level, and message content influence, etc., the model incorporated the time dimension, through the calculation of users’ attribute influence and interactive influence, to comprehensively measure the user influence of Sina Weibo users.

Findings
Compared with other models, the model reflected the dynamics and timeliness of the user influence in a more accurate way. Extensive experiments are conducted on the real-world data set, and the results validate the performance of the approach, and demonstrate the effectiveness of the dynamics and timeliness. Due to the similarity in platform architecture and user behavior between Sina Weibo and Twitter, the calculation model is also applicable to Twitter.

Originality/value
This paper presents a novel computational model for Weibo user influence, which combined multiple indexes such as the user’s attention rate, activity level, and message content influence, etc.