bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extended optical/NIR observations of Type Iax supernova 2014dt: Possible signatures of a bound remnant
Authors: Kawabata Miho , Kawabata Koji S , Maeda Keiich , Yamanaka Masayuki , Nakaoka Tatsuya , Takaki Katsutoshi , Fukushima Daiki , Kojiguchi Naoto , Masumoto Kazunari , Matsumoto Katsura , Akitaya Hiroshi , Itoh Ryosuke , Kanda Yuka , Moritani Yuki , Takata Koji , Uemura Makoto , Ui Takahiro , Yoshida Michitoshi , Hattori Takashi , Lee Chien-Hsiu , Tominaga Nozomu , Nomoto Ken’ichi 
Published: October 2018

Abstract
We present optical and near-infrared observations of the nearby Type Iax supernova (SN) 2014dt from 14 to 410 d after the maximum light. The velocities of the iron absorption lines in the early phase indicated that SN 2014dt showed slower expansion than the well-observed Type Iax SNe 2002cx, 2005hk, and 2012Z. In the late phase, the evolution of the light curve and that of the spectra were considerably slower. The spectral energy distribution kept roughly the same shape after ∼100 d, and the bolometric light curve flattened during the same period. These observations suggest the existence of an optically thick component that almost fully trapped the γ-ray energy from 56Co decay. These findings are consistent with the predictions of the weak deflagration model, leaving a bound white dwarf remnant after the explosion.
ESTIMATION OF PATIENT LENS DOSE ASSOCIATED WITH C-ARM CONE-BEAM COMPUTED TOMOGRAPHY USAGE DURING INTERVENTIONAL NEURORADIOLOGY
Authors: Kawauchi Satoru , Chida Koichi , Moritake Takashi , Matsumaru Yuji , Hamada Yusuke , Sakuma Hideyuki , Yoda Shogo , Sun Lue , Sato Masayuki , Tsuruta Wataro 
Published: October 2018

Abstract
The purpose of this study was to investigate the dose distribution and lens doses associated with C-arm cone-beam computed tomography (CBCT), using a head phantom, and to estimate the contribution ratio of C-arm CBCT to each patient’s lens dose during interventional neuroradiology (‘lens dose ratio’) in 109 clinical cases. In the phantom study, the peak skin doses and respective right and left lens doses of C-arm CBCT were as follows: 63.0 ± 1.9 mGy, 19.7 ± 1.4 mGy and 21.9 ± 0.8 mGy in whole brain C-arm CBCT and 39.2 ± 1.4 mGy, 4.7 ± 0.9 mGy and 3.6 ± 0.3 mGy in high-resolution C-arm CBCT. In the clinical study, the lens dose ratios were 25.4 ± 8.7% in the right lens and 19.1 ± 9.8% in the left lens. This study shows that, on average, ~25% of patients’ total lens dose was contributed by C-arm CBCT.
Roy Porter Student Prize Essay How (Not) to Survive a Plague: The Theology of Fleeing Disease in Sixteenth-century England
Authors: Weinreich Spencer J 
Published: October 2018

Abstract
Early modern medicine favoured flight as the best prophylactic against epidemic disease. Theologically, however, flight savoured of an attempt to defy divine providence, or a dereliction of Christian charity, while staying could seem an act of presumption or recklessness. This essay studies six theologians whose writings on the issue circulated in sixteenth-century England. Long dismissed as inconclusive and derivative, these ‘flight theologies’ can be better understood as products of theological principle and communal experience, whose combined influence precluded definitive prescriptions. Instead, authors marshalled the rhetoric of ‘conscience’ to displace the decision back onto their readers, while retaining interpretive authority over the key factors of Scripture and personal obligations. Flight theology thus seeks less to solve a practical problem, than to produce a particular kind of political subjectivity, bound to the community and predicated on persuasion. In so doing, the discourse fuelled the emergence of an early modern English public sphere.
Women’s Work in Fragile States: Evidence from a Firm-Level Dataset in Somaliland
Authors: Nelson-Nuñez Jami , Cyr Christopher 
Published: October 2018

AbstractWhat explains variation in women’s employment in fragile states with conflict-affected histories and limited state capacity? Employment builds stability and including women in labor markets can yield peace dividends. We use data from a firm-level survey in Somaliland, a de facto state in northern Somalia, to investigate why some firms employ more women than others. We analyze firm characteristics affected by state fragility and conflict, including female firm ownership, diaspora ownership and management, and limited access to services. This research contributes to our understanding of economic growth in fragile contexts and identifies opportunities to address gender inequalities in the developing world.
Design of RNA hairpin modules that predictably tune translation in yeast
Authors: Weenink Tim , van der Hilst Jelle , McKiernan Robert M , Ellis Tom 
Published: October 2018

AbstractModular parts for tuning translation are prevalent in prokaryotic synthetic biology but lacking for eukaryotic synthetic biology. Working in Saccharomyces cerevisiae yeast, we here describe how hairpin RNA structures inserted into the 5′ untranslated region (5′UTR) of mRNAs can be used to tune expression levels by 100-fold by inhibiting translation. We determine the relationship between the calculated free energy of folding in the 5′UTR and in vivo protein abundance, and show that this enables rational design of hairpin libraries that give predicted expression outputs. Our approach is modular, working with different promoters and protein coding sequences, and outperforms promoter mutation as a way to predictably generate a library where a protein is induced to express at a range of different levels. With this new tool, computational RNA sequence design can be used to predictably fine-tune protein production for genes expressed in yeast.
Computational modeling of the crosstalk between macrophage polarization and tumor cell plasticity in the tumor microenvironment
Authors: Li Xuefei , Jolly Mohit Kumar , George Jason T. , Pienta Kenneth J. , Levine Herbert 
Published: October 2018

AbstractTumor microenvironments contain multiple cell types interacting among one another via different signaling pathways. Furthermore, both cancer cells and different immune cells can display phenotypic plasticity in response to these communicating signals, thereby leading to complex spatiotemporal patterns that can impact therapeutic response. Here, we investigate the crosstalk between cancer cells and macrophages in a tumor microenvironment through in silico (computational) co-culture models. In particular, we investigate how macrophages of different polarization (M1 vs. M2) can interact with epithelial-mesenchymal plasticity of cancer cells, and conversely, how cancer cells exhibiting different phenotypes (epithelial vs. mesenchymal) can influence the polarization of macrophages. Based on interactions documented in the literature, an interaction network of cancer cells and macrophages is constructed. The steady states of the network are then analyzed. Various interactions were removed or added into the constructed-network to test the functions of those interactions. Also, parameters in the mathematical models were varied to explore their effects on the steady states of the network. In general, the interactions between cancer cells and macrophages can give rise to multiple stable steady-states for a given set of parameters and each steady state is stable against perturbations. Importantly, we show that the system can often reach one type of stable steady states where cancer cells go extinct. Our results may help inform efficient therapeutic strategies.
A 117 year retrospective analysis of Pennsylvania tick community dynamics
Authors: Pak Damie , Jacobs Steven B. , Sakamoto Joyce M. 
Published: October 2018

AbstractBackgroundTick-borne diseases have been increasing at the local, national, and global levels. Researchers studying ticks and tick-borne disease need a thorough knowledge of the pathogens, vectors, and epidemiology of disease spread. Three surveillance approaches are commonly used to provide insight into tick-borne disease risk: human disease case surveillance, active tick surveillance, and passive tick surveillance. Long-term passive surveillance can provide up-to-date data on the spatial variability and temporal dynamics of ectoparasite communities and shed light into the ecology of rarer tick species. We present a retrospective analysis on compiled data of ticks from Pennsylvania over the last 117 years.MethodsWe compiled data from ticks collected during tick surveillance research, and from citizen-based submissions to the Penn State University Department of Entomology (PSUEnt). Specimens were deposited at the PSUEnt arthropod collections that eventually became The Frost Entomological Museum. While most of the specimens were submitted by the public, a subset of the data were collected through active methods (flagging or dragging, or removal of ticks from wildlife). We analyzed all data from 1900-2017 for tick community composition, host associations, and spatio-temporal dynamics.ResultsIn total there were 4,491 submission lots consisting of 7,132 tick specimens. Twenty-four different species were identified, with the large proportion of submissions represented by five tick species. We observed a shift in tick community composition in which the dominant species of tick (Ixodes cookei) was overtaken in abundance byDermacentor variabilisin the early 1990s, and then replaced in abundance byI. scapularis. We analyzed host data and identified overlaps in host range amongst tick species, suggesting potential hubs of pathogen transfer between different tick vectors and their reservoir hosts.ConclusionsWe highlight the importance of long-term passive tick surveillance in investigating the ecology of both common and rare tick species. Information on the geographic distribution, host-association, and seasonality of the tick community can help researchers and health-officials to identify high-risk areas.
A free boundary model of epithelial dynamics
Authors: Baker Ruth E , Parker Andrew , Simpson Matthew J 
Published: October 2018

AbstractIn this work we analyse a one-dimensional, cell-based model of an epithelial sheet. In this model, cells interact with their nearest neighbouring cells and move deterministically. Cells also proliferate stochastically, with the rate of proliferation specified as a function of the cell length. This mechanical model of cell dynamics gives rise to a free boundary problem. We construct a corresponding continuum-limit description where the variables in the continuum limit description are expanded in powers of the small parameter 1/N, where N is the number of cells in the population. By carefully constructing the continuum limit description we obtain a free boundary partial differential equation description governing the density of the cells within the evolving domain, as well as a free boundary condition that governs the evolution of the domain. We show that care must be taken to arrive at a free boundary condition that conserves mass. By comparing averaged realisations of the cell-based model with the numerical solution of the free boundary partial differential equation, we show that the new mass-conserving boundary condition enables the coarsegrained partial differential equation model to provide very accurate predictions of the behaviour of the cell-based model, including both evolution of the cell density, and the position of the free boundary, across a range of interaction potentials and proliferation functions in the cell based model.
Cleft lip/palate and educational attainment: cause, consequence, or correlation? A Mendelian randomization study
Authors: Dardani Christina , Howe Laurence J , Stergiakouli Evie , Wren Yvonne , Humphries Kerry , Davies Amy , Ho Karen , Mangold Elisabeth , Ludwig Kerstin U , Relton Caroline L , Smith George Davey , Lewis Sarah J , Sandy Jonathan , Davies Neil M , Sharp Gemma C 
Published: October 2018

AbstractImportancePrevious studies have found that children born with a non-syndromic form of cleft lip and/or palate have lower-than-average educational attainment. These differences could be due to a genetic predisposition to low intelligence and academic performance, factors arising due to the cleft phenotype (such as school absence, social stigmatization and impaired speech and language development), or confounding by the prenatal environment. A clearer understanding of this mechanism will inform development of interventions to improve educational attainment in individuals born with a cleft, which could have wide-ranging knock-on effects on their quality of life.ObjectiveTo assess evidence for the hypothesis that common variant genetic liability to non-syndromic cleft lip with or without cleft palate (nsCL/P) influences educational attainment.DesignUsing summary data from genome-wide association studies (GWAS), we performed Linkage Disequilibrium (LD)-score regression and two-sample Mendelian randomization to evaluate the relationship between genetic liability to nsCL/P (GWAS n=3,987) and educational attainment (GWAS n=766,345), and intelligence (GWAS n=257,828).ResultsThere was little evidence for shared genetic aetiology between nsCL/P and educational attainment (rg −0.03, 95% CI −0.14 to 0.08, P 0.58; βMR 0.002, 95% CI −0.001 to 0.005, P 0.417) or intelligence (rg −0.01, 95% CI −0.12 to 0.10, P 0.85; βMR 0.002, 95% CI −0.010 to 0.014, P 0.669).Conclusions and relevanceCommon genetic variants are unlikely to predispose individuals born with nsCL/P to low educational attainment or intelligence. This information will help tailor clinical-, school-, social- and family-level interventions to improve educational attainment in this group.Key PointsQuestionDo children born with a non-syndromic cleft lip with or without palate (nsCL/P) have lower-than average academic achievement because of an underlying genetic predisposition to educational attainment and/or intelligence?FindingsThere was little evidence for shared common variant genetic correlation between nsCL/P, educational attainment and intelligence.MeaningCommon genetic variants are unlikely to predispose individuals born with nsCL/P to low educational attainment or intelligence. This information will help tailor clinical-, school-, social- and family-level interventions to improve educational attainment in this group.
XTalkiiS: a tool for finding data-driven cross-talks between intra-/inter-species pathways
Authors: Azad A. K. M. 
Published: October 2018

AbstractCell-cell communication via pathway cross-talks within a single species have been studied in silico recently to decipher various disease phenotype. However, computational prediction of pathway cross-talks among multiple species in a data-driven manner is yet to be explored. In this article, I present XTalkiiS (Cross-talks between inter-/intra species pathways), a tool to automatically predict pathway cross-talks from data-driven models of pathway network, both within the same organism (intra-species) and between two organisms (inter-species). XTalkiiS starts with retrieving and listing up-to-date pathway information in all the species available in KEGG database using RESTful APIs (exploiting KEGG web services) and an in-house built web crawler. I hypothesize that data-driven network models can be built by simultaneously quantifying co-expression of pathway components (i.e. genes/proteins) in matched samples in multiple organisms. Next, XTalkiiS loads a data-driven pathway network and applies a novel cross-talk modelling approach to determine interactions among known KEGG pathways in selected organisms. The potentials of XTalkiiS are huge as it paves the way of finding novel insights into mechanisms how pathways from two species (ideally host-parasite) may interact that may contribute to the various phenotype of interests such as malaria disease. XTalkiiS is made open sourced at https://github.com/Akmazad/XTalkiiS and its binary files are freely available for downloading from https://sourceforge.net/projects/xtalkiis/.
Gorilla in our Midst: An online behavioral experiment builder
Authors: Anwyl-Irvine Alexander , Massonnié Jessica , Flitton Adam , Kirkham Natasha , Evershed Jo 
Published: October 2018

AbstractBehavioural researchers are increasingly conducting their studies online to gain access to large and diverse samples that would be difficult to get in a laboratory environment. However, there are technical access barriers to building experiments online, and web-browsers can present problems for consistent timing – an important issue with reaction time-sensitive measures. For example, to ensure accuracy and test-retest reliability in presentation and response recording, experimenters need a working knowledge of programming languages such as JavaScript. We review some of the previous and current tools for online behavioural research, and how well they address the issues of usability and timing. We then present The Gorilla Experiment Builder (gorilla.sc) a fully tooled experiment authoring and deployment platform, designed to resolve many timing issues, and make reliable online experimentation open and accessible to a wider range of technical abilities. In order to demonstrate the platform’s aptitude for accessible, reliable and scalable research, we administered the task with a range of participant groups (primary school children and adults), settings (without supervision, at home, and under supervision, in schools and public engagement events), equipment (own computers, computer supplied by researcher), and connection types (personal internet connection, mobile phone 3G/4G). We used a simplified flanker task, taken from the Attentional Networks Task (Rueda, Posner, & Rothbart, 2004). We replicated the ‘conflict network’ effect in all these populations, demonstrating the platform’s capability to run reaction time-sensitive experiments. Unresolved limitations of running experiments online are then discussed, along with potential solutions, and some future features of the platform.
A Universal Algorithm to Detect Rare or Novel Cell Types in High-Throughput Single-Cell Gene Expression Data
Authors: Weiss Zoe , Tsoucas Daphne 
Published: October 2018

AbstractDetecting rare cell types would allow early disease detection of cancers and infections, identification of new cell types, and a deepened understanding of cell differentiation. We developed a universal algorithm to identify rare cell types from a wide variety of single-cell ’omics’ data. We validated our algorithm on single-cell qPCR data from mouse hematopoietic cells and single-cell RNA-seq data from human glioblastoma tumors cells, both with expression values from an ample number of genes. We then applied our algorithm to seq-FISH data from mouse hippocampus cells containing expression values from only 121 genes. Our algorithm detected rare cell types including a putative new hippocampal cell type.Author summaryRare cell type detection would advance early disease diagnosis (e.g., cancer, infection), allow identification of new cell types, and increase understanding of cell differentiation. Current computational methods can detect common cell types, but it remains a challenge to detect rare cell types within cell populations, especially with expression data from a relatively small number of genes. We created a powerful algorithm to detect rare cell types in a population of cells. We validated our algorithm on data from mouse blood stem cells and human glioblastoma tumors cells. When we applied our algorithm to mouse hippocampus data containing expression values from only 121 genes, we detected a putative new brain cell type that no previous algorithm has identified. Our universal algorithm can now be applied to a wide range of data to detect the early onset of diseases and discover new cell types.
Marked point process filter for clusterless and adaptive encoding-decoding of multiunit activity
Authors: Arai Kensuke , Liu Daniel F. , Frank Loren M. , Eden Uri T. 
Published: October 2018

AbstractReal-time, closed-loop experiments can uncover causal relationships between specific neural activity and behavior. An important advance in realizing this is the marked point process filtering framework which utilizes the “mark” or the waveform features of unsorted spikes, to construct a relationship between these features and behavior, which we call the encoding model. This relationship is not fixed, because learning changes coding properties of individual neurons, and electrodes can physically move during the experiment, changing waveform characteristics. We introduce a sequential, Bayesian encoding model which allows incorporation of new information on the fly to adapt the model in real time. A possible application of this framework is to the decoding of the contents of hippocampal ripples in rats exploring a maze. During physical exploration, we observe the marks and positions at which they occur, to update the encoding model, which is employed to decode contents of ripples when rats stop moving, and switch back to updating the model once the rat starts moving again.
Mindfulness meditators do not show differences in electrophysiological measures of error processing
Authors: Bailey Neil W , Raj Kavya , Freedman Gabrielle , Fitzgibbon Bernadette M , Rogasch Nigel C , Van Dam Nicholas T , Fitzgerald Paul B 
Published: October 2018

AbstractMindfulness meditation may improve attention and self-regulation. One component of attention and self-regulation that may allow these improvements is performance monitoring. Neural correlates of performance monitoring can be objectively measured with electroencephalogram (EEG) via the error related negativity (ERN) and error positivity (Pe). Previous research assessing the ERN and Pe in meditators has resulted in inconsistent findings; some have reported alteration in peak amplitudes from both very brief meditation practice and long-term meditation practice, while others have failed to provide evidence for differences in the ERN or Pe. However, recently developed EEG analysis techniques allow for more rigorous analyses than have been used in past investigations. The current study measured the ERN and Pe, as well as post-error alpha suppression, during a Go/Nogo task, and emotional and colour Stroop tasks. The measures were compared between 22 experienced meditators (mean of 8 years of practice) and 20 healthy controls. The results suggested no differences in the ERN, Pe, or post-error alpha suppression (all p > 0.05), even when varying multiple analysis parameters. The study showed equivalent statistical power to previous research, and > 85% power to detect medium effect sizes present in previous research. Bayes Factor analysis indicated the null hypotheses were > 3.5 more likely than any of the alternative hypotheses for the ERN or Pe. These results suggest that meditation may not alter neural activity related to error processing, despite prior research suggesting that it does.