bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topic Tomographies (TopTom): a visual approach to distill information from media streams
Authors: Gobbo B. , Balsamo D. , Mauri M. , Bajardi P. , Panisson A. , Ciuccarelli P. 
Published: July 2019

AbstractIn this paper we present Top Tom, a digital platform whose goal is to provide analytical and visual solutions for the exploration of a dynamic corpus of user‐generated messages and media articles, with the aim of i) distilling the information from thousands of documents in a low‐dimensional space of explainable topics, ii) cluster them in a hierarchical fashion while allowing to drill down to details and stories as constituents of the topics, iii) spotting trends and anomalies. Top Tom implements a batch processing pipeline able to run both in near‐real time with time stamped data from streaming sources and on historical data with a temporal dimension in a cold start mode. The resulting output unfolds along three main axes: time, volume and semantic similarity (i.e. topic hierarchical aggregation). To allow the browsing of data in a multiscale fashion and the identification of anomalous behaviors, three visual metaphors were adopted from biological and medical fields to design visualizations, i.e. the flowing of particles in a coherent stream, tomographic cross sectioning and contrast‐like analysis of biological tissues. The platform interface is composed by three main visualizations with coherent and smooth navigation interactions: calendar view, flow view, and temporal cut view. The integration of these three visual models with the multiscale analytic pipeline proposes a novel system for the identification and exploration of topics from unstructured texts. We evaluated the system using a collection of documents about the emerging opioid epidemics in the United States.
Augmenting Tactile 3D Data Navigation With Pressure Sensing
Authors: Wang Xiyao , Besançon Lonni , Ammi Mehdi , Isenberg Tobias 
Published: July 2019

AbstractWe present a pressure‐augmented tactile 3D data navigation technique, specifically designed for small devices, motivated by the need to support the interactive visualization beyond traditional workstations. While touch input has been studied extensively on large screens, current techniques do not scale to small and portable devices. We use phone‐based pressure sensing with a binary mapping to separate interaction degrees of freedom (DOF) and thus allow users to easily select different manipulation schemes (e. g., users first perform only rotation and then with a simple pressure input to switch to translation). We compare our technique to traditional 3D‐RST (rotation, scaling, translation) using a docking task in a controlled experiment. The results show that our technique increases the accuracy of interaction, with limited impact on speed. We discuss the implications for 3D interaction design and verify that our results extend to older devices with pseudo pressure and are valid in realistic phone usage scenarios.
A Random Sampling O(n) Force‐calculation Algorithm for Graph Layouts
Authors: Gove R. 
Published: July 2019

AbstractThis paper proposes a linear‐time repulsive‐force‐calculation algorithm with sub‐linear auxiliary space requirements, achieving an asymptotic improvement over the Barnes‐Hut and Fast Multipole Method force‐calculation algorithms. The algorithm, named random vertex sampling (RVS), achieves its speed by updating a random sample of vertices at each iteration, each with a random sample of repulsive forces. This paper also proposes a combination algorithm that uses RVS to derive an initial layout and then applies Barnes‐Hut to refine the layout. An evaluation of RVS and the combination algorithm compares their speed and quality on 109 graphs against a Barnes‐Hut layout algorithm. The RVS algorithm performs up to 6.1 times faster on the tested graphs while maintaining comparable layout quality. The combination algorithm also performs faster than Barnes‐Hut, but produces layouts that are more symmetric than using RVS alone. Data and code: https://osf.io/nb7m8/
State‐of‐the‐Art Report: Visual Computing in Radiation Therapy Planning
Authors: Schlachter M. , Raidou R.G. , Muren L.P. , Preim B. , Putora P.M. , Bühler K. 
Published: July 2019

AbstractRadiation therapy (RT) is one of the major curative approaches for cancer. It is a complex and risky treatment approach, which requires precise planning, prior to the administration of the treatment. Visual Computing (VC) is a fundamental component of RT planning, providing solutions in all parts of the process—from imaging to delivery. Despite the significant technological advancements of RT over the last decades, there are still many challenges to address. This survey provides an overview of the compound planning process of RT, and of the ways that VC has supported RT in all its facets. The RT planning process is described to enable a basic understanding in the involved data, users and workflow steps. A systematic categorization and an extensive analysis of existing literature in the joint VC/RT research is presented, covering the entire planning process. The survey concludes with a discussion on lessons learnt, current status, open challenges, and future directions in VC/RT research.
A Review of Guidance Approaches in Visual Data Analysis: A Multifocal Perspective
Authors: Ceneda Davide , Gschwandtner Theresia , Miksch Silvia 
Published: July 2019

AbstractVisual data analysis can be envisioned as a collaboration of the user and the computational system with the aim of completing a given task. Pursuing an effective system‐user integration, in which the system actively helps the user to reach his/her analysis goal has been focus of visualization research for quite some time. However, this problem is still largely unsolved. As a result, users might be overwhelmed by powerful but complex visual analysis systems which also limits their ability to produce insightful results. In this context, guidance is a promising step towards enabling an effective mixed‐initiative collaboration to promote the visual analysis. However, the way how guidance should be put into practice is still to be unravelled. Thus, we conducted a comprehensive literature research and provide an overview of how guidance is tackled by different approaches in visual analysis systems. We distinguish between guidance that is provided by the system to support the user, and guidance that is provided by the user to support the system. By identifying open problems, we highlight promising research directions and point to missing factors that are needed to enable the envisioned human‐computer collaboration, and thus, promote a more effective visual data analysis.
State‐of‐the‐art in Multi‐Light Image Collections for Surface Visualization and Analysis
Authors: Pintus R. , Dulecha T. G. , Ciortan I. , Gobbetti E. , Giachetti A. 
Published: July 2019

AbstractMulti‐Light Image Collections (MLICs), i.e., stacks of photos of a scene acquired with a fixed viewpoint and a varying surface illumination, provide large amounts of visual and geometric information. In this survey, we provide an up‐to‐date integrative view of MLICs as a mean to gain insight on objects through the analysis and visualization of the acquired data. After a general overview of MLICs capturing and storage, we focus on the main approaches to produce representations usable for visualization and analysis. In this context, we first discuss methods for direct exploration of the raw data. We then summarize approaches that strive to emphasize shape and material details by fusing all acquisitions in a single enhanced image. Subsequently, we focus on approaches that produce relightable images through intermediate representations. This can be done both by fitting various analytic forms of the light transform function, or by locally estimating the parameters of physically plausible models of shape and reflectance and using them for visualization and analysis. We finally review techniques that improve object understanding by using illustrative approaches to enhance relightable models, or by extracting features and derived maps. We also review how these methods are applied in several, main application domains, and what are the available tools to perform MLIC visualization and analysis. We finally point out relevant research issues, analyze research trends, and offer guidelines for practical applications.
Lizards possess the most complete tetrapod Hox gene repertoire despite pervasive structural changes in Hox clusters
Authors: Feiner Nathalie , Wood Natalie J. 
Published: July 2019

AbstractHox genes are a remarkable example of conservation in animal development and their nested expression along the head‐to‐tail axis orchestrates embryonic patterning. Early in vertebrate history, two duplications led to the emergence of four Hox clusters (A‐D) and redundancy within paralog groups has been partially accommodated with gene losses. Here we conduct an inventory of squamate Hox genes using the genomes of 10 lizard and 7 snake species. Although the HoxC1 gene has been hypothesized to be lost in the amniote ancestor, we reveal that it is retained in lizards. In contrast, all snakes lack functional HoxC1 and ‐D12 genes. Varying levels of degradation suggest differences in the process of gene loss between the two genes. The vertebrate HoxC1 gene is prone to gene loss and its functional domains are more variable than those of other Hox1 genes. We describe for the first time the HoxC1 expression patterns in tetrapods. HoxC1 is broadly expressed during development in the diencephalon, the neural tube, dorsal root ganglia, and limb buds in two lizard species. Our study emphasizes the value of revisiting Hox gene repertoires by densely sampling taxonomic groups and its feasibility owing to growing sequence resources in evaluating gene repertoires across taxa.
The cost and the value of treatment of medication overuse headache in Italy: a longitudinal study based on patient‐derived data
Authors: Raggi A. , Leonardi M. , Sansone E. , Curone M. , Grazzi L. , D'Amico D. 
Published: July 2019

Background and purposeThe cost of medication overuse headache (MOH) is underestimated. Our aim was to address the cost‐effectiveness of a structured treatment protocol and to present annual cost estimates.MethodsPatients were enrolled on the occasion of a structured treatment protocol, were administered a research protocol addressing direct and indirect costs and were followed up for 3 months.ResultsOf 176 enrolled patients, 138 completed the study. The 3‐month cost per patient fell from €2989 to €1160: the difference was €696 per month for patients treated in the ward and €466 for those treated in day‐hospital; thus it takes 2–3 months to compensate for the protocol's cost. The per‐person annual costs of MOH were €10 533 (95% confidence interval €8700–12 406): direct healthcare costs accounted for 44.8% and indirect costs for 51.5% of the total MOH cost. The annual MOH cost for Italy is estimated at €13.5 billion (95% confidence interval €11.1–15.9 billion).ConclusionThe cost of MOH around the period of a structured treatment protocol is much higher compared to previous estimates. Our protocol is cost‐effective for reducing the economic burden of MOH.
Thirteen years of medication alerts issued by the Brazilian Health Regulatory Agency (ANVISA): What is the profile?
Authors: Ferreira Vitor Costa , Ferreira Gustavo Costa , Baldoni André Oliveira 
Published: July 2019

AbstractRationale, aims, and objectivesAs a pharmacovigilance measure, the Brazilian Health Regulatory Agency (ANVISA) monitors the postmarketing events of medication and issues alerts on actions to be taken and information updates. The present study has the objective of analysing the profile of all the alerts on medication issued by ANVISA between 2006 and 2018.MethodsA descriptive documentary analysis was carried out through the ANVISA website and double checked with two researchers in order to avoid discrepancies in data collection and interpretation of information.ResultsA total of 79 alerts available in the period were analysed, the mean being 6.07 alerts/year and standard deviation of 3.81. The medications most cited in the alerts were antivirals (9.7%), followed by antidiabetics (7.3%) and contraceptives (7.3%). The main problems identified were adverse reactions (50%) and other problems related to safety (15%). The main actions directed by ANVISA were generation of a new contraindication (37.3%) and alteration in the package insert (22.3%).ConclusionAlerts are an important means of communicating new information to health professionals and to society. However, they need better standardization in order to facilitate understanding, dissemination in order to broaden access to information, and studies to corroborate the current literature and improve current pharmacovigilance.
IGF2 enhanced the osteo‐/dentinogenic and neurogenic differentiation potentials of stem cells from apical papilla
Authors: Diao Shu , Yang Haoqing , Cao Yangyang , Yang Dongmei , Fan Zhipeng 
Published: July 2019

AbstractObjectivesIn dental tissue engineering, niche is important for maintaining stem cell function and regenerating the dental tissues. However, there is limited knowledge for the growth factors in niche to maintain the function of stem cells. In this study, we investigated the effect of IGF2, a growth factor in stem cells from apical papilla (SCAPs) niche, on differentiation and proliferation potentials of SCAPs.Materials and methodsRecombinant human IGF2 protein (rhIGF2) was used. Cell counting kit‐8 assay, Carboxyfluorescein succinimidyl ester assay, alkaline phosphatase (ALP) activity, Alizarin Red staining, quantitative calcium analysis, immunofluorescence staining and real‐time RT‐PCR were performed to investigate the cell proliferation and differentiation potentials of SCAPs. And proteomic analysis was used to identify the differential secreted proteins.ResultsBy ALP activity assay, we found that 5 ng/mL rhIGF2 might be the optimal concentration for treatment. Then, Alizarin Red staining, quantitative calcium analysis and osteogenesis‐related gene expression results showed that 5 ng/mL rhIGF2 could enhance the osteo‐/dentinogenic differentiation potentials in SCAPs. Immunofluorescence staining and real‐time RT‐PCR results showed that neurogenic markers were significantly induced by 5 ng/mL rhIGF2 in SCAPs. Then, CCK‐8 assay and CFSE assay results showed that 5 ng/mL rhIGF2 could enhance the cell proliferation in SCAPs. Furthermore, proteomic analysis showed that IGF2 could induce some secreted proteins which function related to the osteogenesis, neurogenesis and cell proliferation.ConclusionsOur results identified that IGF2 might be the potential mediator in niche to promote SCAP function and dental tissue regeneration.
Elucidating the functional evolution of heat sensors amongXenopusspecies adapted to different thermal niches by ancestral sequence reconstruction
Authors: Saito Shigeru , Saito Claire T. , Nozawa Masafumi , Tominaga Makoto 
Published: July 2019

AbstractAmbient temperature fluctuations are detected via the thermosensory system which allows animals to seek preferable thermal conditions or escape from harmful temperatures. Evolutionary changes in thermal perception have thus potentially played crucial roles in niche selection. The genusXenopus(clawed frog) is suitable for investigating the relationship between thermal perception and niche selection due to their diverse latitudinal and altitudinal distributions. Here we performed comparative analyses of the neuronal heat sensors TRPV1 and TRPA1 among closely relatedXenopusspecies (X. borealis,X. muelleri,X. laevis, andX. tropicalis) to elucidate their functional evolution and to assess whether their functional differences correlate with thermal niche selection among the species. Comparison of TRPV1 among four extantXenopusspecies and reconstruction of the ancestral TRPV1 revealed that TRPV1 responses to repeated heat stimulation were specifically altered in the lineage leading toX. tropicaliswhich inhabits warmer niches. Moreover, the thermal sensitivity of TRPA1 was lower inX. tropicalisthan the other species, although the thermal sensitivity of TRPV1 and TRPA1 was not always lower in species that inhabit warmer niches than the species inhabit cooler niches. However, a clear correlation was found in species differences in TRPA1 activity. Heat‐evoked activity of TRPA1 inX. borealisandX. laevis, which are adapted to cooler niches, was significantly higher than inX. tropicalisandX. muelleriwhich are adapted to warmer niches. These findings suggest that the functional properties of heat sensors changed duringXenopusevolution, potentially altering the preferred temperature ranges among species.
The Rationality of Emotional Change: Toward a Process View*
Authors: Na'aman Oded 
Published: July 2019

AbstractThe paper argues against a widely held synchronic view of emotional rationality. I begin by considering recent philosophical literature on various backward‐looking emotions, such as regret, grief, resentment, and anger. I articulate the general problem these accounts grapple with: a certain diminution in backward‐looking emotions seems fitting while the reasons for these emotions seem to persist. The problem, I argue, rests on the assumption that if the facts that give reason for an emotion remain unchanged, the emotion remains fitting. However, I argue there are rationally self‐consuming attitudes: affective attitudes that become less fitting the longer they endure while the facts that give reason for them persist. A widely held synchronic view of fitting affective attitudes denies that fittingness at a time depends on the agent's attitudes at different times and therefore denies that the fittingness of an affective attitude can depend on its duration. Once we reject the synchronic view, we may see that affective attitudes are often fitting due to the fitting processes of which they are part. These fitting processes explain the fitting diminution of backward‐looking emotions as well as other diachronic aspects of the fittingness of emotions.
Alterations in cellular RNA decapping dynamics affect tomato spotted wilt virus cap snatching and infection in Arabidopsis
Authors: Ma Xiaofang , Zhou Yijun , Moffett Peter 
Published: July 2019

Summary

RNA processing and decay pathways have important impacts on RNA viruses, particularly animal‐infecting bunyaviruses, which utilize a cap‐snatching mechanism to translate their mRNAs. However, their effects on plant‐infecting bunyaviruses have not been investigated.

The roles of mRNA degradation and non‐sense‐mediated decay components, including DECAPPING 2 (DCP2), EXORIBONUCLEASE 4 (XRN4), ASYMMETRIC LEAVES2 (AS2) and UP‐FRAMESHIFT 1 (UPF1) were investigated in infection of Arabidopsis thaliana by several RNA viruses, including the bunyavirus, tomato spotted wilt virus (TSWV).

TSWV infection on mutants with decreased or increased RNA decapping ability resulted in increased and decreased susceptibility, respectively. By contrast, these mutations had the opposite, or no, effect on RNA viruses that use different mRNA capping strategies. Consistent with this, the RNA capping efficiency of TSWV mRNA was higher in a dcp2 mutant. Furthermore, the TSWV N protein partially colocalized with RNA processing body (PB) components and altering decapping activity by heat shock or coinfection with another virus resulted in corresponding changes in TSWV accumulation.

The present results indicate that TSWV infection in plants depends on its ability to snatch caps from mRNAs destined for decapping in PBs and that genetic or environmental alteration of RNA processing dynamics can affect infection outcomes.
Preoperative Plan with 3D Printing in Internal and External Fixation for Complex Tibial Plateau Fractures
Authors: Wu Wei‐yong , Xu Wei‐guo , Wan Chun‐you , Fang Min 
Published: July 2019

ObjectiveTo compare short‐term treatment effects of internal and external fixation in the treatment of complicated tibial plateau fractures by preoperative planning with 3D printing.MethodsSixty‐nine patients with tibial plateau fractures were examined. 3D printing was used to establish the model in all patients before the operation. Thirty‐four patients were treated with an external fixator (9‐Schatzker Type V, 25‐Schatzker Type VI) and 35 patients were treated with internal fixation (12‐Schatzker Type V, 23‐Schatzker Type VI). The time span of the study was 2 years after the operation. All patients were followed up in the clinic of the attending physician who recorded patient follow‐up information at the same time. Finally, the Rasmussen functional score, radiographic parameters, complication rates, hospital days and operative parameters of the two groups were analyzed.ResultsThe short‐term (within 2 years) Rasmussen score in the external fixation group was close to that of the internal fixation group; the differences were not significant (P > 0.05). The fractures were reduced adequately using both forms of surgical treatment. There is no significant difference between internal and external fixation in terms of radiographic parameters after 2 years (Mann–Whitney U‐tests, P > 0.05). Thrombosis was detected in 7 cases (2 external fixation, 5 internal fixation). Superficial infection was detected in 3 cases (1 external fixation, 2 internal fixation). Deep infection was detected in 3 cases (0 external fixation, 3 internal fixation). Knee stiffness was detected in 4 cases (2 external fixation, 2 internal fixation); 1 (2.7%) case of screw pullout occurred in the internal fixation group. The external fixation group had shorter operation times (172.94 ± 50.00 min vs 253.86 ± 64.59 min), less bleeding volume (395.88 ± 121.10 mL vs 864.29 ± 238.12 mL), and fewer days (17.03 ± 5.03 days vs 30.17 ± 8.64 days) of hospitalization compared to the internal fixation (t‐test, P = 0.00); subgroup analysis of all patients with complex tibial plateau fractures revealed that for patients with tibial plateau fracture type VI, the functional score of external fixation (26.79 ± 2.04) is better than that (25.54 ± 1.69) of internal fixation (t‐ test, P = 0.026) and the overall infection rate of external fixation is lower than that of internal fixation (χ2‐ test, P = 0.047).ConclusionUsing 3D printed models in combination with external fixation has more advantages for short‐term treatment of complex tibial plateau fractures. In particular, relatively better functional recovery and lower rates of infection can be achieved for Schatzker type VI fractures. The external fixation treatment was preferred in cases of Schatzker VI tibial plateau fractures.