bluuebunny/crossref_metadata_2025 huggingface dataset:
On the diverse and opposing effects of nutrition on pathogen virulence
Authors: Pike Victoria L. , Lythgoe Katrina A. , King Kayla C.
Published: July 2019

Climate change and anthropogenic activity are currently driving large changes in nutritional availability across ecosystems, with consequences for infectious disease. An increase in host nutrition could lead to more resources for hosts to expend on the immune system or for pathogens to exploit. In this paper, we report a meta-analysis of studies on host–pathogen systems across the tree of life, to examine the impact of host nutritional quality and quantity on pathogen virulence. We did not find broad support across studies for a one-way effect of nutrient availability on pathogen virulence. We thus discuss a hypothesis that there is a balance between the effect of host nutrition on the immune system and on pathogen resources, with the pivot point of the balance differing for vertebrate and invertebrate hosts. Our results suggest that variation in nutrition, caused by natural or anthropogenic factors, can have diverse effects on infectious disease outcomes across species.
Single cell chromatin accessibility reveals pancreatic islet cell type- and state-specific regulatory programs of diabetes risk
Authors: Chiou Joshua , Zeng Chun , Cheng Zhang , Han Jee Yun , Schlichting Michael , Huang Serina , Wang Jinzhao , Sui Yinghui , Deogaygay Allison , Okino Mei-Lin , Qiu Yunjiang , Sun Ying , Kudtarkar Parul , Fang Rongxin , Preissl Sebastian , Sander Maike , Gorkin David , Gaulton Kyle J
Published: July 2019

Genetic risk variants for complex, multifactorial diseases are enriched incis-regulatory elements. Single cell epigenomic technologies create new opportunities to dissect cell type-specific mechanisms of risk variants, yet this approach has not been widely applied to disease-relevant tissues. Given the central role of pancreatic islets in type 2 diabetes (T2D) pathophysiology, we generated accessible chromatin profiles from 14.2k islet cells and identified 13 cell clusters including multiple alpha, beta and delta cell clusters which represented hormone-producing and signal-responsive cell states. We cataloged 244,236 islet cell type accessible chromatin sites and identified transcription factors (TFs) underlying both lineage- and state-specific regulation. We measured the enrichment of T2D and glycemic trait GWAS for the accessible chromatin profiles of single cells, which revealed heterogeneity in the effects of beta cell states and TFs on fasting glucose and T2D risk. We further used machine learning to predict the cell type-specific regulatory function of genetic variants, and single cell co-accessibility to link distal sites to putative cell type-specific target genes. We localized 239 fine-mapped T2D risk signals to islet accessible chromatin, and further prioritized variants at these signals with predicted regulatory function and co-accessibility with target genes. At theKCNQ1locus, the causal T2D variant rs231361 had predicted effects on an enhancer with beta cell-specific, long-range co-accessibility to the insulin promoter, and deletion of this enhancer reduced insulin gene and protein expression in human embryonic stem cell-derived beta cells. Our findings provide a cell type- and state-resolved map of gene regulation in human islets, illuminate likely mechanisms of T2D risk at hundreds of loci, and demonstrate the power of single cell epigenomics for interpreting complex disease genetics.
Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1
Authors: Biggs Bradley W. , Bedore Stacy R. , Arvay Erika , Huang Shu , Subramanian Harshith , McIntyre Emily A. , Duscent-Maitland Chantel V. , Neidle Ellen L. , Tyo Keith E.J.
Published: July 2019

One primary objective of synthetic biology is to improve the sustainability of chemical manufacturing. Biological systems can utilize a variety of carbon sources, including waste streams that pose challenges to traditional chemical processing such as lignin biomass, providing opportunity for remediation and valorization of these materials. Success, however, depends on identifying microorganisms that are both metabolically versatile and engineerable. This has been a historic hindrance. Here, we leverage the facile genetics of the metabolically versatile bacterium Acinetobacter baylyi ADP1 to create easy and rapid molecular cloning workflows, a promoter library, ribosomal binding site (RBS) variants, and an unprecedented number of bacterial chromosomal protein expression sites and variants. Moreover, we demonstrate the utility of these tools by examining ADP1’s catabolic repression regulation, creating a strain with improved potential for lignin bioprocessing. Taken together, this work establishes ADP1 as an ideal host for a variety of sustainability and synthetic biology applications.
A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures in mixed phenotype acute leukemia
Authors: Granja Jeffrey M. , Klemm Sandy , McGinnis Lisa M. , Kathiria Arwa S. , Mezger Anja , Parks Benjamin , Gars Eric , Liedtke Michaela , Zheng Grace X.Y. , Chang Howard Y. , Majeti Ravindra , Greenleaf William J.
Published: July 2019

In order to identify the molecular determinants of human diseases, such as cancer, that arise from a diverse range of tissue, it is necessary to accurately distinguish normal and pathogenic cellular programs.1–3Here we present a novel approach for single-cell multi-omic deconvolution of healthy and pathological molecular signatures within phenotypically heterogeneous malignant cells. By first creating immunophenotypic, transcriptomic and epigenetic single-cell maps of hematopoietic development from healthy peripheral blood and bone marrow mononuclear cells, we identify cancer-specific transcriptional and chromatin signatures from single cells in a cohort of mixed phenotype acute leukemia (MPAL) clinical samples. MPALs are a high-risk subtype of acute leukemia characterized by a heterogeneous malignant cell population expressing both myeloid and lymphoid lineage-specific markers.4, 5Our results reveal widespread heterogeneity in the pathogenetic gene regulatory and expression programs across patients, yet relatively consistent changes within patients even across malignant cells occupying diverse portions of the hematopoietic lineage. An integrative analysis of transcriptomic and epigenetic maps identifies 91,601 putative gene-regulatory interactions and classifies a number of transcription factors that regulate leukemia specific genes, includingRUNX1-linked regulatory elements proximal toCD69. This work provides a template for integrative, multi-omic analysis for the interpretation of pathogenic molecular signatures in the context of developmental origin.
The Genome of the Zebra Mussel,Dreissena polymorpha: A Resource for Invasive Species Research
Authors: McCartney Michael A. , Auch Benjamin , Kono Thomas , Mallez Sophie , Zhang Ying , Obille Angelico , Becker Aaron , Abrahante Juan E. , Garbe John , Badalamenti Jonathan P. , Herman Adam , Mangelson Hayley , Liachko Ivan , Sullivan Shawn , Sone Eli D. , Koren Sergey , Silverstein Kevin A. T. , Beckman Kenneth B. , Gohl Daryl M.
Published: July 2019

The zebra mussel,Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources forDreissenaor related bivalves, with nearly 450 million years of divergence between zebra mussels and its closest sequenced relative. Although theD. polymorphagenome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate the highest quality molluscan assembly to date. Through comparative analysis and transcriptomics experiments we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact Steamer-Like Elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found thatD. polymorphahave an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.
Probabilities of multilocus genotypes in SIB recombinant inbred lines
Authors: Jebreen Kamel , Petrizzelli Marianyela , Martin Olivier C.
Published: July 2019

Recombinant Inbred Lines (RILs) are obtained through generations of inbreeding until all alleles are fixed. In 1931 Haldane and Waddington published a landmark paper where they provided the probabilities of achieving any combination of alleles in 2-way RILs for 2 and 3 loci. In the case of SIB RILs where sisters and brothers are crossed at each generation, there has been no progress in treating 4 or more loci, a limitation we overcome here without much increase in complexity. In the general situation ofLloci, the task is to determine 2Lprobabilities, but we find that it is necessary to first calculate the 4L“identical by descent” (IBD) probabilities that a RIL inherits at each locus its DNA from one of the four originating chromosomes. We show that these 4Lprobabilities satisfy a system of linear equations that follow from self consistency. In the absence of genetic interference – crossovers arising independently –, the associated matrix can be written explicitly in terms of the recombination rates between the different loci. We provide the matrices forLup to 4 and also include a computer program to automatically generate the matrices for higher values ofL. Furthermore, our framework can be generalized to recombination rates that are different in female and male meiosis which allows us to show that the Haldane and Waddington 2-locus formula is valid in that more subtle case if the meiotic recombination rate is taken as the average rate across female and male. Once the 4LIBD probabilities are determined, the 2Lprobabilities of RIL genotypes are obtainedviasummations of these quantities.In fine, our computer program allows to determine the probabilities of all the multilocus genotypes produced in such sibling-based RILs forL≤ 10, a huge leap beyond theL= 3 restriction of Haldane and Waddington.
A dual function of TMEM70 in OXPHOS: assembly of complexes I and V
Authors: Sánchez-Caballero Laura , Elurbe Dei M. , Baertling Fabian , Guerrero-Castillo Sergio , van den Brand Mariel , van Strien Joeri , van Dam Teunis J. P. , Rodenburg Richard , Brandt Ulrich , Huynen Martijn A. , Nijtmans Leo G.J.
Published: July 2019

Protein complexes from the oxidative phosphorylation (OXPHOS) system are assembled with the help of proteins called assembly factors. We here delineate the function of the inner mitochondrial membrane protein TMEM70, in which mutations have been linked to OXPHOS deficiencies, using a combination of BioID, complexome profiling and coevolution analyses. TMEM70 interacts with complex I and V and for both complexes the loss of TMEM70 results in the accumulation of an assembly intermediate followed by a reduction of the next assembly intermediate in the pathway. This indicates that TMEM70 has a role in the stability of membrane-bound subassemblies or in the membrane recruitment of subunits into the forming complex. Independent evidence for a role of TMEM70 in OXPHOS assembly comes from evolutionary analyses. The TMEM70/TMEM186/TMEM223 protein family, of which we show that TMEM186 and TMEM223 are mitochondrial in human as well, only occurs in species with OXPHOS complexes. Our results validate the use of combining complexomics with BioID and evolutionary analyses in elucidating congenital defects in protein complex assembly.
Extended Bayesian inference incorporating symmetry bias
Authors: Shinohara Shuji , Manome Nobuhito , Suzuki Kouta , Chung Ung-il , Takahashi Tatsuji , Gunji Pegio-Yukio , Nakajima Yoshihiro , Mitsuyoshi Shunji
Published: July 2019

In this study, we start by proposing a causal induction model that incorporates symmetry bias. This model has two parameters that control the strength of symmetry bias and includes conditional probability and conventional models of causal induction as special cases. It can reproduce causal induction of human judgment with high accuracy. We further propose a human-like Bayesian inference method to replace the conditional probability in Bayesian inference with the aforementioned causal induction model. In this method, two components coexist: the component of Bayesian inference, which updates the degree of confidence for each hypothesis, and the component of inverse Bayesian inference that modifies the model of each hypothesis. In other words, this method allows not only inference but also simultaneous learning. Our study demonstrates that the method with both Bayesian inference and inverse Bayesian inference enables us to deal flexibly with unsteady situations where the target of inference changes occasionally.
Management controls, heterarchy and innovation: a case study of a start-up company
Authors: Taylor David , King Robyn , Smith David
Published: July 2019

Purpose

The purpose of this paper is to consider how organizations with diverse, interdependent functions with differing evaluative principles and differing ideas as to which behaviors are the most desirable, use management controls in their efforts to achieve innovation.

Design/methodology/approach

The authors conducted a case study of TechCo, an Australian technology start-up company, over a 12 month period.

Findings

The authors demonstrate how the clash of differing evaluative principles among interdependent teams led to the organization seeking new ways of organizing, which in turn, enabled the organization to better manage the interdependencies between the diverse functional areas. Additionally, the findings show how, through the use of management control systems, the organization was able to promote idea generation and “buy-in” across all functional areas, order competing priorities for innovation and set the agenda as to what constituted “acceptable” innovation for the organization to pursue.

Originality/value

The authors find that management controls play an important role in managing the tensions between differing evaluative principles in diverse functional areas in a heterarchical organization, and in supporting innovation in such an environment. As such, the authors provide the first research evidence on how management controls are used within a heterarchy to generate and select innovative ideas.
A comparison of text structure and self-regulated strategy instruction for elementary school students’ writing
Authors: Teng (Mark) Feng
Published: July 2019

Purpose

This study aims to examine the writing outcomes of 6th-grade students learning English as a second language.

Design/methodology/approach

In all 45 students in a text structure instruction (TSI) group were compared with 45 students in a self-regulated strategy instruction (SRSI) group and 43 students receiving traditional writing instruction. SRSI was adapted from the self-regulated strategy development (SRSD) model (MacArthur et al., 2015). The SRSD model includes self-regulation writing strategies, text and genre knowledge and think-aloud modeling. Findings allowed for a comparison of TSI and SRSI, in which organization knowledge does not need to be taught using SRSD methods. Measures of writing outcomes, including writing quality and summarization of main ideas, were administered after a one-month intervention.

Findings

Results revealed that, compared with traditional instruction, the TSI and SRSI groups each exhibited better writing outcomes. Compared with the traditional instruction group, each technique had a unique impact: SRSI on writing quality, and TSI on main ideas included in written summaries. Linguistic and textual analyses of students’ writing revealed that the TSI and SRSI group learners both demonstrated high syntactic complexity, content organization and lexical variation in their compositions.

Research limitations/implications

The present study provides empirical evidence that explicit teaching of SRSI writing strategies or TSI can be implemented effectively and elicit gains in elementary school L2 learners’ written output. A clear division does not exist between self-regulated writing strategies and text structure knowledge; the two techniques should be complementary, as suggested in the earlier SRSD model.

Originality/value

Classroom-based research has addressed the need to enhance self-regulated capacity in writing. However, writing has become more challenging for primary school learners. In addition, writing is a cognitively demanding process. The plethora of processes involved in writing may be one of the factors that caused difficulties in writing. Thus, writing proficiency relies on the development of text structure knowledge and the fostering of self-regulation capabilities.
Cross-sectional reshaping of perturbed/unperturbed rectangular jets
Authors: Ghasemi Abbas , Li Xianguo
Published: July 2019

Purpose

This study aims to investigate the cross-sectional reshaping in transitioning/starting rectangular jets of aspect ratio 2 under various inlet perturbation conditions at the Reynolds number of Re = UDh/v = 17,750.

Design/methodology/approach

Large eddy simulation results compared with the phase-locked particle image velocimetry data exhibit the cross-sectional jet deformations from rectangular to rounder shapes. Inflow velocity oscillations are introduced at the fundamental frequency associated with the Kelvin–Helmholtz instability characterized by the spectral analysis of the hotwire data and the linear stability predictions.

Findings

The initially rectangular cross-section of the jet reshapes into the rounder geometries with increased downstream distance while the edges of the jet become distorted due to the shear layer instability more significantly observed near the high curvature corners. The different expansion rates in the longer and shorter edges of the jet and the consequent cross-sectional reshaping are found to be sensitive to small levels of random inlet perturbations. In addition, introducing controlled sinusoidal oscillations results in the formation of more organized trailing shear layer where the stronger vortex rings go through the curvature-induced deformations.

Originality/value

Spatio-temporal study of vortex dynamics in transitioning rectangular jets reveals important information about the effect of the controlled jet forcing on local entrainment. Dynamics of the leading vortex dominates the entrainment in transitioning jets which are commonly used in practical applications. Near-field entrainment is also promoted proportional to the amplitude of the controlled inlet oscillations within the trailing vortex rings.
Double stratified stagnation-point flow of Williamson nanomaterial with entropy generation through a porous medium
Authors: Khan Muhammad Ijaz , Kiyani M.Z. , Hayat Tasawar , Faisal Javed Muhammad , Ahmad I.
Published: July 2019

Purpose

This paper aims to address double-stratified stagnation-point flow of Williamson nanomaterial with entropy generation. Flow through porous medium is discussed. Energy equation is modeled in existence of viscous dissipation, Brownian motion and thermophoresis. Furthermore, convective boundary conditions are considered. Total entropy rate is presented.

Design/methodology/approach

The non-linear flow expressions are converted to ordinary ones by implementation of suitable transformations. The obtained ordinary system is tackled for series solutions via homotopy analysis method.

Findings

Till date no one has considered the irreversibility analysis in stagnation-point flow of Williamson nanomaterial with double stratification, porous medium and convective conditions. The basic objective of present research is to investigate the convective stagnation point flow of Williamson liquid with entropy concept and porous medium.

Originality/value

As per the authors’ knowledge, no such work is yet present in the literature.
China’s emerging partnership network: what, who, where, when and why
Authors: Li Quan , Ye Min
Published: July 2019

Purpose

The purpose of this paper is to explore and test the motivation behind the evolution of China’s vast network of partnerships around the globe since the end of the Cold War.

Design/methodology/approach

After combing through 24 types of partnerships with 78 countries, the authors empirically tested four hypotheses using data from Correlates of War and World Bank.

Findings

The analysis indicates that China’s choice to build such an elaborate network is not random. On the contrary, it is largely determined by three factors: the need to counter the US pressure; the necessity of maintaining peace and stability along its borders and achieving the long-term goal of modernization.

Originality/value

The research is among the first attempts to comprehensively test the possible motivations behind China’s partnership building efforts and provides a stepping stone for analyzing this important aspect of China’s foreign policy.
Leveraging guest-room technology: a tale of two guest profiles
Authors: Erdem Mehmet , Atadil Hilmi A. , Nasoz Pelin
Published: July 2019

Purpose

The purpose of this study is to examine hotel guests’ attitudes toward guest room technologies (GRTs) and determine whether hotel guests’ characteristics and attitudes regarding GRTs vary according to hotel guest typologies.

Design/methodology/approach

The data were gathered from a sample of 508 hotel guests who had stayed in a hotel in the past 12 months via a self-administered survey on Qualtrics survey software. The analysis of the study consisted of two main research steps: identification of cluster groups via the K-means cluster analysis algorithm and discriminant analysis; and performing a series of chi-square analyses to determine whether hotel guests’ characteristics and attitudes vary according to obtained hotel guest typologies.

Findings

Results indicated significant attitudinal (e.g. internet payment preference) and demographic (e.g. age) differences among the obtained hotel guest typologies regarding their attitudes toward GRTs.

Practical implications

The results provide valuable guidance and a pragmatic approach for those hotel managers that aim to generate tailored marketing strategies for guest segments that are interested in GRTs.

Originality/value

This study concentrates on GRTs with a market segmentation approach by using advanced statistical procedures. It contributes to the body of related research literature by offering empirical evidence where the study evaluates the impact of the availability of new GRTs on guest decision-making based on the principles of the theory of planned behavior. Practitioners will be able to use the presented findings to generate marketing and pricing strategies with respect to the technological needs and wants of each typology.
Lack of fire and insect herbivory constrain recruitment in a rare legume from Western Australia
Authors: Cochrane Anne , Monks Leonie
Published: July 2019

We investigated factors influencing recruitment in the rare endemic shrubAcacia insolitasubsp.recurva(Fabaceae) from the heavily cleared south‐west of Western Australia. We examined annual seed production over 4 years, including the impact of herbivory on reproductive output. Conversion of bud to fruit was low (overall 0.02%). The lack of significant difference in canopy dimensions between caged and uncaged plants suggested that vertebrate herbivore grazing was negligible, but invertebrate predation had a negative impact on seed production (loss of >80% of fruiting potential). Soil cores determined the presence of soil‐stored seeds and an experimental burn confirmed that plants are fire‐killed and can regenerate from the seed bank. This seed reserve was found to contain <5 seeds m−2, and both freshly collected seeds and seeds retrieved from the soil had high viability (99%vs. 91%) when subjected to a germination test. Seedling recruitment 29 months post‐fire resulted in a ratio of three seedlings for every adult killed by fire. We also compared reproductive success in this rareAcaciawith its common conspecific and although the rare species produced more flowers, the success of flowering did not translate into better fruit set. We conclude that insect damage to reproductive branchlets and lack of appropriate disturbance are major factors constraining recruitment. Active site management may be required for the continued persistence of this fire‐dependent legume.
Artificial oxygen carrier improves fatigue resistance in slow muscle but not in fast muscle in a rat in situ model
Authors: Kawaguchi Akira T. , Tamaki Tetsuro
Published: July 2019

The effects of liposome‐encapsulated hemoglobin with high O2 affinity (h‐LEH), an artificial O2 carrier in skeletal muscle, were studied by in situ fatigue resistance test in fast‐type plantaris (PLT) and slow‐type soleus (SOL) muscles with or without ischemia in the rat. The distal tendons of PLT and SOL muscles were isolated in situ and individually attached to the force transducers to record the developed tension in response to stimuli (80 Hz tetanus train, 1.5 minutes) to the ipsilateral sciatic nerve. The fatigue resistance test (five sets separated by 2‐minute rests) was evaluated in terms of tension attenuation (fatigue) from the initial to the last tension (A) during each set, attenuation of the initial (B) or last tension (C) in each set, as compared to the first set in the presence or absence of ischemia or h‐LEH (10 mL/kg). While ischemia significantly enhanced fatigue only in PLT, h‐LEH showed no effect regardless of the perfusion pattern (normal/ischemia) or muscle‐type (PLT/SOL) during each set (A). In parameter (B), set‐by‐set fatigue development was observed in PLT, whereas h‐LEH‐SOL showed a trend of advanced fatigue resistance. Such trends became clear in the parameter C (last tension), because h‐LEH‐SOL exerted, rather than decreased, the tension enhancement regardless of the presence or absence of ischemia, whereas there were no h‐LEH effects in PLT. In addition, faster recovery of the nicotinamide adenine dinucleotide content in the muscle after 10 minutes of all fatigue tests was observed in h‐LEH‐SOL, while saline‐SOL still showed a significantly higher value than that of control. These results suggested that additional O2 supply by h‐LEH may accelerate the tricarboxylic acid cycle/electron transport chain in slow‐type aerobic SOL muscle containing abundant mitochondria and contribute to the faster removal of muscle fatigue substances such as lactate.
An analysis of innovation in textile companies: An efficiency approach
Authors: Puertas Medina Rosa , Martí Selva M. Luisa , Calafat Marzal Consuelo
Published: July 2019

The elimination of trade contingency measures in 2005 triggered a process of renewal in the textile sector, requiring major investments. The divide between efficiency and innovation has become an issue of major importance for decision‐making in the Spanish textile sector. This study provides quantitative data on the efficiency levels of innovative Spanish textile companies. The aim is to identify their distinguishing features and establish a possible pattern to follow. In addition, truncated regression is used to estimate the determinants of efficiency, in order to check the significance of innovation processes for firms.
Interactions of nanomaterials with ion channels and related mechanisms
Authors: Yin Suhan , Liu Jia , Kang Yiyuan , Lin Yuqing , Li Dongjian , Shao Longquan
Published: July 2019

The pharmacological potential of nanotechnology, especially in drug delivery and bioengineering, has developed rapidly in recent decades. Ion channels, which are easily targeted by external agents, such as nanomaterials (NMs) and synthetic drugs, due to their unique structures, have attracted increasing attention in the fields of nanotechnology and pharmacology for the treatment of ion channel‐related diseases. NMs have significant effects on ion channels, and these effects are manifested in many ways, including changes in ion currents, kinetic characteristics and channel distribution. Subsequently, intracellular ion homeostasis, signalling pathways, and intracellular ion stores are affected, leading to the initiation of a range of biological processes. However, the effect of the interactions of NMs with ion channels is an interesting topic that remains obscure. In this review, we have summarized the recent research progress on the direct and indirect interactions between NMs and ion channels and discussed the related molecular mechanisms, which are crucial to the further development of ion channel‐related nanotechnological applications.
Latent Space Cartography: Visual Analysis of Vector Space Embeddings
Authors: Liu Yang , Jun Eunice , Li Qisheng , Heer Jeffrey
Published: July 2019

Latent spaces—reduced‐dimensionality vector space embeddings of data, fit via machine learning—have been shown to capture interesting semantic properties and support data analysis and synthesis within a domain. Interpretation of latent spaces is challenging because prior knowledge, sometimes subtle and implicit, is essential to the process. We contribute methods for “latent space cartography”, the process of mapping and comparing meaningful semantic dimensions within latent spaces. We first perform a literature survey of relevant machine learning, natural language processing, and scientific research to distill common tasks and propose a workflow process. Next, we present an integrated visual analysis system for supporting this workflow, enabling users to discover, define, and verify meaningful relationships among data points, encoded within latent space dimensions. Three case studies demonstrate how users of our system can compare latent space variants in image generation, challenge existing findings on cancer transcriptomes, and assess a word embedding benchmark.
DIVA: Exploration and Validation of Hypothesized Drug‐Drug Interactions
Authors: Kakar T. , Qin X. , Rundensteiner E. A. , Harrison L. , Sahoo S. K. , De S.
Published: July 2019

Adverse reactions caused by drug‐drug interactions are a major public health concern. Currently, adverse reaction signals are detected through a tedious manual process in which drug safety analysts review a large number of reports collected through post‐marketing drug surveillance. While computational techniques in support of this signal analysis are necessary, alone they are not sufficient. In particular, when machine learning techniques are applied to extract candidate signals from reports, the resulting set is (1) too large in size, i.e., exponential to the number of unique drugs and reactions in reports, (2) disconnected from the underlying reports that serve as evidence and context, and (3) ultimately requires human intervention to be validated in the domain context as a true signal warranting action. In this work, we address these challenges though a visual analytics system, DIVA, designed to align with the drug safety analysis workflow by supporting the detection, screening, and verification of candidate drug interaction signals. DTVA's abstractions and encodings are informed by formative interviews with drug safety analysts. DIVA's coordinated visualizations realize a proposed novel augmented interaction data model (AIM) which links signals generated by machine learning techniques with domain‐specific metadata critical for signal analysis. DIVA's alignment with the drug review process allows an analyst to interactively screen for important signals, triage signals for in‐depth investigation, and validate signals by reviewing the underlying reports that serve as evidence. The evaluation of DIVA encompasses case‐studies and interviews by drug analysts at the US Food and Drug Administration ‐ both of which confirm that DIVA indeed is effective in supporting analysts in the critical task of exploring and verifying dangerous drug‐drug interactions.
Characterizing Exploratory Visual Analysis: A Literature Review and Evaluation of Analytic Provenance in Tableau
Authors: Battle Leilani , Heer Jeffrey
Published: July 2019

Supporting exploratory visual analysis (EVA) is a central goal of visualization research, and yet our understanding of the process is arguably vague and piecemeal. We contribute a consistent definition of EVA through review of the relevant literature, and an empirical evaluation of existing assumptions regarding how analysts perform EVA using Tableau, a popular visual analysis tool. We present the results of a study where 27 Tableau users answered various analysis questions across 3 datasets. We measure task performance, identify recurring patterns across participants' analyses, and assess variance from task specificity and dataset. We find striking differences between existing assumptions and the collected data. Participants successfully completed a variety of tasks, with over 80% accuracy across focused tasks with measurably correct answers. The observed cadence of analyses is surprisingly slow compared to popular assumptions from the database community. We find significant overlap in analyses across participants, showing that EVA behaviors can be predictable. Furthermore, we find few structural differences between behavior graphs for open‐ended and more focused exploration tasks.
A User‐based Visual Analytics Workflow for Exploratory Model Analysis
Authors: Cashman Dylan , Humayoun Shah Rukh , Heimerl Florian , Park Kendall , Das Subhajit , Thompson John , Saket Bahador , Mosca Abigail , Stasko John , Endert Alex , Gleicher Michael , Chang Remco
Published: July 2019

Many visual analytics systems allow users to interact with machine learning models towards the goals of data exploration and insight generation on a given dataset. However, in some situations, insights may be less important than the production of an accurate predictive model for future use. In that case, users are more interested in generating of diverse and robust predictive models, verifying their performance on holdout data, and selecting the most suitable model for their usage scenario. In this paper, we consider the concept of Exploratory Model Analysis (EMA), which is defined as the process of discovering and selecting relevant models that can be used to make predictions on a data source. We delineate the differences between EMA and the well‐known term exploratory data analysis in terms of the desired outcome of the analytic process: insights into the data or a set of deployable models. The contributions of this work are a visual analytics system workflow for EMA, a user study, and two use cases validating the effectiveness of the workflow. We found that our system workflow enabled users to generate complex models, to assess them for various qualities, and to select the most relevant model for their task.
The Dependent Vectors Operator
Authors: Hofmann Lutz , Sadlo Filip
Published: July 2019

In this paper, we generalize the parallel vectors operator due to Peikert and Roth to arbitrary dimension, i.e., to four‐dimensional fields and beyond. Whereas the original operator tested for parallelism of two (derived) 2D or 3D vector fields, we reformulate the concept in terms of linear dependency of sets of vector fields, and propose a generic technique to extract and filter the solution manifolds. We exemplify our approach for vortex cores, bifurcations, and ridges as well as valleys in higher dimensions.
Robust Reference Frame Extraction from Unsteady 2D Vector Fields with Convolutional Neural Networks
Authors: Kim Byungsoo , Günther Tobias
Published: July 2019

Robust feature extraction is an integral part of scientific visualization. In unsteady vector field analysis, researchers recently directed their attention towards the computation of near‐steady reference frames for vortex extraction, which is a numerically challenging endeavor. In this paper, we utilize a convolutional neural network to combine two steps of the visualization pipeline in an end‐to‐end manner: the filtering and the feature extraction. We use neural networks for the extraction of a steady reference frame for a given unsteady 2D vector field. By conditioning the neural network to noisy inputs and resampling artifacts, we obtain numerically stabler results than existing optimization‐based approaches. Supervised deep learning typically requires a large amount of training data. Thus, our second contribution is the creation of a vector field benchmark data set, which is generally useful for any local deep learning‐based feature extraction. Based on Vatistas velocity profile, we formulate a parametric vector field mixture model that we parameterize based on numerically‐computed example vector fields in near‐steady reference frames. Given the parametric model, we can efficiently synthesize thousands of vector fields that serve as input to our deep learning architecture. The proposed network is evaluated on an unseen numerical fluid flow simulation.
Visualization Support for Developing a Matrix Calculus Algorithm: A Case Study
Authors: Giesen Joachim , Klaus Julien , Laue Sören , Schreck Ferdinand
Published: July 2019

The development of custom interactive visualization tools for specific domains and applications has been made much simpler recently by a surge of visualization tools, libraries and frameworks. Most of these tools are developed for classical data science applications, where a user is supported in analyzing measured or simulated data. But recently, there has also been an increasing interest in visual support for understanding machine learning algorithms and frameworks, especially for deep learning. Many, if not most, of the visualization support for (deep) learning addresses the developer of the learning system and not the end user (data scientist). Here we show on a specific example, namely the development of a matrix calculus algorithm, that supporting visualizations can also greatly benefit the development of algorithms in classical domains like in our case computer algebra. The idea is similar to visually supporting the understanding of learning algorithms, namely provide the developer with an interactive, visual tool that provides insights into the workings and, importantly, also into the failures of the algorithm under development. Developing visualization support for matrix calculus development went similar as the development of more traditional visual support systems for data analysts. First, we had to acquaint ourselves with the problem, its language and challenges by talking to the core developer of the matrix calculus algorithm. Once we understood the challenge, it was fairly easy to develop visual support that streamlined the development of the matrix calculus algorithm significantly.
Ray Tracing Generalized Tube Primitives: Method and Applications
Authors: Han Mengjiao , Wald Ingo , Usher Will , Wu Qi , Wang Feng , Pascucci Valerio , Hansen Charles D. , Johnson Chris R.
Published: July 2019

We present a general high‐performance technique for ray tracing generalized tube primitives. Our technique efficiently supports tube primitives with fixed and varying radii, general acyclic graph structures with bifurcations, and correct transparency with interior surface removal. Such tube primitives are widely used in scientific visualization to represent diffusion tensor imaging tractographies, neuron morphologies, and scalar or vector fields of 3D flow. We implement our approach within the OSPRay ray tracing framework, and evaluate it on a range of interactive visualization use cases of fixed‐ and varying‐radius streamlines, pathlines, complex neuron morphologies, and brain tractographies. Our proposed approach provides interactive, high‐quality rendering, with low memory overhead.
Visual Analysis of Charge Flow Networks for Complex Morphologies
Authors: Kottravel S. , Falk M. , Masood T. Bin , Linares M. , Hotz I.
Published: July 2019

In the field of organic electronics, understanding complex material morphologies and their role in efficient charge transport in solar cells is extremely important. Related processes are studied using the Ising model and Kinetic Monte Carlo simulations resulting in large ensembles of stochastic trajectories. Naive visualization of these trajectories, individually or as a whole, does not lead to new knowledge discovery through exploration. In this paper, we present novel visualization and exploration methods to analyze this complex dynamic data, which provide succinct and meaningful abstractions leading to scientific insights. We propose a morphology abstraction yielding a network composed of material pockets and the interfaces, which serves as backbone for the visualization of the charge diffusion. The trajectory network is created using a novel way of implicitly attracting the trajectories to the skeleton of the morphology relying on a relaxation process. Each individual trajectory is then represented as a connected sequence of nodes in the skeleton. The final network summarizes all of these sequences in a single aggregated network. We apply our method to three different morphologies and demonstrate its suitability for exploring this kind of data.
Kyrix: Interactive Pan/Zoom Visualizations at Scale
Authors: Tao Wenbo , Liu Xiaoyu , Wang Yedi , Battle Leilani , Demiralp Çağatay , Chang Remco , Stonebraker Michael
Published: July 2019

Pan and zoom are basic yet powerful interaction techniques for exploring large datasets. However, existing zoomable UI toolkits such as Pad++ and ZVTM do not provide the backend database support and data‐driven primitives that are necessary for creating large‐scale visualizations. This limitation in existing general‐purpose toolkits has led to many purpose‐built solutions (e.g. Google Maps and ForeCache) that address the issue of scalability but cannot be easily extended to support visualizations beyond their intended data types and usage scenarios. In this paper, we introduce Kyrix to ease the process of creating general and large‐scale web‐based pan/zoom visualizations. Kyrix is an integrated system that provides the developer with a concise and expressive declarative language along with a backend support for performance optimization of large‐scale data. To evaluate the scalability of Kyrix, we conducted a set of benchmarked experiments and show that Kyrix can support high interactivity (with an average latency of 100 ms or below) on pan/zoom visualizations of 100 million data points. We further demonstrate the accessibility of Kyrix through an observational study with 8 developers. Results indicate that developers can quickly learn Kyrix's underlying declarative model to create scalable pan/zoom visualizations. Finally, we provide a gallery of visualizations and show that Kyrix is expressive and flexible in that it can support the developer in creating a wide range of customized visualizations across different application domains and data types.
Efficient Optimal Overlap Removal: Algorithms and Experiments
Authors: Meulemans W.
Published: July 2019

Motivated by visualizing spatial data using proportional symbols, we study the following problem: given a set of overlapping squares of varying sizes, minimally displace the squares as to remove the overlap while maintaining the orthogonal order on their centers. Though this problem is NP‐hard, we show that rotating the squares by 45 degrees into diamonds allows for a linear or convex quadratic program. It is thus efficiently solvable even for relatively large instances.

This positive result and the flexibility offered by constraint programming allow us to study various trade‐offs for overlap removal. Specifically, we model and evaluate through computational experiments the relations between displacement, scale and order constraints for static data, and between displacement and temporal coherence for time‐varying data. Finally, we also explore the generalization of our methodology to other shapes.
Agreement on endoscopic ultrasonography‐guided tissue specimens: Comparing a 20‐G fine‐needle biopsy to a 25‐G fine‐needle aspiration needle among academic and non‐academic pathologists
Authors: van Riet Priscilla A. , Cahen Djuna L. , Biermann Katharina , Hansen Bettina , Larghi Alberto , Rindi Guido , Fellegara Giovanni , Arcidiacono Paolo , Doglioni Claudio , Liberta Decarli Nicola , Iglesias‐Garcia Julio , Abdulkader Ihab , Lazare Iglesias Hector , Kitano Masayuki , Chikugo Takaaki , Yasukawa Satoru , van der Valk Hans , Nguyen Nam Quoc , Ruszkiewicz Andrew , Giovannini Marc , Poizat Flora , van der Merwe Schalk , Roskams Tania , Santo Erwin , Marmor Silvia , Chang Kenneth , Lin Fritz , Farrell James , Robert Marie , Bucobo Juan Carlos , Heimann Alan , Baldaque‐Silva Francisco , Fernández Moro Carlos , Bruno Marco J.
Published: July 2019

Background and Aim

A recently carried out randomized controlled trial showed the benefit of a novel 20‐G fine‐needle biopsy (FNB) over a 25‐G fine‐needle aspiration (FNA) needle. The current study evaluated the reproducibility of these findings among expert academic and non‐academic pathologists.

Methods

This study was a side‐study of the ASPRO (ASpiration versus PROcore) study. Five centers retrieved 74 (59%) consecutive FNB and 51 (41%) FNA samples from the ASPRO study according to randomization; 64 (51%) pancreatic and 61 (49%) lymph node specimens. Samples were re‐reviewed by five expert academic and five non‐academic pathologists and rated in terms of sample quality and diagnosis. Ratings were compared between needles, expert academic and non‐academic pathologists, target lesions, and cytology versus histological specimens.

Results

Besides a higher diagnostic accuracy, FNB also provided for a better agreement on diagnosing malignancy (ĸ = 0.59 vs ĸ = 0.76, P < 0.001) and classification according to Bethesda (ĸ = 0.45 vs ĸ = 0.61, P < 0.001). This equally applied for expert academic and non‐academic pathologists and for pancreatic and lymph node specimens. Sample quality was also rated higher for FNB, but agreement ranged from poor (ĸ = 0.04) to fair (ĸ = 0.55). Histology provided better agreement than cytology, but only when a core specimen was obtained with FNB (P = 0.004 vs P = 0.432).

Conclusion

This study shows that the 20‐G FNB outperforms the 25‐G FNA needle in terms of diagnostic agreement, independent of the background and experience of the pathologist. This endorses use of the 20‐G FNB needle in both expert and lower volume EUS centers.
Creative Leadership: Embedding Global Ideas in a Local Context
Authors: Gadzheva Ivelina
Published: July 2019

In Bulgaria, design is still seen in terms of “making pretty” or, simply, “making things.” This founder of Design for All Bulgaria is helping people see how design can be a way to address social, economic, environmental, and technical challenges.

A Bulgarian designer tackles her country’s attitude about “design as art or product‐making” with a human‐centered approach to big issues like health and ageing.
Building the Veterans Experience Office: CX and the Public Sector
Authors: Morton Barbara C. , Becker Lee
Published: July 2019

Building a Veterans Experience Office—with the goal of being the #1 customer experience office in the federal government—required a completely new view at the enterprise level.

Building leadership at the Veterans Administration—with the help of human‐centered design.