bluuebunny/crossref_metadata_2025_split huggingface dataset:
Requirements for coregistration accuracy in on-scalp MEG
Authors: Zetter Rasmus , Iivanainen Joonas , Stenroos Matti , Parkkonen Lauri 
Published: August 2017

AbstractRecent advances in magnetic sensing has made on-scalp magnetoencephalography (MEG) possible. In particular, optically-pumped magnetometers (OPMs) have reached sensitivity levels that enable their use in MEG. In contrast to the SQUID sensors used in current MEG systems, OPMs do not require cryogenic cooling and can thus be placed within millimetres from the head, enabling the construction of sensor arrays that conform to the shape of an individual’s head. To properly estimate the location of neural sources within the brain, one must accurately know the position and orientation of sensors in relation to the head. With the adaptable on-scalp MEG sensor arrays, this coregistration becomes more challenging than in current SQUID-based MEG systems that use rigid sensor arrays.Here, we used simulations to quantify how accurately one needs to know the position and orientation of sensors in an on-scalp MEG system. The effects that different types of localisation errors have on forward modelling and source estimates obtained by minimum-norm estimation, dipole fitting, and beamforming are detailed.We found that sensor position errors generally have a larger effect than orientation errors and that these errors affect the localisation accuracy of superficial sources the most. To obtain similar or higher accuracy than with current SQUID-based MEG systems, RMS sensor position and orientation errors should be < 4 mm and < 10°, respectively.
Large-scale determination and characterization of cell type-specific regulatory elements in the human genome
Authors: Wang Can , Zhang Shihua 
Published: August 2017

AbstractHistone modifications have been widely elucidated to play vital roles in gene regulation and cell identity. The Roadmap Epigenomics Consortium generated a reference catalogue of several key histone modifications across >100s of human cell types and tissues. Decoding these epigenomes into functional regulatory elements is a challenging task in computational biology. To this end, we adopted a differential chromatin modification analysis framework to comprehensively determine and characterize cell type-specific regulatory elements (CSREs) and their histone modification codes in the human epigenomes of five histone modifications across 127 tissues or cell types. The CSREs show significant relevance with cell type-specific biological functions and diseases and cell identity. Clustering of CSREs with their specificity signals reveals diverse histone codes, demonstrating the diversity of functional roles of CSREs within the same cell or tissue. Last but not least, dynamics of CSREs from close cell types or tissues can give a detailed view of developmental processes such as normal tissue development and cancer occurrence.
Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function
Authors: Benton Mary Lauren , Talipineni Sai Charan , Kostka Dennis , Capra John A. 
Published: August 2017

ABSTRACTNon-coding gene regulatory enhancers are essential to transcription in mammalian cells. As a result, a large variety of experimental and computational strategies have been developed to identify cis-regulatory enhancer sequences. In practice, most studies consider enhancers identified by only a single method, and the concordance of enhancers identified by different methods has not been comprehensively evaluated. Here, we assess the similarities of enhancer sets identified by ten representative strategies in four biological contexts and evaluate the robustness of downstream conclusions to the choice of identification strategy. All pairs of enhancer sets we evaluated overlap significantly more than expected by chance; however, we also found significant dissimilarity between enhancer sets in their genomic characteristics, evolutionary conservation, and association with functional loci within each context. We find most regions identified as enhancers are supported by only one method. The disagreement is sufficient to influence interpretation of GWAS SNPs and eQTL, and to lead to disparate conclusions about enhancer biology and disease mechanisms. We also find only limited evidence that regions identified by multiple enhancer identification methods are better candidates than those identified by a single method. Our results highlight the inherent complexity of enhancer biology and argue that current approaches have yet to adequately account for enhancer diversity. As a result, we cannot recommend the use of any single enhancer identification strategy in isolation. To facilitate assessment of enhancer diversity on studies’ conclusions, we developed creDB, a database of enhancer annotations designed to integrate into bioinformatics workflows. While our findings highlight a major challenge to mapping the genetic architecture of complex disease and interpreting regulatory variants found in patient genomes, a systematic understanding of similarities and differences in enhancer identification methodology will ultimately enable robust inferences about gene regulatory sequences.
Gaussian decomposition of high-resolution melt curve derivatives for measuring genome-editing efficiency
Authors: Zaboikin Michail , Freter Carl , Srinivasakumar Narasimhachar 
Published: August 2017

AbstractWe describe a method for measuring genome editing efficiency fromin silicoanalysis of high-resolution melt curve data. The melt curve data derived from amplicons of genome-edited or unmodified target sites were processed to remove the background fluorescent signal emanating from free fluorophore and then corrected for temperature-dependent quenching of fluorescence of double-stranded DNA-bound fluorophore. Corrected data were normalized and numerically differentiated to obtain the first derivatives of the melt curves. These were then mathematically modeled as a sum or superposition of minimal number of Gaussian components. Using Gaussian parameters determined by modeling of melt curve derivatives of unedited samples, we were able to model melt curve derivatives from genetically altered target sites where the mutant population could be accommodated using an additional Gaussian component. From this, the proportion contributed by the mutant component in the target region amplicon could be accurately determined. Mutant component computations compared well with the mutant frequency determination from next generation sequencing data. The results were also consistent with our earlier studies that used difference curve areas from high-resolution melt curves for determining the efficiency of genome-editing reagents. The advantage of the described method is that it does not require calibration curves to estimate proportion of mutants in amplicons of genome-edited target sites.
Towards a reliable, automated method of individual alpha frequency (IAF) quantification
Authors: Corcoran Andrew W. , Alday Phillip M. , Schlesewsky Matthias , Bornkessel-Schlesewsky Ina 
Published: August 2017

AbstractIndividual alpha frequency (IAF) is a promising electrophysiological marker of interindividual differences in cognitive function. IAF has been linked with trait-like differences in information processing and general intelligence, and provides an empirical basis for the definition of individualised frequency bands. Despite its widespread application, however, there is little consensus on the optimal method for estimating IAF, and many common approaches are prone to bias and inconsistency. Here, we describe an automated strategy for deriving two of the most prevalent IAF estimators in the literature: peak alpha frequency (PAF) and centre of gravity (CoG). These indices are calculated from resting-state power spectra that have been smoothed using a Savitzky-Golay filter (SGF). We evaluate the performance characteristics of this analysis procedure in both empirical and simulated EEG datasets. Applying the SGF technique to resting-state data fromn= 63 healthy adults furnished 61 PAF, and 62 CoG estimates. The statistical properties of these estimates were consistent with previous reports. Simulation analyses revealed that the SGF routine was able to reliably extract target alpha components, even under relatively noisy spectral conditions. The routine consistently outperformed a simpler method of automated peak detection that did not involve spectral smoothing. The SGF technique is fast, open-source, and available in two popular programming languages (MATLAB and Python), and thus can easily be integrated within the most popular M/EEG toolsets (EEGLAB, FieldTrip and MNE-Python). As such, it affords a convenient tool for improving the reliability and replicability of future IAF-related research.
Evolution of mechanisms that control mating inDrosophilamales
Authors: Ahmed Osama M. , Avila-Herrera Aram , Tun Khin May , Serpa Paula H. , Peng Justin , Parthasarathy Srinivas , Knapp Jon-Michael , Stern David L. , Davis Graeme W. , Pollard Katherine S. , Shah Nirao M. 
Published: August 2017

SUMMARYGenetically wired neural mechanisms inhibit mating between species because even naive animals rarely mate with other species. These mechanisms can evolve through changes in expression or function of key genes in specific sensory pathways or central circuits. Gr32a is a gustatory chemoreceptor that, inD. melanogaster, is essential to inhibit interspecies courtship and sense quinine. Similar toD. melanogaster,D. simulansGr32a is expressed in foreleg tarsi, sensorimotor appendages that inhibit interspecies courtship in both species, and it is required to sense quinine. Nevertheless, Gr32a is not required to inhibit interspecies mating byD. simulansmales. However, and similar to its function inD. melanogaster, Ppk25, a member of the Pickpocket family, promotes conspecific courtship inD. simulans. Taken together, we have identified shared as well as distinct evolutionary solutions to chemosensory processing of tastants as well as cues that inhibit or promote courtship in two closely relatedDrosophilaspecies.
Application of MCDM-based TOPSIS method for the selection of optimal process parameter in turning of pure titanium
Authors: Khan Akhtar , Maity Kalipada 
Published: August 2017

Purpose
The purpose of this paper is to explore a multi-criteria decision-making (MCDM) methodology to determine an optimal combination of process parameters that is capable of generating favorable dimensional accuracy and product quality during turning of commercially pure titanium (CP-Ti) grade 2.

Design/methodology/approach
The present paper recommends an optimal combination of cutting parameters with an aim to minimize the cutting force (Fc), surface roughness (Ra), machining temperature (Tm) and to maximize the material removal rate (MRR) after turning of CP-Ti grade 2. This was achieved by the simultaneous optimization of the aforesaid output characteristics (i.e. Fc, Ra, Tm, and MRR) using the MCDM-based TOPSIS method. Taguchi’s L9 orthogonal array was used for conducting the experiments. The output responses (cutting force: Fc, surface roughness: Ra, machining temperature: Tm and MRR) were integrated together and presented in terms of a single signal-to-noise ratio using the Taguchi method.

Findings
The results of the proposed methodology depict that the higher MRR with desirable surface quality and the lower cutting force and machining temperature were observed at a combination of cutting variables as follows: cutting speed of 105 m/min, feed rate of 0.12 mm/rev and depth of cut of 0.5 mm. The analysis of variance test was conducted to evaluate the significance level of process parameters. It is evident from the aforesaid test that the depth of cut was the most significant process parameter followed by cutting speed.

Originality/value
The selection of an optimal parametric combination during the machining operation is becoming more challenging as the decision maker has to consider a set of distinct quality characteristics simultaneously. This situation necessitates an efficient decision-making technique to be used during the machining operation. From the past literature, it is noticed that only a few works were reported on the multi-objective optimization of turning parameters using the TOPSIS method so far. Thus, the proposed methodology can help the decision maker and researchers to optimize the multi-objective turning problems effectively in combination with a desirable accuracy.
Agile manufacturing: a systematic review of literature and implications for future research
Authors: Potdar Pavan Kumar , Routroy Srikanta , Behera Astajyoti 
Published: August 2017

Purpose
Agile manufacturing (AM) has evolved as a revolutionary way of manufacturing the products while managing the uncertainties, product introduction time, responsiveness, innovation, superior quality, etc. along the supply chain to satisfy the ever increasing customer demand and to maximize the profit. The purpose of this paper is to critically analyze the literature related to various dimensions of AM and to report the findings.

Design/methodology/approach
This paper presents the reviews of 300 scholarly articles from 1993 to 2016 by various researchers and practitioners on AM collected from different sources, i.e. Google Scholar and ResearchGate. The information related to AM is also captured during industrial visits to different Indian manufacturing plants.

Findings
AM definitions are reported along divergent scopes and objectives in the literature. The researchers have given importance on performance measurement and process analysis through empirical and descriptive analysis whereas its implementation issues are neglected. It is also observed that the effort made on AM is significant for manufacturing industries which is overlooked in service industries.

Practical implications
This literature review has identified many research gaps in AM which were not paid attention before. Researchers can address these research gaps for strengthening the AM implementation.

Originality/value
In total, 300 research papers are reviewed and analyzed to capture the various aspects of AM and its related issues but not restricted to research methodologies, author profiles, types of industries, tools/techniques/methodology used, etc.
Does foreign direct investment spillover total factor productivity growth? A study of Indian drugs and pharmaceutical industry
Authors: Arora Nitin , Lohani Preeti 
Published: August 2017

PurposeForeign firms have certain advantages which may spillover to domestic firms in the form of improvements in total factor productivity (TFP) growth. The purpose of this paper is to empirically observe the presence of TFP spillovers of foreign direct investment (FDI) to domestic firms through analyzing source of TFP growth in Indian drugs and pharmaceutical industry.Design/methodology/approachThis paper examines the sources of TFP spillovers of FDI in Indian drugs and pharmaceutical industry over the period 1999 to 2014. The data of 304 firms has been used for estimation of the growth rates of TFP and its sources under stochastic frontier analyses based Malmquist productivity index framework. For frontier estimation, the Wang and Ho (2010) model has been executed using translog form of production function.FindingsThe results show that there exists significant TFP spillover effect from the presence of foreign equity in drugs and pharmaceutical industry of India. The results also show that the major source of TFP fluctuations in the said industry is managerial efficiency that has been significantly affected by FDI spillover variables. In sum, the phenomenon of significant Intra-industry (horizontal) efficiency led productivity spillovers of FDI found valid in case of Indian drugs and pharmaceutical industry.Research limitations/implicationsThe number of foreign firms is very less to imitate the significant impact of foreign investment on TFP growth of Indian pharmaceutical industry at aggregated level; and the Wang and Ho (2010) model is failing to capture direct impact of FDI on technological change under Malmquist framework.Practical implicationsSince, there exists dominance of domestic firms in Indian drugs and pharmaceutical industry, the planners should follow the policy which not only attract FDI but also benefit domestic firms; for example, developing modern infrastructure and institution which will further help domestic firms to absorb spillovers provided by the Multinational Corporations and also accelerate the growth and development of the economy.Social implicationsIn no case, the foreign firms should dominate the market share otherwise the efficiency spillover effect will be negative and the domestic firms will be destroyed under the self-centric approach of foreign firms protected by the recent patent laws.Originality/valueThe study is a unique attempt to discuss the production structure and sources of TFP spillovers of FDI in Indian drugs and pharmaceutical industry with such a wide coverage of 304 firms over a period of 16 years under Wang and Ho (2010) model’s framework. The existing studies on TFP spillovers are using either a small sample size of firms or based upon traditional techniques of measuring spillover effects.
Physician verbal compliance-gaining strategies and patient satisfaction
Authors: Olynick Janna , Iliopulos Alexandra , Li Han Z. 
Published: August 2017

Purpose
The patient healthcare experience is a complex phenomenon, as is encouraging patient compliance with medical advice. To address this multifaceted relationship, the purpose of this paper is to explore the ways resident physicians verbally encourage patient compliance and the relationship between these compliance-seeking strategies and patient satisfaction.

Design/methodology/approach
A total of 40 medical interviews between resident physicians and patients were audio-recorded, transcribed, coded, and analysed. Patient questionnaires were also administered and analysed.

Findings
It was found that resident physicians used indirect orders most frequently, followed by motivation, persuasion, scheduling, and direct orders. It was also found that female patients received (marginally) more messages than male patients; female residents used more messages with female patients than with male patients; female residents used more persuasion messages with female patients than with male patients; male residents were less likely than female residents to use motivational messages with female patients; and compliance was significantly correlated with expertise satisfaction, overall satisfaction, and communication satisfaction.

Originality/value
This study advances existing research by examining various ways in which residents verbally encourage patient compliance and the relationship between these messages and patient satisfaction. Findings can be used to inform physicians on strategies to encourage patient adherence to medication regimen, appointments, and lifestyle changes.
Effect of local instability on fire response of steel beams
Authors: Kodur Venkatesh , Naser Mohannad Z. 
Published: August 2017

PurposeThis purpose of this paper is to quantify the effect of local instability arising from high shear loading on response of steel girders subjected to fire conditions.Design/methodology/approachA three-dimensional nonlinear finite element model able to evaluate behavior of fire-exposed steel girders is developed. This model, is capable of predicting fire response of steel girders taking into consideration flexural, shear and deflection limit states.FindingsResults obtained from numerical studies show that shear capacity can degrade at a higher pace than flexural capacity under certain loading scenarios, and hence, failure can result from shear effects prior to attaining failure in flexural mode.Originality/valueThe developed model is unique and provides valuable insight (and information) to the fire response of typical hot-rolled steel girder subjected to high shear loading.
An Evidence‐Based Forensic Taxonomy of Windows Phone Communication Apps
Authors: Cahyani Niken Dwi Wahyu , Martini Ben , Choo Kim‐Kwang Raymond , Ab Rahman Nurul Hidayah , Ashman Helen 
Published: August 2017

AbstractCommunication apps can be an important source of evidence in a forensic investigation (e.g., in the investigation of a drug trafficking or terrorism case where the communications apps were used by the accused persons during the transactions or planning activities). This study presents the first evidence‐based forensic taxonomy of Windows Phone communication apps, using an existing two‐dimensional Android forensic taxonomy as a baseline. Specifically, 30 Windows Phone communication apps, including Instant Messaging (IM) and Voice over IP (VoIP) apps, are examined. Artifacts extracted using physical acquisition are analyzed, and seven digital evidence objects of forensic interest are identified, namely: Call Log, Chats, Contacts, Locations, Installed Applications, SMSs and User Accounts. Findings from this study would help to facilitate timely and effective forensic investigations involving Windows Phone communication apps.
The effects of hydropeaking on riverine plants: a review
Authors: Bejarano María D. , Jansson Roland , Nilsson Christer 
Published: August 2017

ABSTRACTHydropeaking refers to frequent, rapid and short‐term fluctuations in water flow and water levels downstream and upstream of hydropower stations. Such fluctuations are becoming increasingly common worldwide and are known to have far‐reaching effects on riverine vegetation. Novel hydrology caused by hydropeaking has no natural correspondence in freshwater systems, and hence few species have adaptations to all its aspects. Here, we review the literature on hydropeaking effects on riverine plants and define the state of the information on this human alteration of riverine ecosystems. We focus on riparian plants, but also draw on information from aquatic plant species, which exhibit a wide variety of adaptations to inundation and associated processes. Riparian plants face both physiological and physical constraints because of the shifts between submergence and drainage, and erosion of substrates. At the population level, hydropeaking may favour dispersal within, but not between, reservoirs, but may hamper germination, establishment, growth and reproduction. At the community level, strong filtering towards easily dispersed, flexible, flood‐tolerant and amphibious plants is expected, although few species share these traits. Hence, most riparian plant species are expected to disappear or be pushed towards the upper boundaries of the regulated river margin. Future research should examine more closely global variation in hydropeaking effects, including other taxonomic groups of species and the diversity of hydropeaking regimes. There is also a need for studies focusing on identifying the boundaries within which hydropeaking could operate without impairing plant life.