bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of interferential stimulation of the human brain with electrode arrays
Authors: Huang Yu , Datta Abhishek , Parra Lucas C. 
Published: September 2019

AbstractObjectiveInterferential stimulation (IFS) has generated considerable interest recently because of its potential to achieve focal electric fields in deep brain areas with transcranial currents. Conventionally, IFS applies sinusoidal currents through two electrode pairs with close-by frequencies. Here we propose to use an array of electrodes instead of just two electrode pairs; and to use algorithmic optimization to identify the currents required at each electrode to target a desired location in the brain.ApproachWe formulate rigorous optimization criteria for IFS to achieve either maximal modulation-depth or maximally focal stimulation. We find the solution for optimal modulation-depth analytically and maximize for focal stimulation numerically.Main resultsMaximal modulation is achieved when IFS equals conventional high-definition multi-electrode transcranial electrical stimulation (HD-TES) with a modulated current source. This optimal solution can be found directly from a current-flow model, i.e. the “lead field” without the need for algorithmic optimization. Once currents are optimized numerically to achieve optimal focal stimulation, we find that IFS can indeed be more focal than conventional HD-TES, both at the cortical surface and deep in the brain. Generally, however, stimulation intensity of IFS is weak and the locus of highest intensity does not match the locus of highest modulation.SignificanceThis proof-of-principle study shows the potential of IFS over HD-TES for focal non-invasive deep brain stimulation. Future work will be needed to improve on intensity of stimulation and convergence of the optimization procedure.
MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data
Authors: Lin Hsin-Nan , Hsu Wen-Lian 
Published: September 2019

AbstractWith the advance of next-generation sequencing (NGS) technologies, more and more medical and biological researches adopt NGS technologies to characterize the genetic variations between individuals. The identification of personal genome variants using NGS technology is a critical factor for the success of clinical genomics studies. It requires an accurate and consistent analysis procedure to distinguish functional or disease-associated variants from false discoveries due to sequencing errors or misalignments. In this study, we integrate the algorithms for read mapping and variant calling to develop an efficient and versatile NGS analysis tool, called MapCaller. It not only maps every short read onto a reference genome, but it also detects single nucleotide variants, indels, inversions and translocations at the same time. We evaluate the performance of MapCaller with existing variant calling pipelines using three simulated datasets and four real datasets. The result shows that MapCaller can identify variants accurately. Moreover, MapCaller runs much faster than existing methods. It is available at https://github.com/hsinnan75/MapCaller.
Tissue-ABPP enables high-resolution confocal fluorescence imaging of serine hydrolase activity in cryosections – Application to glioma brain unveils activity hotspots originating from tumor-associated neutrophils
Authors: Aaltonen Niina , Singha Prosanta K. , Jakupović Hermina , Wirth Thomas , Samaranayake Haritha , Pasonen-Seppänen Sanna , Rilla Kirsi , Varjosalo Markku , Edgington-Mitchell Laura E. , Kasperkiewicz Paulina , Drag Marcin , Kälvälä Sara , Moisio Eemeli , Savinainen Juha R. , Laitinen Jarmo T. 
Published: September 2019

AbstractSerine hydrolases (SHs) are a functionally diverse family of enzymes playing pivotal roles in health and disease and have emerged as important therapeutic targets in many clinical conditions. Activity-based protein profiling (ABPP) using fluorophosphonate (FP) probes has been a powerful chemoproteomic approach in studies unveiling roles of SHs in various biological systems. The ABPP approach utilizes cell/tissue proteomes and features the FP warhead, linked to a fluorescent reporter for in-gel fluorescence imaging or a biotin tag for streptavidin enrichment and LC-MS/MS-based target identification. Here, we advance the ABPP methodology to glioma brain cryosections, enabling high-resolution confocal fluorescence imaging of SH activity in different cell types of the tumor microenvironment, identified by using extensive immunohistochemistry on activity probe labeled sections. We name this technique tissue-ABPP to distinguish it from conventional gel-based ABPP. We show heightened SH activity in glioma vs. normal brain and unveil activity hotspots originating from tumor-associated neutrophils. Thorough optimization and validation is provided by parallel gel-based ABPP combined with LC-MS/MS-based target verification. Tissue-ABPP enables a wide range of applications for confocal imaging of SH activity in any type of tissue or animal species.
Lens Transmittance Shapes UV Sensitivity in the Eyes of Frogs from Diverse Ecological and Phylogenetic Backgrounds
Authors: Yovanovich Carola A. M. , Pierotti Michele E. R. , Kelber Almut , Jorgewich-Cohen Gabriel , Ibáñez Roberto , Grant Taran 
Published: September 2019

ABSTRACTThe amount of short wavelength (UV, violet and blue) light that reaches the retina depends on the transmittance properties of the ocular media, especially the lens, and varies greatly across species in all vertebrate groups studied previously. We measured the lens transmittance in 32 anuran amphibians with different habits, geographic distributions, and phylogenetic positions and used them together with eye size and pupil shape to evaluate the relationship with diel activity pattern, elevation and latitude. We found an unusually high lens UV transmittance in the most basal species, and a range that extends into the visible spectrum for the rest of the sample, with lenses even absorbing violet light in some diurnal species. However, other diurnal frogs had lenses that transmit UV light like the nocturnal species. This unclear pattern in the segregation of ocular media transmittance and diel activity is shared with other vertebrates and is consistent with the absence of significant correlations in our statistical analyses. Although we did not detect a significant phylogenetic effect, closely related species tend to have similar transmittances, irrespective of whether they share the same diel pattern or not, suggesting that ocular media transmittance properties might be related to phylogeny.
Acute toxicity of the plant volatile indole depends on herbivore specialization
Authors: Maurya Abhinav K. , Patel Rakhi C. , Frost Christopher J. 
Published: September 2019

AbstractHerbivore-induced plant volatiles (HIPVs) provide direct benefits to plants as antimicrobials and herbivore repellents, but their potential as direct toxins to herbivores is unclear. Here we assayed the larvicidal activity of six common HIPVs from three different biochemical pathways and tested the hypothesis that the larvicidal activity of HIPVs is related to the host specialization of the insect pest. We first assessed β-caryophyllene, linalool, z-3-hexenyl acetate, z-3-hexenol, e-2-hexenol, and indole against the beet armyworm (Spodoptera exigua), and found that indole was 7-fold more toxic compared to the other volatiles when incorporated into diet. Then, we tested the larvicidal activity of indole against six common, destructive pest caterpillars with varying host ranges. Consistent with our hypothesis, indole toxicity varied with caterpillar host range: indole toxicity was seven-fold higher in more specialized insect species relative to generalist insect species. That said, the LC50 of indole was comparable to other reported anti-herbivore agents even against the generalist caterpillars. Yet, indole in headspace had neither larvicidal nor ovicidal activity on any caterpillar species tested. These results support a key ecological precept regarding tradeoffs between host specialization and chemical detoxification, and also indicate that indole functions as a direct defense against herbivores that could be potentially useful in integrated pest management strategies.Key messageWe measured the direct toxicity of six common HIPVs against the beet armyworm.Indole was the most toxic HIPV against the beet armyworm.We determined the toxicity of indole against six different pest caterpillar species.Toxicity of indole was associated with the host preference of the insect species.Indole exposure in headspace had no effect on egg hatching or caterpillar survival.Indole has the potential to be developed as an insecticide against crop pests.Author Contribution StatementCJF and AKM designed research. AKM and RCP conducted experiments. AKM and CJF analyzed data and wrote the manuscript. All authors read and approved the manuscript.
Effect of interictal epileptiform discharges on EEG-based functional connectivity networks
Authors: Hu Derek K. , Shrey Daniel W. , Lopour Beth A. 
Published: September 2019

AbstractObjectiveFunctional connectivity networks (FCNs) based on interictal electroencephalography (EEG) can identify pathological brain networks associated with epilepsy. FCNs are altered by interictal epileptiform discharges (IEDs), but it is unknown whether this is due to the morphology of the IED or the underlying pathological activity. Therefore, we characterized the impact of IEDs on the FCN through simulations and EEG analysis.MethodsWe introduced simulated IEDs to sleep EEG recordings of eight healthy controls and analyzed the effect of IED amplitude and rate on the FCN. We then generated FCNs based on epochs with and without IEDs and compared them to the analogous FCNs from eight subjects with infantile spasms (IS), based on 1,340 visually marked IEDs. Differences in network structure and strength were assessed.ResultsIEDs in IS subjects caused increased connectivity strength but no change in network structure. In controls, simulated IEDs with physiological amplitudes and rates did not alter network strength or structure.ConclusionsIncreases in connectivity strength in IS subjects are not artifacts caused by the interictal spike waveform and may be related to the underlying pathophysiology of IS.SignificanceDynamic changes in EEG-based FCNs during IEDs may be valuable for identification of pathological networks associated with epilepsy.HighlightsInfantile spasms subjects exhibit broadly increased connectivity strength during interictal spikesFunctional connectivity network structure is unaltered by interictal spikes in infantile spasmsSimulated spikes in healthy control EEG did not alter network strength or structure
Interhemispheric gamma synchrony between parvalbumin interneurons supports behavioral adaptation
Authors: Cho Kathleen K.A. , Davidson Thomas J. , Marshall Jesse D. , Schnitzer Mark J. , Sohal Vikaas S. 
Published: September 2019

AbstractOrganisms must learn novel strategies to adapt to changing environments. Synchrony, which enhances neuronal communication, might create dynamic brain states, facilitating such adaptation. Although synchronization is common in neural systems, its functional significance remains controversial. We studied the role of gamma-frequency (~40 Hz) synchronization, promoted by parvalbumin interneurons, in mice learning multiple new cue-reward associations. Voltage imaging revealed cell type-specific increases of interhemispheric gamma synchrony within prefrontal parvalbumin interneurons, when mice received feedback that previously-learned associations were no longer valid. Disrupting this synchronization by delivering out-of-phase optogenetic stimulation caused mice to perseverate on outdated associations, an effect not reproduced by stimulating in-phase or out-of-phase at other frequencies. Gamma synchrony was specifically required when new associations utilized familiar cues that were previously irrelevant to behavioral outcomes, not when associations involved novel cues, or for reversing previously learned associations. Thus, gamma synchrony is indispensable for reappraising the behavioral salience of external cues.
Electrostatics and Solvation: Essential Determinants of Chromatin Compaction
Authors: Bendandi A. , Dante S. , Rehana Zia S. , Diaspro A. , Rocchia W. 
Published: September 2019

ABSTRACTChromatin compaction is a process of fundamental importance in Biology, as it greatly influences cellular function and gene expression. The dynamics of compaction is determined by the interactions between DNA and histones, which are mainly mechanical and electrostatic. The high charge of DNA makes electrostatics extremely important for chromatin topology and dynamics. Besides their mechanical and steric role in the chromatin fibre, linker DNA length and linker histone presence and binding position also bear great electrostatic consequences. Electrostatics in chromatin is also indirectly linked to the DNA sequence: the presence of high-curvature AT-rich segments in DNA can cause conformational variations with electrostatic repercussions, attesting to the fact that the role of DNA is both structural and electrostatic. Electrostatics in this system has been analysed by extensively examining at the computational level the repercussions of varying ionic concentration, using all-atom, coarse-grained, and continuum models. There have been some tentative attempts to describe the force fields governing chromatin conformational changes and the energy landscapes of these transitions, but the intricacy of the system has hampered reaching a consensus. Chromatin compaction is a very complex issue, depending on many factors and spanning orders of magnitude in space and time in its dynamics. Therefore, comparison and complementation of theoretical models with experimental results is fundamental. Here, we present existing approaches to analyse electrostatics in chromatin and the different points of view from which this issue is treated. We pay particular attention to solvation, often overlooked in chromatin studies. We also present some numerical results on the solvation of nucleosome core particles. We discuss experimental techniques that have been combined with computational approaches and present some related experimental data such as the Z-potential of nucleosomes at varying ionic concentrations. Finally, we discuss how these observations support the importance of electrostatics and solvation in chromatin models.SIGNIFICANCEThis work explores the determinants of chromatin compaction, focusing on the importance of electrostatic interactions and solvation. Chromatin compaction is an intrinsically multiscale issue, since processes concerning chromatin occur on a wide range of spatial and temporal scales. Since DNA is a highly charged macromolecule, electrostatic interactions are extremely significant for chromatin compaction, an effect examined in this work from many angles, such as the importance of ionic concentration and different ionic types, DNA-protein interactions, and solvation. Solvation is often overlooked in chromatin studies, especially in coarse-grained models, where the nucleosome core, the building block of the chromatin fibre, is represented as a rigid body, even though it has been observed that solvation influences chromatin even at the base-pair level.
Methodology for the preparation of rescue plans – a Polish case study
Authors: Kunikowski Grzegorz , Kosieradzka Anna , Kąkol Urszula 
Published: September 2019

Purpose
The purpose of this paper is to present a proposal for the methodology of developing rescue plans and the concepts of applying recommended response schedules in the context of the State Fire Service’s planning responsibilities (preparation) and public administration (reconciliation and approval), according to the legal order in force in Poland. In the proposed concept, recommended schedules are built on the basis of the matches and successes identified according to the criteria, i.e. the best carried out rescue actions from the register of reports.

Design/methodology/approach
The paper is based on the analysis of existing legal status and policy in Poland as well as the selected relevant academic literature.

Findings
The result is the formulation of a methodology for drawing up the rescue plans to the extent required by law and proposing a concept for the method of developing and applying recommended response schedules, supporting operational planning and conducting rescue operations.

Practical implications
The proposed methodology is to support the procedure of drawing up rescue plans by implying and implementing them into IT solutions. The suggested recommended response schedules, based on observations and conclusions from the analysis of the past rescue operations, may present circumstances and sequences of the use of forces and measures that have had beneficial effects in the past. An in-depth analysis of historical data from the conducted rescue operations may also be used to determine time indicators for the response phase.

Originality/value
The proposed solutions complement the methods currently used by public administration in Poland. The concept can also be inspiring for the State Fire Service (PSP) which has its own analytical tools in the form of a decision support system and registers of rescue operations carried out. The PSP may undertake the practical verification of the presented methodology for preparing rescue plans and recommended response schedules.
Transcending the threshold limitation: a fifth industrial revolution?
Authors: Callaghan Chris William 
Published: September 2019

Purpose
The purpose of this paper is to present the argument that there exists a threshold limitation to new knowledge creation, associated with a global productivity growth slowdown, a global decline in research and development (R&D) productivity and a decline in the growth of globalisation.

Design/methodology/approach
Taking the form of a conceptual paper, this paper seeks to advance the polemic that despite discussions of a ‘fourth industrial revolution,’ there has been no substantive change in a global decline in productivity growth, particularly in developed countries. Specific threats are identified and related to the consequences of technological proliferation in the absence of an effective research response to address them. Certain theoretical propositions are derived, with the suggestion that novel theory promises a ‘fifth industrial revolution,’ one that might ultimately reverse the downward trend in global productivity growth.

Findings
Drawing on management theory, derivation of the theoretical propositions suggests the existence of a mechanism related to research productivity enhancement. Discussions suggest that this mechanism might ultimately explain how the R&D productivity decline, evident since the 1970s, may ultimately be reversed.

Originality/value
The paper seeks to provoke novel thinking about the consequences of a failure to develop a research agenda explicitly focused on the attainment of economies of scale in the research process itself.
The impact of financial regulation policy uncertainty on bank profits and risk
Authors: Killins Robert Neil , Johnk David W. , Egly Peter V. 
Published: September 2019

Purpose
The purpose of this paper is to explore the impact of financial regulation policy uncertainty (FRPU) on bank profit and risk.

Design/methodology/approach
This study applies dynamic panel techniques and uses the Baker et al. (2016) FRPU index and macroeconomic variables to assess FRPU’s impact on bank profit and risk using Federal Deposit Insurance Corporation call reports from Q1 2000 to Q4 2016 for over 4,760 commercial banks.

Findings
The effect of FRPU on profitability (Return on Assets [ROA] and Return on Equity [ROE]) and risk (standard deviation of ROA and ROE) produces complex results. FRPU negatively (positively) impacts profits for small and large banks (money center banks). There is a positive impact on FRPU for small and medium-sized banks, with no impact reported for the large and money center banks.

Practical implications
Findings lead to several implications for financial services regulators, investors and executives as summarized in the conclusion. It is essential to ensure that clear communication channels are open especially to small and medium-sized banks for proper strategic planning, given their greater sensitivity to regulatory uncertainty.

Originality/value
This paper contributes to the literature as follows. First, it explores the impact of FRPU on bank profits and risk using a novel index introduced by Baker et al. (2016). This news-based continuous measure presents a bank profit modeling approach that differs from traditional event study methodology. Second, a large sample of US commercial banks is used which represents an important departure from banking regulation studies.
Nonconformity and socialism: the case of J. G. Greenhough, 1880–1914
Authors: Ryan Liam 
Published: September 2019

Abstract
This article examines the life, thought and activism of the prominent Baptist minister John Gershom Greenhough. Existing scholarly and popular narratives generally focus on the key role played by Nonconformity in nurturing the labour movement in late Victorian and Edwardian Britain. Using Greenhough as a case study this article posits an alternative interpretation of this relationship, contending that the individualistic religious culture of Nonconformity was often deeply hostile to socialism. This hostility motivated Greenhough, and others like him, to abandon their historical allegiance to the Liberal party in the early twentieth century in favour of the Conservatives. More broadly, this article investigates the process of political and ideological conversion and challenges dominant historical readings that characterize anti-socialism as being synonymous with middle-class economic self-interest.
The earls of Edward III and the polity: the earls of Arundel and Northampton in the localities, 1330–60
Authors: Raven Matt 
Published: September 2019

Abstract
This article examines the retinues of two English earls from 1330–60 to ascertain the extent and nature of their local influence, within a wider context of military activity and the changing form of local government and peacekeeping. It demonstrates that the followers of the earl of Northampton in Essex were recruited largely for military purposes but that those of the earl of Arundel in Sussex enjoyed a substantial degree of influence over local government. Ultimately, this article argues that comital influence in local government was imposed by Edward III as part of the growth of government through the mid fourteenth century.