bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio-temporal correlations between catastrophe events in a microtubule bundle: a computational study
Authors: Diwe Makarand , Gopalakrishnan Manoj
Published: July 2019

We explore correlations between dynamics of different microtubules in a bundle, via numerical simulations, using a one-dimensional stochastic model of a microtubule. The GTP-bound tubulins undergo diffusion-limited binding to the tip. Random hydrolysis events take place along the filament, and converts GTP-tubulin to GDP-tubulin. The filament starts depolymerising when the monomer at the tip becomes GDP-bound; in this case, detachment of GDP-tubulin ensues and continues until either GTP-bound tubulin is exposed or complete depolymerisation is achieved. In the latter case, the filament is defined to have undergone a “catastrophe”. Our results show that, in general, the dynamics of growth and catastrophe in different filaments are coupled to each other; closer the filaments are, the stronger the coupling. In particular, all filaments grow slower, on average, when brought closer together. The reduction in growth velocity also leads to more frequent catastrophes. More dramatically, catastrophe events in the different filaments forming a bundle are found to be correlated; a catastrophe event in one filament is more likely to be followed by a similar event in the same filament. This propensity of bunching disappears when the filaments move farther apart.
Loop-closure Kinetics Reveal a Stable, Right-handed DNA Intermediate in Cre Recombination
Authors: Shoura Massa J. , Giovan Stefan M. , Vetcher Alexandre V. , Ziraldo Riccardo , Hanke Andreas , Levene Stephen D.
Published: July 2019

In Cre site-specific recombination, the synaptic intermediate is a recombinase homotetramer containing a pair of DNA target sites. The strand-exchange mechanism proceeds via a Holliday-junction (HJ) intermediate; however, the geometry of the DNA segments in the synapse has remained highly controversial. In particular, all crystallographic structures are consistent with an achiral planar Holliday-junction (HJ) structure, whereas topological assays based on Cre-mediated knotting of plasmid DNAs are consistent with a right-handed chiral junction. Here we use the kinetics of loop closure involving closely spaced (131-151 bp), directly repeated loxP sites to investigate thein-aqueoensemble of conformations for the longest-lived looped DNA intermediate. Fitting the experimental site-spacing dependence of the loop-closure probability,J, to a statistical-mechanical theory of DNA looping provides evidence for substantial out-ofplane HJ distortion. This result unequivocally stands in contrast to the square-planar intermediate geometry determined from crystallographic data for the Cre-loxP system and other int-superfamily recombinases.Jmeasurements carried out with an isomerization-deficient Cre mutant suggest that the apparent geometry of the wild-type complex may result from the temporal averaging of diverse right-handed and achiral structures. Applied to Cre recombinase, and other biological systems, our approach bridges the static pictures provided by crystal structures and the natural dynamics of macromoleculesin vivo. This approach thus advances a more comprehensive dynamic analysis of large nucleoprotein structures and their mechanisms.
The role of preadaptation, propagule pressure and competition in the colonization of new habitats
Authors: Alzate Adriana , Onstein Renske E. , Etienne Rampal S. , Bonte Dries
Published: July 2019

To successfully colonize new habitats, organisms not only need to gain access to it, but also need to cope with the selective pressures imposed by the local biotic and abiotic conditions. The number of immigrants, the preadaptation to the local habitat and the presence of competitors are important factors determining the success of colonization. Here, using an experimental set-up, we test the combined effect of propagule pressure, preadaptation and interspecific competition on the colonization success of new habitats using the two-spotted spider mite (Tetranychus urticae) as our model system and the red spider mite (Tetranychus evansi) as a competitor. Our results show that propagule pressure and preadaptation positively affect colonization success. More successful populations reach larger final population sizes either by having higher per capita growth rate (due to preadaptation effect) or by starting a population with a larger number of individuals. Although populations are more successful colonizing non-competitive environments than competitive ones, propagule pressure and preadaptation counteract the negative effects of competition, promoting colonization success. Our results show the importance of propagule pressure and preadaptation to cope both with the exigencies of the new environment and the community context for successful colonization of new habitats.
Excitatory neurons are more disinhibited than inhibitory neurons by chloride dysregulation in the spinal dorsal horn
Authors: Lee Kwan Yeop , Ratté Stéphanie , Prescott Steven A.
Published: July 2019

Neuropathic pain is a debilitating condition caused by the abnormal processing of somatosensory input. Synaptic inhibition in the spinal dorsal horn plays a key role in that processing. Mechanical allodynia – the misperception of light touch as painful – occurs when inhibition is compromised. Disinhibition is due primarily to chloride dysregulation caused by hypofunction of the potassium-chloride co-transporter KCC2. Here we show, in rats, that excitatory neurons are disproportionately affected. This is not because chloride is differentially dysregulated in excitatory and inhibitory neurons, but, rather, because excitatory neurons rely more heavily on inhibition to counterbalance strong excitation. Receptive fields in both cell types have a center-surround organization but disinhibition unmasks more excitatory input to excitatory neurons. Differences in intrinsic excitability also affect how chloride dysregulation affects spiking. These results deepen understanding of how excitation and inhibition are normally balanced in the spinal dorsal horn, and how their imbalance disrupts somatosensory processing.
High-content interrogation of human induced pluripotent stem cell-derived cortical organoid platforms
Authors: Durens Madel , Nestor Jonathan , Herold Kevin , Niescier Robert F. , Lunden Jason W. , Phillips Andre W. , Lin Yu-Chih , Nestor Michael W.
Published: July 2019

The need for scalable and high-throughput approaches to screening using 3D human stem cell models remains a central challenge in using stem cell disease models for drug discovery. It is imperative to develop standardized systems for phenotypic screening, yet most researchers screen cells across different platforms using a multitude of assays. In this study, we have developed a workflow centered on a small array of assays that can be employed to screen 3D stem cell cultures across a set of platforms. This workflow can be used as a starting point for a standardized approach to phenotypic screening. In this manuscript we hope to provide a roadmap for groups looking to start high-content screening using 3D organoid systems. To do this, we employ serum-free embryoid bodies (SFEBs) created from human induced pluripotent stem cells (hiPSCs). SFEBs are used in this study because they do not display the same level of heterogeneity observed in other neural organoid systems and they are amenable to high content imaging without cryosectioning. They contain populations of excitatory and inhibitory neurons that form synaptically active networks1 and medium- to high-throughput electrophysiology can be performed using SFEBs via the multielectrode array (MEA). The assays outlined in this study allow SFEBs to be scanned for neurite outgrowth, cell number and electrophysiological activity. SFEBs derived from control and disease hiPSCs can be used in combination with high-throughput screening assays to generate sufficient statistical power to compensate for the biological and experimental variability common in 3D cultures, while significantly decreasing processing speed, thus making this an efficient starting point for phenotypic drug screening.
Astaxanthin extends lifespan via altered biogenesis of the mitochondrial respiratory chain complex III
Authors: Hoffman Ronit , Sultan Laure D. , Saada Ann , Hirschberg Joseph , Osterzetser-Biran Oren , Gruenbaum Yosef
Published: July 2019

Astaxanthin is aketo-carotenoid produced in some bacteria and algae, which has very important industrial applications (i.e., in cosmetics, coloring additive in aquaculture and as a dietary supplement for human). Here, we analyzed the molecular basis of Astaxanthin-mediated prolongevity in the model organism,Caenorhabditis elegans. The increased lifespan effects of Astaxanthin are restricted inC. elegansto the adult phase and are uninfluenced by various other carotenoids tested. Genetic analyses indicated that the Astaxanthin-mediated life-extension relies on mitochondria activity, via the Rieske iron-sulfur polypeptide-1 (ISP-1), but is not influenced by the functions of other known longevity-related gene-loci, includingCLK-1, DAF-2,DAT-16,EAT-2,GAS-1 GLP-1orMEV-1. Biochemical analyses of native respiratory complexes showed that Astaxanthin affects the biogenesis of holo-complex III (and likely supercomplex I+III, as well). Effects on holo-CIII assembly and activity were also indicated byin-vitroassays, with mitochondria isolated from worms, rodents, human and plants, which were treated with Astaxanthin. These data indicated a cross-species effect on the oxidative phosphorylation (OXPHOS) machinery by the carotenoid, and provide with further insights into the molecular mechanism of animals longevity extension by Astaxanthin.

Significance Statement

Astaxanthin is a widely consumed pigment by animals and human. In this study we find that Astaxanthin, but not other tested carotenoids, significantly extends the lifespan of animals by affecting respiratory complex III (CIII) biogenesis of the mitochondria, in plants, C. elegans, rodents and human. We further propose a model to try explaining this effect of astaxanthin on animals’ longevity.
Astrocytic striatal GABA transporter activity governs dopamine release and shows maladaptive downregulation in early parkinsonism
Authors: Roberts Bradley M. , Doig Natalie M. , Brimblecombe Katherine R. , Lopes Emanuel F. , Siddorn Ruth E. , Threlfell Sarah , Connor-Robson Natalie , Bengoa-Vergniory Nora , Pasternack Nicholas , Wade-Martins Richard , Magill Peter J. , Cragg Stephanie J.
Published: July 2019

Striatal dopamine (DA) is critical for action and learning. Recent data show DA release is under tonic inhibition by striatal GABA. Ambient striatal GABA tone on striatal projection neurons can be governed by plasma membrane GABA uptake transporters (GATs) on astrocytes. However, whether striatal GATs and astrocytes determine DA output are unknown. We reveal that DA release in mouse dorsolateral striatum, but not nucleus accumbens core, is governed by GAT-1 and GAT-3. These GATs are partly localized to astrocytes, and are enriched in dorsolateral striatum compared to accumbens core. In a mouse model of early parkinsonism, GATs were downregulated and tonic GABAergic inhibition of DA release augmented, with corresponding attenuation of GABA co-release from dopaminergic axons. These data define previously unappreciated and important roles for GATs and astrocytes in determining DA release in striatum, and reveal a maladaptive plasticity in early parkinsonism that impairs DA output in vulnerable striatal regions.

Highlights

GABA transporters set the level of GABA inhibition of DA output in dorsal striatum

Astrocytes facilitate DA release levels by limiting tonic GABA inhibition

Tonic inhibition of DA release is augmented in a mouse model of early parkinsonism

DA and GABA co-release are reduced in a mouse model of early parkinsonism
Microclimate, CO2and CH4concentration on Blue tits (Cyanistes caeruleus) nests: effects of brood size, nestling age and on ectoparasites
Authors: Castaño-Vázquez Francisco , Merino Santiago , Cuezva Soledad , Sánchez Sergio
Published: July 2019

The presence of nestlings and other nest dwelling living beings in nests built in cavities could alter the composition of gases inside the cavity. In addition, this different concentration of gases could be used by some parasites as a cue to localize their hosts. Here, we explored the temporal variation in the concentration and isotopic signature of carbon dioxide (CO2) and methane (CH4) inside nest boxes of blue titsCyanistes caeruleusduring the nestling period (days 3, 8, 13, 20 and 21 post-hatching). Concentration of gases and isotopic signature were significantly different inside of nests than outside (forest) during the nestling period. CO2concentration was higher inside nest while CH4was lower than in forest air. The differences in the concentration of CO2between nest boxes and forest were higher on days 8th and 20th of nestling age than in other ages while the CH4was lower on day 20th of nestling age than in other ages. Moreover, CO2variation was positive and significantly related with brood size and negative and significantly with hatching date. The difference of CO2between inside of nests and forest on 8th day of nestling age were negative and significantly related to flea larvae abundance as measured at the end of the nestling period. A significant positive relationship was found between the difference of CH4between nests and forest and the final abundance of flea larvae for the same nestling age. In addition, flea larvae abundance was positive and significantly related with the relative humidity in nests at 8 days of nestling age. Moreover, blowfly pupae abundance was negative and significantly related with the difference of temperature in nests at 3 day of nestling age. The condition of blue tit females was negative and significantly related with the abundance of blowfly pupae.
Cooperative control of dual-arm robots in different human-robot collaborative tasks
Authors: Yu Xinbo , Zhang Shuang , Sun Liang , Wang Yu , Xue Chengqian , Li Bin
Published: July 2019

Purpose

This paper aims to propose cooperative control strategies for dual-arm robots in different human–robot collaborative tasks in assembly processes. The authors set three different regions where robot performs different collaborative ways: “teleoperate” region, “co-carry” region and “assembly” region. Human holds the “master” arm of dual-arm robot to operate the other “follower” arm by our proposed controller in “teleoperation” region. Limited by the human arm length, “follower” arm is teleoperated by human to carry the distant object. In the “co-carry” region, “master” arm and “follower” arm cooperatively carry the object to the region close to the human. In “assembly” region, “follower” arm is used for fixing the object and “master” arm coupled with human is used for assembly.

Design/methodology/approach

A human moving target estimated method is proposed for decreasing efforts for human to move “master” arm, radial basis functions neural networks are used to compensate for uncertainties in dynamics of both arms. Force feedback is designed in “master” arm controller for human to perceive the movement of “follower” arm. Experimental results on Baxter robot platform show the effectiveness of this proposed method.

Findings

Experimental results on Baxter robot platform show the effectiveness of our proposed methods. Different human-robot collaborative tasks in assembly processes are performed successfully under our cooperative control strategies for dual-arm robots.

Originality/value

In this paper, cooperative control strategies for dual-arm robots have been proposed in different human–robot collaborative tasks in assembly processes. Three different regions where robot performs different collaborative ways are set: “teleoperation” region, “co-carry” region and “assembly” region.
The impact of monetary policy on option-implied stock market expectations
Authors: Wang Xiaoyu , Zhai Jia , Xie Dejun , Jiang Jingjing
Published: July 2019

Purpose

The purpose of this paper is to investigate the impact of Federal Open Market Committee (FOMC) meetings and the changes of the target rates on stock market uncertainty.

Design/methodology/approach

Multivariate regression analysis is applied to the historical data of VIX, FOMC meetings and target rates. Subtle relations are revealed by further categorizing the FOMC meetings into being scheduled and unscheduled and distinguishing the signs of the changes in VIX and target rates. CPI and the prime rate are used for robustness test.

Findings

The authors first examine the relation between FOMC meetings and target surprises; the results indicate that unscheduled FOMC meetings heavily impact the target surprises. Then, the authors investigate the relation between FOMC meetings and VIX changes; the results show that both unscheduled and scheduled FOMC meetings impact VIX, where the impacts of scheduled FOMC meetings are more substantial. The authors also analyze the responses of VIX to the target surprises, and the results reveal that there is an asymmetric effect of target surprises on VIX, where the influences of the scheduled positive target surprises are more significant. Finally, by examining the relation between the FOMC meeting and the risk-neutral density of the VIX option, the authors conclude that both KURT and SKEW are more affected by unscheduled FOMC meetings.

Originality/value

Deeper dimensions of the relations between VIX, FOMC meetings and target rates are analyzed and more insightful understandings of such relations are gained.
Effects of hydrogen relative humidity on the performance of an air-breathing PEM fuel cell
Authors: Chen Zhenxiao , Ingham Derek , Ismail Mohammed , Ma Lin , Hughes Kevin J. , Pourkashanian Mohamed
Published: July 2019

Purpose

The purpose of this paper is to investigate the effects of hydrogen humidity on the performance of air-breathing proton exchange membrane (PEM) fuel cells.

Design/methodology/approach

An efficient mathematical model for air-breathing PEM fuel cells has been built in MATLAB. The sensitivity of the fuel cell performance to the heat transfer coefficient is investigated first. The effect of hydrogen humidity is also studied. In addition, under different hydrogen humidities, the most appropriate thickness of the gas diffusion layer (GDL) is investigated.

Findings

The heat transfer coefficient dictates the performance limiting mode of the air-breathing PEM fuel cell, the modelled air-breathing fuel cell is limited by the dry-out of the membrane at high current densities. The performance of the fuel cell is mainly influenced by the hydrogen humidity. Besides, an optimal cathode GDL and relatively thinner anode GDL are favoured to achieve a good performance of the fuel cell.

Practical implications

The current study improves the understanding of the effect of the hydrogen humidity in air-breathing fuel cells and this new model can be used to investigate different component properties in real designs.

Originality/value

The hydrogen relative humidity and the GDL thickness can be controlled to improve the performance of air-breathing fuel cells.
Examining the role of narratives in civic crowdfunding: linguistic style and message substance
Authors: Lee Chang Heon , Bian Yiyang , Karaouzene Rajaa , Suleiman Nasreen
Published: July 2019

Purpose

The purpose of this paper is to explore how linguistic style and message substance influence persuasion in civic crowdfunding marketplaces in which written narrative pitch become a vital communication to attract private contributions to public goods and services. Drawing on the elaboration likelihood model (ELM), the authors operationalize the linguistic style of the narrative pitch as language power and message substance as issue-relevant argument quality. In this paper, the authors examine how characteristics of both style and message are related to the outcome of civic crowdfunded projects.

Design/methodology/approach

The data on civic crowdfunding projects were retrieved from Spacehive, the platform that dedicated mainly to civic projects ranging from community programs, social-oriented enterprises, to infrastructure or facility development. Each of the narrative samples is analyzed using a computerized text analysis package called the Linguistic Inquiry and Word Count to extract the features of the linguistic style and message substance in the narratives. The logistic regression models are estimated to assess the impact of both linguistic style and message substance on crowdfunding decisions.

Findings

The results show that funding outcomes can be improved with psychological language dimensions (i.e. positive affective and perceptual language). However, extensive use of social language does not help project creators to increase their chance of funding performance; but instead, such language reduces the likelihood of project success. Additionally, message substance or issue-relevant information such as money and risk language influences funding outcome.

Originality/value

Very few empirical studies investigated the differential effects of language style and message substance on funding performance of crowdfunding campaigns. The authors draw upon the dual process of persuasion as a theoretical base to identify a comprehensive set of linguistic style and message substance and to examine the role of such features in an emerging civic crowdfunding market. This study advances the application of the dual process in ELM by identifying and examining distinct persuasive cues originating from linguistics styles and message contents.
Towards a diversified knowledge organization system
Authors: Zhitomirsky-Geffet Maayan
Published: July 2019

Purpose

The need for inclusive and logically consistent representation of diverse and even confronting viewpoints on the domain knowledge has been widely discussed in the literature in the past decade. The purpose of this paper is to propose a generic model for building an open coherent diversified knowledge organization system (KOS).

Design/methodology/approach

The proposed model incorporates a generic epistemological component, the validity scope type, assigned to each statement in the constructed KOS. Statements are clustered by their association with various validity scope types into internally coherent subsystems. These subsystems form a knowledge organization network connected through the universal (consensual) subsystems with more than one validity scope type. The model extends the Galili’s Cultural Content Representation paradigm, which divides the knowledge content of a scientific theory into two confronting parts: body and periphery.

Findings

The knowledge organization network model makes it possible to comparatively examine similarities and differences among various viewpoints and theories on the domain knowledge. The presented approach conforms with the principle of Open Knowledge Network initiative for creation of open accessible knowledge.

Practical implications

The proposed model can be used for ontological reasoning by a variety of information services, such as ontology-based decision-support and learning systems, diversified search and customer management applications.

Social implications

The model enables explicit representation of social and cultural minority voices and historical knowledge in the KOS.

Originality/value

The main contribution of the proposed model is that it generalizes and enhances various previously proposed representations of epistemological aspects of KOS and allows for multiple inter-linked subsystems to coherently co-exist as part of the extensible network.
Infliximab reduces activated myeloid dendritic cells, different macrophage subsets and CXCR3‐positive cells in granuloma annulare
Authors: Bürgler Christina , Vinay Keshavamurthy , Häfliger Stefanie , Klötgen Hans‐Wilhelm , Yawalkar Nikhil
Published: July 2019

Disseminated granuloma annulare (GA) is a rare granulomatous dermatitis of unknown etiology. Treatment is often challenging and lack of a uniformly effective treatment, adds to the disease morbidity. Tumor necrosis factor (TNF)‐α is an important cytokine in granuloma formation and previous reports have shown improvement of disseminated GA with anti‐TNF‐α therapy. Nevertheless, the underlying mechanism of actions of TNF‐α inhibitors in GA remains unclear. Our aim was to evaluate alterations in the inflammatory infiltrate in a patient who experienced complete clearance of GA after treatment with infliximab. A skin biopsy was obtained before and 24 weeks after treatment with infliximab 5 mg/kg at weeks 0, 2, 6, 14 and 24. Immunohistochemical stains were performed in pre‐ and post‐treatment biopsy specimens using CD1a, CD4, CD8, CD11c, CD32, CD68, CD69, CD163, CD183 and human leukocyte antigen (HLA)‐DR to characterize alterations of the infiltrates. Parallel with clinical improvement, we observed a marked decrease in myeloid (CD11c) dendritic cells, different macrophage subsets (CD68, CD32, CD163) and T cells. In addition, a marked reduction of activation markers (HLA‐DR, CD69) and CD183+ (CXCR3) cells was observed in post‐treatment biopsy specimens. In conclusion, the clinical improvement of disseminated GA by infliximab is paralleled by inhibition of activated myeloid dendritic cells, different macrophage subsets and type 1 T cells.
The tropical backyard: performing environmental difference
Authors: Law Lisa
Published: July 2019

This paper extends debates investigating the importance of domestic yards and gardens in shaping identities and the everyday practices and performances of human–nature interaction in a tropical city. It presents findings from a pilot study investigating backyards in a small but ethnically diverse neighbourhood in Cairns, Australia—a site that raises questions about the normative constructions of “nature” in much of the literature. The paper explores how Cairns residents make sense of their backyards, especially in terms of how they relate to them as “tropical”. Living in Cairns means managing excess water during the rainy season, dealing with new kinds of pests, and being critically conscious of the temperate bias of Australian garden retailers and house/garden magazines. The paper frames these experiences within a longer tradition of tropicality or a (western) way of making sense of/imagining tropical regions and environmental difference. In so doing, it opens up a new cultural geography of the suburbs, displaces normative constructions of “nature” and shows how the legacies of European colonialism still play out in a dominant Australian culture.
Valuing product innovation: genetically engineered varieties in US corn and soybeans
Authors: Ciliberto Federico , Moschini GianCarlo , Perry Edward D.
Published: July 2019

We develop a discrete‐choice model of differentiated products for US corn and soybean seed demand to study the welfare impact of genetically engineered (GE) crop varieties. Using a unique data set spanning the period 1996–2011, we find that the welfare impact of the GE innovation is significant. In the last five years of the period analyzed, our preferred counterfactual indicates that total surplus due to GE traits was $5.18 billion per year, with seed manufacturers appropriating 56% of this surplus. The seed industry obtained more surplus from GE corn, whereas farmers received more surplus from GE soybeans.
Detection, molecular characterisation and aspects involving the transmission of tomato chlorotic dwarf viroid in eggplant
Authors: Gramazio Pietro , Lerma María D. , Villanueva Gloria , Vilanova Santiago , García‐Fortea Edgar , Mangino Giulio , Figàs Maria R. , Arrones Andrea , Alonso David , San Bautista Alberto , Soler Salvador , Prohens Jaime , Plazas Mariola
Published: July 2019

Tomato chlorotic dwarf viroid (TCDVd) is a pospiviroid that causes severe disease symptoms in tomato. TCDVd is also naturally found in other crops and plants, in most occasions being asymptomatic. Apart from the natural hosts reported up to now, artificial inoculations have revealed that TCDVd can infect other plants, including eggplant (Solanum melongena). In a screening of seedlings of eggplant from a breeding programme we detected a pospiviroid, which we identified as TCDVd, representing the first report of natural infection of eggplant by TCDVd. The new TCDVd isolate of eggplant was detected by reverse transcription polymerase chain reaction (RT‐PCR) using primers TG21/CT20, initially designed to detect potato spindle tuber viroid. The new isolate sequence is close to a Brugmansia sanguinea isolate of TCDVd from the Netherlands, and most of the nucleotidic changes with respect to this isolate and to the reference genome sequence of TCDVd are found in the TR region. Naturally infected plants of eggplant with this TCDVd isolate did not display any disease symptoms. We demonstrated that in eggplant TCDVd is mechanically transmitted with low to moderate efficiency with cultivation practices, but not by plant‐to‐plant contact. Tomato plants artificially inoculated with the eggplant isolate of TCDVd tested positive for the presence of the viroid at 50 days after inoculation, but did not display any disease symptoms. Seed transmission to germinated seedlings of eggplant was variable among progenies from infected plants, ranging from 7.7% to 100.0%. Disinfection of seeds with chemical treatments with sodium hypochlorite and trisodium phosphate solutions plus thermotherapy at 80°C for 24 hr or 90°C for 6 hr was ineffective in reducing the rate of transmission by seed. We did not find evidence of horizontal transmission of TCDVd by pollen, but vertical transmission was highly efficient when healthy eggplant plants were pollinated with infected pollen. Our results indicate that asymptomatic infection of eggplant by TCDVd and high seed and pollen transmission rates may contribute to the spread of this viroid. The information we obtained is useful in order to implement measures for the prevention, control and eradication of TCDVd in eggplant crops, as well as to avoid their transmission to other hosts.
Risk Factors for Overdose in Young People Who Received Substance Use Disorder Treatment
Authors: Yule Amy M. , Carrellas Nicholas W. , DiSalvo Maura , Lyons Rachael M. , McKowen James W. , Nargiso Jessica E. , Bergman Brandon G. , Kelly John F. , Wilens Timothy E.
Published: July 2019

Background and Objectives

To identify substance and psychiatric predictors of overdose (OD) in young people with substance use disorders (SUDs) who received treatment.

Methods

We conducted a retrospective review of consecutive medical records of young people who were evaluated in a SUD program between 2012 and 2013 and received treatment. An independent group of patients from the same program who received treatment and had a fatal OD were also included in the sample. OD was defined as substance use associated with a significant impairment in level of consciousness without intention of self‐harm, or an ingestion of a substance that was reported as a suicide attempt. t Tests, Pearson's χ2, and Fisher's exact tests were performed to identify predictors of OD after receiving treatment.

Results

After initial evaluation, 127 out of 200 patients followed up for treatment and were included in the sample. Ten (8%) of these patients had a nonfatal OD. Nine patients who received treatment and had a fatal OD were also identified. The sample's mean age was 20.2 ± 2.8 years. Compared with those without OD, those with OD were more likely to have a history of intravenous drug use (odds ratio [OR]: 36.5, P < .001) and mood disorder not otherwise specified (OR: 4.51, P = .01).

Discussion and Conclusions

Intravenous drug use and mood dysregulation increased risk for OD in young people who received SUD treatment.

Scientific Significance

It is important to identify clinically relevant risk factors for OD specific to young people in SUD treatment due to the risk for death associated with OD. (Am J Addict 2019;28:382–389)
The efficacy of HBOC‐201 in ex situ gradual rewarming kidney perfusion in a rat model
Authors: Mahboub Paria , Aburawi Mohamed , Karimian Negin , Lin Florence , Karabacak Murat , Fontan Fermin , Tessier Shannon N. , Markmann James , Yeh Heidi , Uygun Korkut
Published: July 2019

Gradual rewarming from hypothermic to normothermic is a novel perfusion modality with superior outcome to sudden rewarming to normothermic. However, the identification of an oxygen carrier that could function at a temperature range from 4 to 7°C or whether it is necessary to use oxygen carrier during kidney rewarming, remains unresolved. This study was designed to test the use of a hemoglobin‐based oxygen carrier (HBOC) during gradual kidney rewarming as an alternative to simple dissolved oxygen. In this study, 10 rat kidneys were randomly divided into the control and the HBOC group. In the control group, no oxygen carrier was used during rewarming perfusion and the perfusion solution was oxygenated only by applying diffused carbogen flow. The protocol mimicked a donor after circulatory death (DCD) kidney transplantation, where after 30 minutes warm ischemia and 120 minutes cold storage in University of Wisconsin solution, the DCD kidneys underwent gradual rewarming from 10 to 37°C during 90 minutes with or without HBOC. This was followed by 30 minutes of warm ischemia in room temperature to mimic the anastomosis time and 120 minutes of reperfusion at 37°C to mimic the early post‐transplant state of the graft. The HBOC group demonstrated superior kidney function which was highlighted by higher ultrafiltrate production, better glomerular filtration rate and improved sodium reabsorption. There was no significant difference between the 2 groups regarding the hemodynamics, tissue injury, and adenosine triphosphate levels. In conclusion, this study suggests better renal function recovery in DCD kidneys after rewarming with HBOC compared to rewarming without an oxygen carrier.
The effect of gastrectomy on regorafenib exposure and progression‐free survival in patients with advanced gastrointestinal stromal tumours
Authors: Lubberman Floor J.E. , van der Graaf Winette T.A. , Xu Lei , Cleton Adriaan , Demetri George D. , Gelderblom Hans , van Erp Nielka P.
Published: July 2019

Aims

We investigated whether major gastrectomy influences the plasma exposure of regorafenib and treatment outcome.

Methods

Efficacy and pharmacokinetic data from 133 gastrointestinal stromal tumour patients included in a phase III trial were analysed. Patients were subdivided into 2 groups according to the extent of the gastrectomy (no/nonsignificant gastrectomy and major gastrectomy). Progression‐free survival (PFS) on regorafenib was measured and regorafenib and its pharmacological active metabolites plasma exposure were measured.

Results

A total of 133 patient were included, of whom 27 underwent major gastrectomy. In patients with no/nonsignificant gastrectomy the median PFS was 145 (interquartile range 43–281) days. The PFS in patients with a major gastrectomy was 172 (interquartile range 57–280) days. Regorafenib pharmacokinetic samples were collected in 80 patients of which 19 patients with a major gastrectomy and 61 patients with no/nonsignificant gastric surgery. The average ± standard deviation total concentration of regorafenib including the metabolites M‐2 and M‐5 was 6.9 ± 1.53 μmol/L and 6.7 ± 1.56 μmol/L in patient with major gastrectomy and no/nonsignificant gastrectomy respectively.

Conclusion

Our study shows that major gastrectomy did not influence plasma exposure of regorafenib and metabolites. In addition, no difference in PFS between the subgroups was seen.
Toward Understanding Representation Methods in Visualization Recommendations through Scatterplot Construction Tasks
Authors: L'Yi Sehi , Chang Youli , Shin DongHwa , Seo Jinwook
Published: July 2019

Most visualization recommendation systems predominantly rely on graphical previews to describe alternative visual encodings. However, since InfoVis novices are not familiar with visual representations (e.g., interpretation barriers [GTS10]), novices might have difficulty understanding and choosing recommended visual encodings. As an initial step toward understanding effective representation methods for visualization recommendations, we investigate the effectiveness of three representation methods (i.e., previews, animated transitions, and textual descriptions) under scatterplot construction tasks. Our results show how different representations individually and cooperatively help users understand and choose recommended visualizations, for example, by supporting their expect‐and‐confirm process. Based on our study results, we discuss design implications for visualization recommendation interfaces.
Visualizing for the Non‐Visual: Enabling the Visually Impaired to Use Visualization
Authors: Choi Jinho , Jung Sanghun , Park Deok Gun , Choo Jaegul , Elmqvist Niklas
Published: July 2019

The majority of visualizations on the web are still stored as raster images, making them inaccessible to visually impaired users. We propose a deep‐neural‐network‐based approach that automatically recognizes key elements in a visualization, including a visualization type, graphical elements, labels, legends, and most importantly, the original data conveyed in the visualization. We leverage such extracted information to provide visually impaired people with the reading of the extracted information. Based on interviews with visually impaired users, we built a Google Chrome extension designed to work with screen reader software to automatically decode charts on a webpage using our pipeline. We compared the performance of the back‐end algorithm with existing methods and evaluated the utility using qualitative feedback from visually impaired users.
Towards Glyphs for Uncertain Symmetric Second‐Order Tensors
Authors: Gerrits Tim , Rössl Christian , Theisel Holger
Published: July 2019

Measured data often incorporates some amount of uncertainty, which is generally modeled as a distribution of possible samples. In this paper, we consider second‐order symmetric tensors with uncertainty. In the 3D case, this means the tensor data consists of 6 coefficients – uncertainty, however, is encoded by 21 coefficients assuming a multivariate Gaussian distribution as model. The high dimension makes the direct visualization of tensor data with uncertainty a difficult problem, which was until now unsolved. The contribution of this paper consists in the design of glyphs for uncertain second‐order symmetric tensors in 2D and 3D. The construction consists of a standard glyph for the mean tensor that is augmented by a scalar field that represents uncertainty. We show that this scalar field and therefore the displayed glyph encode the uncertainty comprehensively, i.e., there exists a bijective map between the glyph and the parameters of the distribution. Our approach can extend several classes of existing glyphs for symmetric tensors to additionally encode uncertainty and therefore provides a possible foundation for further uncertain tensor glyph design. For demonstration, we choose the well‐known superquadric glyphs, and we show that the uncertainty visualization satisfies all their design constraints.
A Geometric Optimization Approach for the Detection and Segmentation of Multiple Aneurysms
Authors: Lawonn Kai , Meuschke Monique , Wickenhöfer Ralph , Preim Bernhard , Hildebrandt Klaus
Published: July 2019

We present a method for detecting and segmenting aneurysms in blood vessels that facilitates the assessment of risks associated with the aneurysms. The detection and analysis of aneurysms is important for medical diagnosis as aneurysms bear the risk of rupture with fatal consequences for the patient. For risk assessment and treatment planning, morphological descriptors, such as the height and width of the aneurysm, are used. Our system enables the fast detection, segmentation and analysis of single and multiple aneurysms. The method proceeds in two stages plus an optional third stage in which the user interacts with the system. First, a set of aneurysm candidate regions is created by segmenting regions of the vessels. Second, the aneurysms are detected by a classification of the candidates. The third stage allows users to adjust and correct the result of the previous stages using a brushing interface. When the segmentation of the aneurysm is complete, the corresponding ostium curves and morphological descriptors are computed and a report including the results of the analysis and renderings of the aneurysms is generated. The novelty of our approach lies in combining an analytic characterization of aneurysms and vessels to generate a list of candidate regions with a classifier trained on data to identify the aneurysms in the candidate list. The candidate generation is modeled as a global combinatorial optimization problem that is based on a local geometric characterization of aneurysms and vessels and can be efficiently solved using a graph cut algorithm. For the aneurysm classification scheme, we identified four suitable features and modeled appropriate training data. An important aspect of our approach is that the resulting system is fast enough to allow for user interaction with the global optimization by specifying additional constraints via a brushing interface.
Linking and Layout: Exploring the Integration of Text and Visualization in Storytelling
Authors: Zhi Qiyu , Ottley Alvitta , Metoyer Ronald
Published: July 2019

Modern web technologies are enabling authors to create various forms of text visualization integration for storytelling. This integration may shape the stories' flow and thereby affect the reading experience. In this paper, we seek to understand two text visualization integration forms: (i) different text and visualization spatial arrangements (layout), namely, vertical and slideshow; and (ii) interactive linking of text and visualization (linking). Here, linking refers to a bidirectional interaction mode that explicitly highlights the explanatory visualization element when selecting narrative text and vice versa. Through a crowdsourced study with 180 participants, we measured the effect of layout and linking on the degree to which users engage with the story (user engagement), their understanding of the story content (comprehension), and their ability to recall the story information (recall). We found that participants performed significantly better in comprehension tasks with the slideshow layout. Participant recall was better with the slideshow layout under conditions with linking versus no linking. We also found that linking significantly increased user engagement. Additionally, linking and the slideshow layout were preferred by the participants. We also explored user reading behaviors with different conditions.
Tasks, Techniques, and Tools for Genomic Data Visualization
Authors: Nusrat S. , Harbig T. , Gehlenborg N.
Published: July 2019

Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of investigators. Addressing this need has become crucial in genomics, as biomedical research is increasingly data‐driven and many studies lack well‐defined hypotheses. A key challenge in data‐driven research is to discover unexpected patterns and to formulate hypotheses in an unbiased manner in vast amounts of genomic and other associated data. Over the past two decades, this has driven the development of numerous data visualization techniques and tools for visualizing genomic data. Based on a comprehensive literature survey, we propose taxonomies for data, visualization, and tasks involved in genomic data visualization. Furthermore, we provide a comprehensive review of published genomic visualization tools in the context of the proposed taxonomies.
The State of the Art in Visualizing Multivariate Networks
Authors: Nobre C. , Meyer M. , Streit M. , Lex A.
Published: July 2019

Multivariate networks are made up of nodes and their relationships (links), but also data about those nodes and links as attributes. Most real‐world networks are associated with several attributes, and many analysis tasks depend on analyzing both, relationships and attributes. Visualization of multivariate networks, however, is challenging, especially when both the topology of the network and the attributes need to be considered concurrently. In this state‐of‐the‐art report, we analyze current practices and classify techniques along four axes: layouts, view operations, layout operations, and data operations. We also provide an analysis of tasks specific to multivariate networks and give recommendations for which technique to use in which scenario. Finally, we survey application areas and evaluation methodologies.
The State of the Art in Visual Analysis Approaches for Ocean and Atmospheric Datasets
Authors: Afzal S. , Hittawe M.M. , Ghani S. , Jamil T. , Knio O. , Hadwiger M. , Hoteit I.
Published: July 2019

The analysis of ocean and atmospheric datasets offers a unique set of challenges to scientists working in different application areas. These challenges include dealing with extremely large volumes of multidimensional data, supporting interactive visual analysis, ensembles exploration and visualization, exploring model sensitivities to inputs, mesoscale ocean features analysis, predictive analytics, heterogeneity and complexity of observational data, representing uncertainty, and many more. Researchers across disciplines collaborate to address such challenges, which led to significant research and development advances in ocean and atmospheric sciences, and also in several relevant areas such as visualization and visual analytics, big data analytics, machine learning and statistics. In this report, we perform an extensive survey of research advances in the visual analysis of ocean and atmospheric datasets. First, we survey the task requirements by conducting interviews with researchers, domain experts, and end users working with these datasets on a spectrum of analytics problems in the domain of ocean and atmospheric sciences. We then discuss existing models and frameworks related to data analysis, sense‐making, and knowledge discovery for visual analytics applications. We categorize the techniques, systems, and tools presented in the literature based on the taxonomies of task requirements, interaction methods, visualization techniques, machine learning and statistical methods, evaluation methods, data types, data dimensions and size, spatial scale and application areas. We then evaluate the task requirements identified based on our interviews with domain experts in the context of categorized research based on our taxonomies, and existing models and frameworks of visual analytics to determine the extent to which they fulfill these task requirements, and identify the gaps in current research. In the last part of this report, we summarize the trends, challenges, and opportunities for future research in this area.

(see http://www.acm.org/about/class/class/2012)