bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water waves excited by near-impulsive wind forcing
Authors: Zavadsky Andrey , Shemer Lev 
Published: September 2017

Only limited information is currently available on the evolution of waves generated by wind that varies in time, and in particular on the initial stages of wind–wave growth from rest under a suddenly applied wind forcing. The emerging wind–wave field varies in time as well as in space. Detailed knowledge of wave parameter distributions under those conditions contributes to a better understanding of the mechanisms of wind wave generation. In the present study, the instantaneous surface elevation and two components of the instantaneous surface slope were recorded at various fetches in a small-scale experimental facility under nearly impulsive wind forcing. Numerous independent realizations have been recorded for each selection of operational conditions. Sufficient data at a number of fetches were accumulated to calculate reliable ensemble-averaged statistical parameters of the evolving random wind–wave field as a function of the time elapsed from activation of wind forcing. Distinct stages in the wave evolution process from appearance of initial ripples to emergence of a quasi-steady wind–wave field were identified. The experimental results during each stage of evolution were analysed in view of the viscous instability theory by Kawai (J. Fluid Mech., vol. 93, 1979, pp. 661–703) and the resonance model by Phillips (J. Fluid Mech., vol. 2, 1957, pp. 417–445).
Throat swabs have no influence on the management of patients with sore throats
Authors: Cheung L , Pattni V , Peacock P , Sood S , Gupta D 
Published: September 2017

AbstractBackground:Throat swabs are neither specific nor sensitive for micro-bacteria causing sore throat symptoms; however, current guidelines suggest they are still useful in some cases.Method:Retrospective and prospective analyses were conducted of throat swabs requested within the months of January 2016 and August 2016, respectively.Results:The study comprised 247 patients. Fifty-nine (24 per cent) had a positive culture. Forty-six grew group A beta-haemolytic streptococci, with the remainder growing candida (n = 10), coliform (n = 1) and klebsiella (n = 2). There was no significant difference in culture rates between primary or secondary care sources (χ2 = 0.56, p = 0.45). None of the swabs influenced a variation in patient management from local antimicrobial policies. Current practice has an estimated annual financial impact of £3 434 340 on the National Health Service.Conclusion:Throat swabs do not influence the antimicrobial treatment for patients with sore throats, even under current guidelines, and incur unnecessary cost. Current clinical guidelines could be reviewed to reduce the number of throat swabs being conducted unnecessarily.
A GAME-THEORETIC ANALYSIS OF PASCAL’S WAGER
Authors: Tarar Ahmer 
Published: September 2017

Abstract:Formal analyses of Pascal’s Wager have almost all been decision-theoretic, with a human as the sole decision-maker. This paper analyses Pascal’s Wager in a game-theoretic setting in which the deity whose existence the human is considering wagering on is also a decision-maker. There is an equilibrium in which the human chooses to wager that the deity exists and Pascal’s Wager thus operates, but also one in which the human does not wager. Thus, in a game-theoretic setting, Pascal’s Wager is indeterminate: wagering and not wagering are both consistent with equilibrium behaviour.
Citation Practices of the International Criminal Court: The Situation in Darfur, Sudan
Authors: MANLEY STEWART 
Published: September 2017

AbstractThis article analyzes the 9,203 citations made by the International Criminal Court (ICC) in its cases involving Sudan. To date, few empirical studies have assessed the citation practices of courts and even fewer of international courts. The data is rich. It reveals, for instance, the changing nature of the Court's citations over time, the disproportionate distribution of citations among chambers, the potential impact of party pleadings on citations, and the allocation of citations to previous rulings of the Court, other international tribunals and domestic courts. The article also explores possible explanations for the patterns that emerge and assesses what the patterns may mean for the Court. Unlike most other citation analyses, the study provides the additional benefit of having categorized the citations based on their function, distinguishing for instance between citations that the Court uses to help it decide legal and factual issues, and those it does not.
Fine-temporal forecasting of outbreak probability and severity: Ross River virus in Western Australia
Authors: KOOLHOF I. S. , BETTIOL S. , CARVER S. 
Published: September 2017

SUMMARYHealth warnings of mosquito-borne disease risk require forecasts that are accurate at fine-temporal resolutions (weekly scales); however, most forecasting is coarse (monthly). We use environmental and Ross River virus (RRV) surveillance to predict weekly outbreak probabilities and incidence spanning tropical, semi-arid, and Mediterranean regions of Western Australia (1991–2014). Hurdle and linear models were used to predict outbreak probabilities and incidence respectively, using time-lagged environmental variables. Forecast accuracy was assessed by model fit and cross-validation. Residual RRV notification data were also examined against mitigation expenditure for one site, Mandurah 2007–2014. Models were predictive of RRV activity, except at one site (Capel). Minimum temperature was an important predictor of RRV outbreaks and incidence at all predicted sites. Precipitation was more likely to cause outbreaks and greater incidence among tropical and semi-arid sites. While variable, mitigation expenditure coincided positively with increased RRV incidence (r2 = 0·21). Our research demonstrates capacity to accurately predict mosquito-borne disease outbreaks and incidence at fine-temporal resolutions. We apply our findings, developing a user-friendly tool enabling managers to easily adopt this research to forecast region-specific RRV outbreaks and incidence. Approaches here may be of value to fine-scale forecasting of RRV in other areas of Australia, and other mosquito-borne diseases.
Emotion perception improvement following high frequency transcranial random noise stimulation of the inferior frontal cortex
Authors: Penton Tegan , Dixon Laura , Evans Lauren Jayne , Banissy Michael J. 
Published: September 2017

AbstractFacial emotion perception plays a key role in interpersonal communication and is a precursor for a variety of socio-cognitive abilities. One brain region thought to support emotion perception is the inferior frontal cortex (IFC). The current study aimed to examine whether modulating neural activity in the IFC using high frequency transcranial random noise stimulation (tRNS) could enhance emotion perception abilities. In Experiment 1, participants received either tRNS to IFC or sham stimulation prior to completing facial emotion and identity perception tasks. Those receiving tRNS significantly outperformed those receiving sham stimulation on facial emotion, but not identity, perception tasks. In Experiment 2, we examined whether baseline performance interacted with the effects of stimulation. Participants completed a facial emotion and identity discrimination task prior to and following tRNS to either IFC or an active control region (area V5/MT). Baseline performance was a significant predictor of emotion discrimination performance change following tRNS to IFC. This effect was not observed for tRNS targeted at V5/MT or for identity discrimination. Overall, the findings implicate the IFC in emotion processing and demonstrate that tRNS may be a useful tool to modulate emotion perception when accounting for individual differences in factors such as baseline task performance.
Screening candidate microRNA-mRNA regulatory pairs for predicting the response to chemoradiotherapy in rectal cancer by a bioinformatics approach
Authors: Peng Qiliang , Zhu Junjia , Shen Peipei , Yao Wenyan , Lei Yu , Zou Li , Xu Yingying , Shen Yuntian , Zhu Yaqun 
Published: September 2017

AbstractExtensive efforts have been undertaken in search of biomarkers for predicting the chemoradiotherapy response in rectal cancer. However, most attention on treatment efficiency prediction in carcinoma is addicted to single or limited molecules. Network biomarkers are considered to outperform single molecules in predictive power. In this study, candidate microRNAs (miRNAs) were identified from the PubMed citations and miRNA expression profiles. Targets of miRNAs were obtained from four experimentally confirmed interactions and three computationally predicted databases. Functional enrichment analysis of all the targets revealed their associations with chemoradiotherapy response, indicating they could be promising biomarkers. Two lists of key target mRNAs of the candidate miRNAs were retrieved from protein–protein interaction (PPI) network and mRNA expression profiles, respectively. Pathway analysis and literature validation revealed that the mRNA lists were highly related to the ionizing radiation. The above miRNAs along with the key miRNA targets provide potential miRNA-mRNA regulatory pairs as network biomarkers in which all the network components may be used for predicting the chemoradiotherapy response. These results demonstrated that the network biomarkers could provide a useful model for predicting the chemoradiotherapy response and help in further understanding the molecular basis of response differences, which should be prioritized for further study.
Morphologically constrained and data informed cell segmentation of budding yeast
Authors: Bakker Elco , Swain Peter S , Crane Matthew M 
Published: September 2017

Abstract

Motivation
Although high-content image cytometry is becoming increasingly routine, processing the large amount of data acquired during time-lapse experiments remains a challenge. The majority of approaches for automated single-cell segmentation focus on flat, uniform fields of view covered with a single layer of cells. In the increasingly popular microfluidic devices that trap individual cells for long term imaging, these conditions are not met. Consequently, most techniques for segmentation perform poorly. Although potentially constraining the generalizability of software, incorporating information about the microfluidic features, flow of media and the morphology of the cells can substantially improve performance.

Results
Here we present DISCO (Data Informed Segmentation of Cell Objects), a framework for using the physical constraints imposed by microfluidic traps, the shape based morphological constraints of budding yeast and temporal information about cell growth and motion to allow tracking and segmentation of cells in microfluidic devices. Using manually curated datasets, we demonstrate substantial improvements in both tracking and segmentation when compared with existing software.

Availability and implementation
The MATLAB code for the algorithm and for measuring performance is available at https://github.com/pswain/segmentation-software and the test images and the curated ground-truth results used for comparing the algorithms are available at http://datashare.is.ed.ac.uk/handle/10283/2002.

Supplementary information
Supplementary data are available at Bioinformatics online.
Risk of Pulmonary Embolism in Patients With Isolated Great Saphenous Vein Thrombus
Authors: Gupta Akshya , Pandya Vijay , Baran Timothy , Dogra Vikram S. 
Published: September 2017

Abstract
Risks associated with isolated great saphenous vein (GSV) thrombosis remain controversial. The purpose of this study is to identify the risk of pulmonary embolism (PE) in patients with isolated GSV thrombosis, particularly those with thrombus within 3 cm of the sapheno-femoral junction. A retrospective chart review of color flow Doppler lower extremity venous ultrasound examinations from an academic hospital from 2011 to 2016 was conducted. Seventy-eight patients were identified as having acute thrombus in their GSV and were then further stratified based on the presence or absence of concomitant deep venous thrombosis (DVT). A control group of 49 patients who presented with leg swelling and were found to have a normal color flow Doppler examination was also identified. Patients without thrombus (n = 49), patients with isolated GSV thrombus (n = 29), and patients with GSV thrombus with concomitant DVT (n = 49) underwent full chart review to determine whether any patients developed PE. This was diagnosed specifically by computed tomography angiogram or ventilation/perfusion scan, within 60 days of initial diagnosis of lower extremity thrombus. In our analysis, there was no significant difference in the risk of PE in patients with isolated GSV thrombus compared with a control group of normal patients (3.5% vs 2.0%, P = 0.38). However, patients with GSV thrombus and concomitant DVT had a significantly increased risk of PE compared with patients with isolated GSV thrombus (26.5% vs 3.5%, P = 0.01). We found that the risk of PE in patients with isolated GSV thrombus is not significantly increased compared with a normal cohort.
The evolving spirit: morals and mutualism in Arabella Buckley's evolutionary epic
Authors: Larsen Jordan 
Published: September 2017

Contemporaries of Charles Darwin were divided on reconciling his theory of natural selection with religion and morality. Although Alfred Russel Wallace stands out as a spiritualist advocate of natural selection who rejected a natural origin of morality, the science popularizer and spiritualist Arabella Buckley (1840–1929) offers a more representative example of how theists, whether spiritualist or more orthodox in their religion, found reconciliation. Unlike Wallace, Buckley emphasized the lawful evolution of morality and of the soul, drawing from the theological tradition of traducianism. Significantly, Buckley argued for a mutualistic and deeply theistic interpretation of Darwinian evolution, particularly the evolution of morals, without sacrificing the uniformity of natural law. Though Buckley's understanding of the evolutionary epic has been represented as emphasizing mutualism (Gates 1998) and spiritualist theology (Lightman 2007), here I demonstrate that her distinctive addition to the debate lies in her unifying theory of traducianism. In contrast to other authors, I argue that through Buckley we better understand Victorian spiritualism as more of a religion than an occult science. However, it was a conception of religion that, through her evolutionary traducianism, bridged science and spiritualism. This offers historians a more complex but satisfying image of the Victorian worldview after Darwin.
Caffeic Acid Phenethyl Ester (CAPE) Inhibits Growth of Chromosomally instablebub1Δ mutant inSaccharomyces cerevisiae
Authors: Azman Zeynep N. , Kiyici Aysel , Oncel Mufide , Yilmaz H. Ramazan , Gunduz Esra , Gunduz Mehmet , Basrai Munira A. , Ciftci-Yilmaz Sultan 
Published: September 2017

AbstractChromosomal instability (CIN) is a hallmark of cancer cells. Spindle Assembly Checkpoint (SAC) proteins such as Bub1 monitor errors in chromosome segregation and cause cell cycle delay to prevent CIN. Altered expression ofBUBlis observed in several tumor samples and cancer cell lines which display CIN. Caffeic Acid Phenethyl Ester (CAPE) which is an active component of propolis obtained from bee hives has anti-inflammatory antioxidant and anticarcinogenic properties. We used budding yeastS. cerevisiaeas a model organism to investigate the molecular mechanism by which CAPE can inhibit the growth of cells with high levels of CIN. Here we show that CAPE leads to growth inhibition ofbub1Δ strains. CAPE treatment suppressed chromosome mis-segregation inbub1Δstrain possibly due to apoptosis of chromosomally instablebub1Δ cells. We propose that CAPE may serve as a potential therapeutic agent for treatment ofBUB1deficient cancers and other cancers that exhibit CIN.
A topographic visual pathway into the central brain of Drosophila
Authors: Timaeus Lorin , Geid Laura , Hummel Thomas 
Published: September 2017

SummaryThe visual system is characterized by a strict topographic organization from the retina towards multiple layers of synaptic integration. Recent studies in Drosophila have shown that in the transition from the optic lobes to the central brain, due to convergence of columnar neurons onto optic glomeruli, distinct synaptic units employed in the computation of different visual features, the retinotopic representation is lost in these circuits. However, functional imaging revealed aspatial representation of visual cuesin the Drosophila central complex, raising the question about the underlying circuitry, which bypasses optic glomerulus convergence.While characterizing afferent arborizations within Drosophila visual glomeruli, we discovered a spatial segregation of topographic and non-topographic projections from distinct molecular classes of medulla projection neurons,medullo-tubercular(MeTu) neurons, into a specific central brain glomerulus, theanterior optic tubercle(AOTu). Single cell analysis revealed that topographic information is organized by ensembles of MeTu neurons (type 1), forming parallel channels within the AOTu, while a separate class of MeTu neurons (type 2) displays convergent projection, associated with a loss of spatial resolution. MeTu afferents in the AOTu synapse onto a matching topographic field of output projection neurons, thesetubercular-bulbar(TuBu) neurons relay visual information towards dendritic fields of central complex ring neurons in the bulb neuropil. Within the bulb, neuronal proximity of the topographic AOTu map as well as channel identity is maintained despite the absence of a stereotyped map organization, providing the structural basis for spatial representation of visual information in the central complex (CX). TuBu neurons project onto dendritic fields of efferent ring neurons, where distinct sectors of the bulb correspond to a distinct ring domain in the ellipsoid body. We found a stereotypic circuitry for each analyzed TuBu class, thus the individual channels of peripheral topography are maintained in the central complex structure. Together with previous data showing rough topography within the lobula AOTu domain, our results on the organization of medulla projection neurons define the AOTu neuropil as the main relay station for spatial information from the optic lobes into the central brain.
Numb prevents a complete EMT by modulating Notch signalling
Authors: Bocci Federico , Jolly Mohit Kumar , Tripathi Satyendra C. , Aguilar Mitzi , Hanash Samir M , Levine Herbert , Onuchic José N. 
Published: September 2017

AbstractEpithelial-Mesenchymal Transition (EMT) plays key roles during embryonic development, wound healing, and cancer metastasis. Cells in a partial EMT or hybrid epithelial/mesenchymal (E/M) phenotype tend to exhibit collective cell migration, forming clusters of circulating tumour cells – the primary drivers of metastasis. Activation of cell-cell signalling pathways such as Notch fosters a partial or complete EMT, yet the mechanisms enabling cluster formation remain poorly understood. Using an integrated computational-experimental approach, we examine the role of Numb – an inhibitor of Notch intercellular signalling – in mediating EMT and clusters formation of hybrid E/M cells. Knockdown of Numb in stable hybrid E/M cells H1975 results in a full EMT, thereby showing that Numb acts as a brake for a full EMT. Consistent with this observation, we show via a mathematical model that Numb inhibits a full EMT by stabilizing a hybrid E/M phenotype. Thus, Numb can behave as a ‘phenotypic stability factor’ by modulating Notch-driven EMT. By generalizing the mathematical model to a multi-cell level, Numb is predicted to alter the balance of hybrid E/M versus mesenchymal cells in clusters, potentially resulting in a higher tumour-initiation ability. Finally, Numb correlates with a poor survival in multiple independent lung and ovarian cancer datasets, hence confirming its relationship with increased cancer aggressiveness.Major Findings: we adopt an integrative computational-experimental approach to identify that Numb, an inhibitor of Notch signalling, can stabilize a hybrid epithelial/mesenchymal (E/M) phenotype. We show that knockdown of Numb in H1975 cells that display a stable hybrid E/M state is sufficient to destabilize a hybrid E/M state and push them to a full EMT phenotype. Next, we develop a mechanism-based mathematical model that recapitulates this ability of Numb in maintaining a hybrid E/M state, and predicts that Numb can alter the relative frequency of hybrid E/M and mesenchymal cells at a tissue level or in clusters of circulating tumor cells (CTCs) – the primary drivers of metastasis. Finally, we show that across cancer types, Numb correlates with worse patient survival, thus reinforcing the emerging notion that a hybrid E/M, but not necessarily a completely mesenchymal, phenotype associates with elevated tumour progression.
What exactly is ‘N’ in cell culture and animal experiments?
Authors: Lazic Stanley E. , Clarke-Williams Charlie J. , Munafò Marcus R. 
Published: September 2017

AbstractBiologists establish the existence of experimental effects by applying treatments or interventions to biological entities or units, such as people, animals, slice preparations, or cells. When done appropriately, independent replication of the entity-intervention pair contributes to the sample size (N) and forms the basis of statistical inference. However, sometimes the appropriate entity-intervention pair may not be obvious, and the wrong choice can make an experiment worthless. We surveyed a random sample of published animal experiments from 2011 to 2016 where interventions were applied to parents but effects examined in the offspring, as regulatory authorities have provided clear guidelines on replication with such designs. We found that only 22% of studies (95% CI = 17% to 29%) replicated the correct entity-intervention pair and thus made valid statistical inferences. Approximately half of the studies (46%, 95% CI = 38% to 53%) had pseudoreplication while 32% (95% CI = 26% to 39%) provided insufficient information to make a judgement. Pseudoreplication artificially inflates the sample size, leading to more false positive results and inflating the apparent evidence supporting a scientific claim. It is hard for science to advance when so many experiments are poorly designed and analysed. We argue that distinguishing between biological units, experimental units, and observational units clarifies where replication should occur, describe the criteria for genuine replication, and provide guidelines for designing and analysingin vitro, ex vivo,andin vivoexperiments.