bluuebunny/crossref_metadata_2025 huggingface dataset:
HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices
Authors: Spöri Yann , Flot Jean‐François
Published: July 2020

Haplotype webs (haplowebs) and conspecificity matrices have recently been proposed as graphical methods for species delimitation. However, performing such analyses by hand can be error‐prone and time‐consuming, and no program is currently available to generate these graphs automatically.

Here we present two online tools called HaplowebMaker and CoMa (short for ‘Conspecificity Matrices') that fill this gap. Starting from one or several FASTA sequence alignments, HaplowebMaker generates median‐joining (or minimum spanning) networks, then adds connections between sequences found co‐occurring in heterozygous individuals, thereby turning each network into a haploweb. HaplowebMaker also returns a partition matrix summarizing the partitions inferred from each marker using the criterion of mutual allelic exclusivity. CoMa then turns the partition matrix into a conspecificity matrix and orders it, producing a figure in which each species is revealed as a square along the diagonal.

HaplowebMaker and CoMa are open source and written in Haxe; webserver implementations are available at https://eeg‐ebe.github.io/HaplowebMaker and https://eeg‐ebe.github.io/CoMa/.
Revisiting the minimum set cover, the maximal coverage problems and a maximum benefit area selection problem to make climate‐change‐concerned conservation plans effective
Authors: Alagador Diogo , Cerdeira Jorge Orestes
Published: July 2020

Informed decisions for the selection of protected areas (PAs) are grounded in two general problems in Operations Research: the minimum set covering problem (minCost), where a set of ecological constraints are established as conservation targets and the minimum cost PAs are found, and the maximal coverage problem (maxCoverage) where the constraint is uniquely economic (i.e. a fixed budget) and the goal is to maximize the number of species having conservation targets adequately covered.

We adjustminCostandmaxCoverageto accommodate the dynamic effects of climate change on species’ ranges. The selection of sites is replaced by the selection of time‐ordered sequences of sites (climate change corridors), and an estimate of the persistence of each species in corridors is calculated according to the expected suitability of each site in the respective time period and the capacity of species to disperse between consecutive sites along corridors. In these problems, conservation targets are expressed as desired (and attainable) species persistence levels. We also introduce a novel problem (minShortfall) that combinesminCostandmaxCoverage. Unlike these two problems,minShortfallallows persistence targets to be missed and minimizes the sum of those gaps (i.e. target shortfalls), subject to a limited budget.

We illustrate the three problems with a case study using climatic suitability estimates for 10 mammal species in the Iberian Peninsula under a climate change scenario until 2080. We compare solutions of the three problems with respect to species persistence and PA costs, under distinct settings of persistence targets, number of target‐fulfilled species and budgets. The solutions from different problems differed with regard to the areas to prioritize, their timings and the species whose persistence targets were fulfilled. This analysis also allowed identifying groups of species sharing corridors in optimal solutions, thus allowing important financial savings in site protection.

We suggest that enhancing species persistence is an adequate approach to cope with habitat shifts due to climate change. We trust the three problems discussed can provide complementary and valuable support for planners to anticipate decisions in order that the negative effects of climate change on species’ persistence are minimized.
Glycome profiling by lectin microarray reveals dynamic glycan alterations during epidermal stem cell aging
Authors: Oinam Lalhaba , Changarathil Gopakumar , Raja Erna , Ngo Yen Xuan , Tateno Hiroaki , Sada Aiko , Yanagisawa Hiromi
Published: July 2020

Aging in the epidermis is marked by a gradual decline in barrier function, impaired wound healing, hair loss, and an increased risk of cancer. This could be due to age‐related changes in the properties of epidermal stem cells and defective interactions with their microenvironment. Currently, no biochemical tools are available to detect and evaluate the aging of epidermal stem cells. The cellular glycosylation is involved in cell–cell communications and cell–matrix adhesions in various physiological and pathological conditions. Here, we explored the changes of glycans in epidermal stem cells as a potential biomarker of aging. Using lectin microarray, we performed a comprehensive glycan profiling of freshly isolated epidermal stem cells from young and old mouse skin. Epidermal stem cells exhibited a significant difference in glycan profiles between young and old mice. In particular, the binding of a mannose‐binder rHeltuba was decreased in old epidermal stem cells, whereas that of an α2‐3Sia‐binder rGal8N increased. These glycan changes were accompanied by upregulation of sialyltransferase, St3gal2 and St6gal1 and mannosidase Man1a genes in old epidermal stem cells. The modification of cell surface glycans by overexpressing these glycogenes leads to a defect in the regenerative ability of epidermal stem cells in culture. Hence, our study suggests the age‐related global alterations in cellular glycosylation patterns and its potential contribution to the stem cell function. These glycan modifications detected by lectins may serve as molecular markers for aging, and further functional studies will lead us to a better understanding of the process of skin aging.
The effects of shrub encroachment on bird occupancy vary with land use in an African savanna
Authors: Stanton R. A. , Fletcher R. J. , Sibiya M. , Monadjem A. , McCleery R. A.
Published: July 2020

Land‐cover and land‐use change are major drivers of global biodiversity loss. Savannas are experiencing shrub encroachment and land‐use changes that affect animal communities, yet how the effects of shrub encroachment vary with land use remains unclear. We also need to determine which species traits explain the effects of shrub encroachment and land‐use changes to identify potential drivers of community change and predict species' responses to conservation efforts. We sampled birds across gradients of shrub encroachment and land use (protected savanna, pastures, homestead lands, and sugarcane) in the lowveld savanna of Eswatini to: (1) test for the effects of shrub encroachment, land‐use change, and their potential synergies on the occurrence of 48 species of birds; and (2) determine which species traits (those associated with nesting, foraging, or vulnerability to predation) explained species' associations with shrub encroachment and land‐use change. We used Bayesian multispecies occupancy models to account for imperfect detection, interpret species responses, and understand the effects of species traits. We found evidence for community‐wide synergies between shrub encroachment and land‐use effects on birds that varied with species' diets. Agricultural intensification had negative effects on the occurrence of most species examined, while shrub cover typically had positive effects which were stronger in pastures and homestead lands than in protected areas. The negative effects of land‐use change were greatest for insectivores and cavity nesters, whereas insectivore occurrence increased with shrub cover, collectively indicating that nesting and foraging traits best explained species responses to land‐use and land‐cover change in the region. Our results suggest that shrub cover management for bird conservation should vary with land use: shrubs could be thinned in protected areas without reducing bird occupancy but shrubs in homesteads should be retained.
A European consensus statement on the use of four‐factor prothrombin complex concentrate for cardiac and non‐cardiac surgical patients
Authors: Erdoes G. , Koster A. , Ortmann E. , Meesters M. I. , Bolliger D. , Baryshnikova E. , Martinez Lopez De Arroyabe B. , Ahmed A. , Lance M. D. , Ranucci M. , von Heymann C. , Agarwal S. , Ravn H. B.
Published: July 2020

Modern four‐factor prothrombin complex concentrate was designed originally for rapid targeted replacement of the coagulation factors II, VII, IX and X. Dosing strategies for the approved indication of vitamin K antagonist‐related bleeding vary greatly. They include INR and bodyweight‐related protocols as well as fixed dose regimens. Particularly in the massively bleeding trauma and cardiac surgery patient, four‐factor prothrombin complex concentrate is used increasingly for haemostatic resuscitation. Members of the Transfusion and Haemostasis Subcommittee of the European Association of Cardiothoracic Anaesthesiology performed a systematic literature review on four‐factor prothrombin complex concentrate. The available evidence has been summarised for dosing, efficacy, drug safety and monitoring strategies in different scenarios. Whereas there is evidence for the efficacy of four‐factor prothrombin concentrate for a variety of bleeding scenarios, convincing safety data are clearly missing. In the massively bleeding patient with coagulopathy, our group recommends the administration of an initial bolus of 25 IU.kg‐1. This applies for: the acute reversal of vitamin K antagonist therapy; haemostatic resuscitation, particularly in trauma; and the reversal of direct oral anticoagulants when no specific antidote is available. In patients with a high risk for thromboembolic complications, e.g. cardiac surgery, the administration of an initial half‐dose bolus (12.5 IU.kg‐1) should be considered. A second bolus may be indicated if coagulopathy and microvascular bleeding persists and other reasons for bleeding are largely ruled out. Tissue‐factor‐activated, factor VII‐dependent and heparin insensitive point‐of‐care tests may be used for peri‐operative monitoring and guiding of prothrombin complex concentrate therapy.
Why does COVID‐19 kill more elderly men than women? Is there a role for testosterone?
Authors: Papadopoulos Vassilios , Li Lu , Samplaski Mary
Published: July 2020

Background

Recent epidemiological data indicate that there may be a gender predisposition to COVID‐19, with men predisposed to being most severely affected, and older men accounting for most deaths.

Objectives

Provide a review of the research literature, propose hypotheses, and therapies based on the potential link between testosterone (T) and COVID‐19 induced mortality in elderly men.

Materials and Methods

A search of publications in academic electronic databases, and government and public health organization web sites on T, aging, inflammation, severe acute respiratory syndrome (SARS) due to coronavirus (CoV) 2 (SARS‐CoV‐2) infection, and COVID‐19 disease state and outcomes was performed.

Results

The link between T, the immune system, and male aging is well‐established, as is the progressive decline in T levels with aging. In women, T levels drop before menopause and variably increase with advanced age. Elevated IL‐6 is a characteristic biomarker of patients infected with COVID‐19 and has been linked to the development of the acute respiratory distress syndrome (ARDS). Thus far, half of the admitted COVID‐19 patients developed ARDS, half of these patients died, and elderly male patients have been more likely to develop ARDS and die. Low T is associated with ARDS. These data suggest that low T levels may exacerbate the severity of COVID‐19 infection in elderly men. It may also stand to reason that normal T levels may offer some protection against COVID‐19. SARS‐CoV‐2 binds to the angiotensin‐converting enzyme 2, present in high levels in the testis.

Conclusion

At present, it is not known whether low T levels in aging hypogonadal males create a permissive environment for severe responses to COVID‐19 infection or if the virus inhibits androgen formation. Given the preponderance of COVID‐19 related mortality in elderly males, additional testing for gonadal function and treatment with T may be merited.
The role of RIPK3‐regulated cell death pathways and necroptosis in the pathogenesis of cardiac ischaemia‐reperfusion injury
Authors: Ying Luo , Benjanuwattra Juthipong , Chattipakorn Siriporn C. , Chattipakorn Nipon
Published: July 2020

Despite advancements in management of acute myocardial infarction, this disease remains one of the leading causes of death. Timely reestablishment of epicardial coronary blood flow is the cornerstone of therapy; however, substantial amount of damage can occur as a consequence of cardiac ischaemia/reperfusion (I/R) injury. It has been previously proposed that the pathway leading to major cell death, apoptosis, is responsible for cardiac I/R injury. Nevertheless, there is compelling evidence to suggest that necroptosis, a programmed necrosis, contributes remarkably to both myocardial injury and microcirculatory dysfunction following cardiac I/R injury. Receptor‐interacting protein kinase 1 (RIPK1), RIPK3, and mixed‐lineage kinase domain‐like pseudokinase (MLKL) are shown as the major mediators of necroptosis. In addition to the traditional perception that RIPK1/RIPK3/MLKL‐dependent plasma membrane rupture is fundamental to this process, several RIPK3‐related pathways such as endoplasmic reticulum stress and mitochondrial fragmentation have also been implicated in cardiac I/R injury. In this review, reports from both in vitro and in vivo studies regarding the roles of necroptosis and RIPK3‐regulated necrosis in cardiac I/R injury have been collectively summarized and discussed. Furthermore, reports on potential interventions targeting these processes to attenuate cardiac I/R insults to the heart have been presented in this review. Future investigations adding to the knowledge obtained from these previous studies are needed in the pursuit of discovering the most effective pharmacological agent to improve cardiac I/R outcomes.
Clinical outcomes and adverse events in patients hospitalised with COVID‐19, treated with off‐label hydroxychloroquine and azithromycin
Authors: Kelly Mary , O'Connor Ròisìn , Townsend Liam , Coghlan Miriam , Relihan Eileen , Moriarty Miriam , Carr Bernard , Melanophy Gail , Doyle Caitriona , Bannan Ciaran , O'Riordan Ruth , Merry Concepta , Clarke Susie , Bergin Colm
Published: July 2020

Aims

To assess clinical outcomes and adverse drug events in patients hospitalised with COVID‐19 treated with off‐label hydroxychloroquine (HCQ) and azithromycin (Az).

Methods

We performed a retrospective analysis of hospitalised patients who had a positive polymerase chain reaction test for SARS‐CoV‐2 and received HCQ plus Az or no targeted therapy. The primary end point was clinical improvement on day 7 defined as either hospital discharge or an improvement of 2 points on a 6‐category ordinal scale. Secondary outcomes included mortality at day 28, intensive care admission, requirement for mechanical ventilation and incidence of adverse events.

Results

Data from a total of 134 patients were evaluated; 82 patients received HCQ/Az and 52 patients received no targeted therapy. Clinical improvement was seen in 26.8% of patients who received HCQ/Az but this was not significant. The rates of intensive care transfer and mechanical ventilation were higher in the treatment group, but these differences were not significant. Mortality at day 28 was significantly higher in the treatment group (P = .03). Hypoglycaemia elevated liver function tests and QT prolongation were monitored in both groups. The risk of QT prolongation was significantly higher in the treatment group. Treatment was stopped early in 6 (7.3%) patients due to adverse events.

Conclusion

Although patients who received HCQ/Az were more severely ill the administration of these repurposed drugs did not result in clinical improvement and was associated with a significant increase in toxicity. This descriptive study highlights the importance of monitoring all repurposed agents for adverse events.
Developmental population pharmacokinetics of caffeine in Chinese premature infants with apnoea of prematurity: A post‐marketing study to support paediatric labelling in China
Authors: Gao Xiang‐Bo , Zheng Yi , Yang Fan , Wang Chen‐Hong , Jiang Zhou‐Hong , Wu Yue‐E , Jacqz‐Aigrain Evelyne , Ni Shao‐Qing , Zhao Wei
Published: July 2020

Aims

The aim of the study was to evaluate the suitability of the current caffeine dosing regimen for the Chinese population using modelling and simulation approach.

Methods

Pharmacokinetic samples were collected from 99 Chinese newborns with premature apnoea. The median (range) of gestational age and postmenstrual age were 28.3 (25.0–33.4) weeks and 31.1 (26.4–38.0) weeks, respectively. Newborns were receiving caffeine citrate at a loading dose of 20 mg/kg/d and a maintenance dose of 5–10 mg/kg/d. Caffeine concentrations and CYP1A2 polymorphisms were investigated. Population pharmacokinetic modelling of caffeine in Chinese preterm newborn on a population‐wide scale was conducted using NONMEM.

Results

A 1‐compartment model with first‐order elimination was used to describe population pharmacokinetic. With current weight implemented using 0.75 allometric scaling, clearance (CL) was positively related to current weight and postmenstrual age, but a negative relationship was observed with serum creatinine concentration. Eight genotypes of CYP1A2 were tested and none of them had a significant impact on caffeine pharmacokinetic parameters. Interindividual variability of CL and volume of distribution was 7.70 and 65.9%. The median (range) of 95% confidence intervals of CL were 0.0128 (0.0128–0.0131) L/h/kg. Monte Carlo simulation demonstrated that 80% (loading dose) and 98% (maintenance dose) of premature infants treated with a labelled dosing regimen attained the concentration target range of 5–20 mg/L.

Conclusion

A population PK model of caffeine was developed in Chinese newborns. Body weight‐implemented allometric scaling, postmenstrual age and serum creatinine concentration markedly affected caffeine clearance. The labelled dosing regimen is suitable for Chinese premature infants.
Congenital tumors of the central nervous system: an institutional review of 64 cases with emphasis on tumors with unique histologic and molecular characteristics
Authors: Viaene Angela N. , Pu Cunfeng , Perry Arie , Li Marilyn M. , Luo Minjie , Santi Mariarita
Published: July 2020

Congenital brain tumors are rare accounting for 0.5%–1.9% of all pediatric brain tumors. While different criteria have been used to classify a tumor as congenital, those diagnosed prior to 6 months of age are considered to be “probably” congenital in origin. We performed an institutional review of all central nervous system (CNS) tumors (surgical and autopsy specimens from 1990 to 2019) in patients less than 6 months old. Sixty‐four unique cases were identified, and these accounted for 2.0% of all CNS tumor specimens at our institution. The most common tumor types were high‐grade gliomas, low‐grade gliomas and medulloblastomas. Atypical teratoid rhabdoid tumors, choroid plexus tumors and germ cell tumors also accounted for a significant portion of the cohort. Seven tumors were diagnosed prenatally. The most common clinical presentation at diagnosis was increased head circumference. At the conclusion of the study, over half of the patients were alive including all patients with WHO grade I and II tumors. Ninety‐two percent of cases were classifiable using the 2016 WHO system, and when available, molecular findings supported the histologic diagnoses. However, several gliomas had unusual histologic features and did not correspond to a well‐defined entity. Molecular testing was essential for accurate classification of a subset of these tumors, and several high‐grade gliomas exhibited fusions considered unique to infantile gliomas, including those involving theMET, ALKand NTRK genes. To our knowledge, this cohort represents the largest single‐institution study of congenital CNS tumors and highlights many ways in which congenital CNS tumors are distinct from CNS tumors of older pediatric patients and adults.
Safety perspectives on presently considered drugs for the treatment of COVID‐19
Authors: Penman Sophie L. , Kiy Robyn T. , Jensen Rebecca L. , Beoku‐Betts Christopher , Alfirevic Ana , Back David , Khoo Saye H. , Owen Andrew , Pirmohamed Munir , Park B. Kevin , Meng Xiaoli , Goldring Christopher E. , Chadwick Amy E.
Published: July 2020

Intense efforts are underway to evaluate potential therapeutic agents for the treatment of COVID‐19. In order to respond quickly to the crisis, the repurposing of existing drugs is the primary pharmacological strategy. Despite the urgent clinical need for these therapies, it is imperative to consider potential safety issues. This is important due to the harm–benefit ratios that may be encountered when treating COVID‐19, which can depend on the stage of the disease, when therapy is administered and underlying clinical factors in individual patients. Treatments are currently being trialled for a range of scenarios from prophylaxis (where benefit must greatly exceed risk) to severe life‐threatening disease (where a degree of potential risk may be tolerated if it is exceeded by the potential benefit). In this perspective, we have reviewed some of the most widely researched repurposed agents in order to identify potential safety considerations using existing information in the context of COVID‐19.
Child development assessment: Practitioner input in the revision for Griffiths III
Authors: Green Elizabeth M. , Stroud Louise , Marx Candice , Cronje Johan
Published: July 2020

Introduction

The input from practitioners in developmental assessment test revision is a crucial and leading component of the project. This paper highlights six key phases of the Griffiths III revision process and the value of having a guiding plan that includes test practitioner input.

Methods

The revision of the Griffiths III consisted of six separate phases that were supported by practitioner and user input and feedback. These six phases and practitioner views ensured that the necessary core constructs and new areas for item development were included in the revised version. These processes also underscored the construct development and task review, item design, piloting and standardization of the revised version, as well as its production, release and subsequent training methods.

Results

The six guiding phases provided a methodologically robust frame to the revision process. Practitioners valued an overall developmental measure with discrete data about and within the ‘avenues of learning’ allowing them to analyse a child's strengths and weaknesses. Communication with practitioners across the world demonstrated the wide disparity of culture and environments that the Griffiths Scales are deployed in. It is not possible to design a revised scale that is appropriate for all areas of use, so in this revision process, it was decided to design the scales as culturally fair as possible and support practitioners in other countries to translate and validate the scales for use.

Conclusions

The revision of the Griffiths III found test users to be valuable sources of information on the basis of their experiences with the test and professional knowledge. Creating a continuous feedback mechanism within a phased process provided opportunities for the revision team to engage meaningfully with the data being obtained as well as test users to advance the scope and quality of the test. Revision teams are encouraged to consider the process and engagement methods explored in this study during their projects.
Fathers’ Involvement in Chinese Societies: Increasing Presence, Uneven Progress
Authors: Li Xuan
Published: July 2020

Chinese fathers, who have been understudied, traditionally were expected to act as emotionally distant educators and disciplinarians of their children as well as heads of the household. Their dual roles as parents and as men evolved during modern social transformations following divergent paths, with their parental role departing from the Confucian patriarchal ideal further than did their gender role. Today, in Chinese societies, fathers are more involved in child‐rearing and warmer to their children than their predecessors, but comparable progress toward a quantitatively and qualitatively equal division of child‐rearing responsibilities between parents remains lacking. Chinese fathers’ involvement varies by geolocation, social class, and maternal support; their participation in their children’s lives benefits children’s adjustment, possibly through secure father–child attachment, and is influenced by the relationship between fathers and mothers. Researchers should address how Chinese fathers’ increasing but gendered involvement affects children’s and families’ functioning, study fathers in diverse families, and incorporate grandparents into research on fathering.
Effect of Twinning on Chinese and English Vocabulary Knowledge
Authors: Wong Simpson W.L. , Cheung Him , Zheng Mo , Yang Xiujie , McBride Catherine , Ho Connie Suk‐Han , Leung Judy Sze‐Man , Chow Bonnie Wing‐Yin , Waye Mary Miu Yee
Published: July 2020

Vocabulary knowledge was tested in a native (Cantonese‐Chinese) and foreign (English) language in 150 twins and 150 singletons aged 6–11 years, matched on age, gender, grade level, nonverbal intelligence, parents’ education, family income, and number of siblings and household members. The singletons clearly outperformed the twins on the native vocabulary, but this “twinning effect” was much less noticeable for the foreign vocabulary. The effect on English vocabulary was further reduced after exposure to English at home was controlled. Given that these participants learned most of their English in school rather than home, the present findings support the notion that the twinning effect is associated with increased competition for family interaction in twins compared with singletons.
Rapamycin-based graft-versus-host disease prophylaxis increases the immunosuppressivity of myeloid-derived suppressor cells without affecting T cells and anti-tumor cytotoxicity
Authors: Scheurer J , Reisser T , Leithäuser F , Messmann J J , Holzmann K , Debatin K-M , Strauss G
Published: July 2020

The immunosuppressant rapamycin (RAPA) inhibits mammalian target of rapamycin (mTOR) functions and is applied after allogeneic bone marrow transplantation (BMT) to attenuate the development of graft-versus-host disease (GVHD), although the cellular targets of RAPA treatment are not well defined. Allogeneic T cells are the main drivers of GVHD, while immunoregulatory myeloid-derived suppressor cells (MDSCs) were recently identified as potent disease inhibitors. In this study, we analyzed whether RAPA prevents the deleterious effects of allogeneic T cells or supports the immunosuppressive functions of MDSCs in a BMT model with major histocompatibility complex (MHC) classes I and II disparities. RAPA treatment efficiently attenuated clinical and histological GVHD and strongly decreased disease-induced mortality. Although splenocyte numbers increased during RAPA treatment, the ratio of effector T cells to MDSCs was unaltered. However, RAPA treatment induced massive changes in the genomic landscape of MDSCs preferentially up-regulating genes responsible for uptake or signal transduction of lipopeptides and lipoproteins. Most importantly, MDSCs from RAPA-treated mice exhibited increased immunosuppressive potential, which was primarily inducible nitric oxide synthase (iNOS)-dependent. Surprisingly, RAPA treatment had no impact on the genomic landscape of T cells, which was reflected by unchanged expression of activation and exhaustion markers and cytokine profiles in T cells from RAPA-treated and untreated mice. Similarly, T cell cytotoxicity and the graft-versus-tumor effect were maintained as co-transplanted tumor cells were efficiently eradicated, indicating that the immunosuppressant RAPA might be an attractive approach to strengthen the immunosuppressive function of MDSCs without affecting T cell immunity.
Salivary cortisol, cortisone and serum cortisol concentrations are related to age and body mass index in healthy children and young people
Authors: Titman Andrew , Price Victoria , Hawcutt Daniel , Chesters Chris , Ali Murtaza , Cacace Gianluca , Lancaster Gill A. , Peak Matthew , Blair Joanne C.
Published: July 2020

Background

Saliva is an ideal medium in which to measure cortisol in children. However, there are very few data reporting salivary cortisol or cortisone concentrations in healthy children since the introduction of liquid chromatography‐mass spectrometry (LC‐MS/MS) to routine laboratory practice.

Design

Early morning serum cortisol, salivary cortisol and cortisone were measured on fasting samples, and salivary hormones were measured in samples collected every 2 hours during waking hours, and 30 minutes after waking the following morning.

Participants

43 healthy paediatric volunteers (19 female), median age 11.5 years, range 6.2‐18.7, participated.

Results

Early morning serum cortisol (265 nmol/L, 156‐516) correlated strongly with salivary cortisol (4.7 nmol/L, 1.1‐14.6) and cortisone (28.8 nmol/L, 11.7‐56.6),P < .0001 for both. Serum cortisol, salivary cortisol and salivary cortisone correlated directly with age (P < .0001,P = .002 andP = .015, respectively), and salivary cortisone/cortisol ratio correlated indirectly with age (P = .007). Between 08.00 and 21.00, area under the curve for salivary cortisol (mean ± 1 SD) was 41.8 ± 19.1 and for cortisone 213.0 ± 61.2. Salivary cortisol was undetectable in 25/130 (19%) of samples collected after 13.00, while cortisone was always detectable.

Discussion

Salivary cortisol and cortisone concentrations are strongly related to serum cortisol concentrations; however, cortisone may be a preferable measure as cortisol is often undetectable. Age may be an important factor in the interpretation of early morning cortisol measurements made in serum and saliva.
Loss‐of‐function mutation in DNAH8 induces asthenoteratospermia associated with multiple morphological abnormalities of the sperm flagella
Authors: Yang Yihong , Jiang Chuan , Zhang Xueguang , Liu Xue , Li Jinghong , Qiao Xiaoyong , Liu Hongqian , Shen Ying
Published: July 2020

Asthenozoospermia is a common cause of male infertility associated with the reduced motility and/or abnormal morphology of spermatozoa, although its etiology remains incompletely understood. Multiple morphological abnormalities of the sperm flagella (MMAF) is one of the main causes of asthenozoospermia. However, the MMAF‐associated genes identified to date cannot explain all the human MMAF cases. Herein, a loss‐of‐function mutation of DNAH8 was identified in an asthenozoospermia patient with MMAF. Moreover, the negative effect of this mutation on DNAH8 expression was confirmed by immunofluorescence staining and western blotting. Remarkably, it is the first time that DNAH8 is suggested to be associated with human MMAF. Our findings provide strong evidence that a loss‐of‐function mutation in DNAH8 can cause male infertility with MMAF and that DNAH8 is essential for sperm flagellar formation.
Representative Isovalue Detection and Isosurface Segmentation Using Novel Isosurface Measures
Authors: Wang Cuilan
Published: July 2020

Interval volume is the volume of the region between two isosurfaces. This paper proposes a novel measure, called VOA measure, that is computed based on interval volume and isosurface area. This measure represents the rate of change of distance between isosurfaces with respect to isovalue. It can be used to detect representative isovalues of the dataset since two isosurfaces near material boundaries tend to be much closer to each other than two isosurfaces in material interiors, assuming they have the same isovalue difference. For the same isosurface, some portion of it may pass through the boundary of two materials and some portion of it may pass through the interior of a material. To separate the portions of an isosurface that represent different features of the dataset, another novel isosurface measure is introduced. This measure is calculated based on the Euclidean distance of individual sample points on two isosurfaces. The effectiveness of the two new measures in detecting significant isovalues and segmenting isosurfaces are demonstrated in the paper.
Bombalytics: Visualization of Competition and Collaboration Strategies of Players in a Bomb Laying Game
Authors: Agarwal Shivam , Wallner Günter , Beck Fabian
Published: July 2020

Competition and collaboration form complex interaction patterns between the agents and objects involved. Only by understanding these interaction patterns, we can reveal the strategies the participating parties applied. In this paper, we study such competition and collaboration behavior for a computer game. Serving as a testbed for artificial intelligence, the multiplayer bomb laying game Pommerman provides a rich source of advanced behavior of computer agents. We propose a visualization approach that shows an overview of multiple games, with a detailed timeline‐based visualization for exploring the specifics of each game. Since an analyst can only fully understand the data when considering the direct and indirect interactions between agents, we suggest various visual encodings of these interactions. Based on feedback from expert users and an application example, we demonstrate that the approach helps identify central competition strategies and provides insights on collaboration.
Ocupado: Visualizing Location‐Based Counts Over Time Across Buildings
Authors: Oppermann Michael , Munzner Tamara
Published: July 2020

Understanding how spaces in buildings are being used is vital for optimizing space utilization, for improving resource allocation, and for the design of new facilities. We present a multi‐year design study that resulted in Ocupado, a set of visual decision‐support tools centered around occupancy data for stakeholders in facilities management and planning. Ocupado uses WiFi devices as a proxy for human presence, capturing location‐based counts that preserve privacy without trajectories. We contribute data and task abstractions for studying space utilization for combinations of data granularities in both space and time. In addition, we contribute generalizable design choices for visualizing location‐based counts relating to indoor environments. We provide evidence of Ocupado's utility through multiple analysis scenarios with real‐world data refined through extensive stakeholder feedback, and discussion of its take‐up by our industry partner.
A Visual Analytics Approach to Facilitate Crime Hotspot Analysis
Authors: de Queiroz Neto José F. , Santos Emanuele , Vidal Creto Augusto , Ebert David S.
Published: July 2020

Computer‐based technology has played a significant role in crime prevention over the past 30 years, especially with the popularization of spatial databases and crime mapping systems. Police departments frequently use hotspot analysis to identify regions that should be a priority in receiving preventive resources. Practitioners and researchers agree that tracking crime over time and identifying its geographic patterns are vital information for planning efficiently. Frequently, police departments have access to systems that are too complicated and excessively technical, leading to modest usage. By working closely together with domain experts from police agencies of two different countries, we identified and characterized five domain tasks inherent to the hotspot analysis problem and developed SHOC, a visualization tool that strives for simplicity and ease of use in helping users to perform all the domain tasks. SHOC is included in a visual analytics system that allows users without technical expertise to annotate, save, and share analyses. We also demonstrate that our system effectively supports the completion of the domain tasks in two different real‐world case studies.
Boxer: Interactive Comparison of Classifier Results
Authors: Gleicher Michael , Barve Aditya , Yu Xinyi , Heimerl Florian
Published: July 2020

Machine learning practitioners often compare the results of different classifiers to help select, diagnose and tune models. We present Boxer, a system to enable such comparison. Our system facilitates interactive exploration of the experimental results obtained by applying multiple classifiers to a common set of model inputs. The approach focuses on allowing the user to identify interesting subsets of training and testing instances and comparing performance of the classifiers on these subsets. The system couples standard visual designs with set algebra interactions and comparative elements. This allows the user to compose and coordinate views to specify subsets and assess classifier performance on them. The flexibility of these compositions allow the user to address a wide range of scenarios in developing and assessing classifiers. We demonstrate Boxer in use cases including model selection, tuning, fairness assessment, and data quality diagnosis.
Short‐Contact Touch‐Manipulation of Scatterplot Matrices on Wall Displays
Authors: Riehmann P. , León G. Molina , Reibert J. , Echtler F. , Froehlich B.
Published: July 2020

This paper presents a short‐contact multitouch vocabulary for interacting with scatterplot matrices (SPLOMs) on wall‐sized displays. Fling‐based gestures overcome central interaction challenges of such large displays by avoiding long swipes on the typically blunt surfaces, frequent physical navigation by walking for accessing screen areas beyond arm's reach in the horizontal direction and uncomfortable postures for accessing screen areas in the vertical direction. Furthermore, we make use of the display's high resolution and large size by supporting the efficient specification of two‐tiered focus + context regions which are consistently propagated across the SPLOM. These techniques are complemented by axis‐centered and lasso‐based selection techniques for specifying subsets of the data. An expert review as well as a user study confirmed the potential and general usability of our seamlessly integrated multitouch interaction techniques for SPLOMs on large vertical displays.
Fiber Surfaces for many Variables
Authors: Blecha C. , Raith F. , Präger A. J. , Nagel T. , Kolditz O. , Maßmann J. , Röber N. , Böttinger M. , Scheuermann G.
Published: July 2020

Scientific visualization deals with increasingly complex data consisting of multiple fields. Typical disciplines generating multivariate data are fluid dynamics, structural mechanics, geology, bioengineering, and climate research. Quite often, scientists are interested in the relation between some of these variables. A popular visualization technique for a single scalar field is the extraction and rendering of isosurfaces. With this technique, the domain can be split into two parts, i.e. a volume with higher values and one with lower values than the selected isovalue. Fiber surfaces generalize this concept to two or three scalar variables up to now. This article extends the notion further to potentially any finite number of scalar fields. We generalize the fiber surface extraction algorithm of Raith et al. [RBN∗19] from 3 to d dimensions and demonstrate the technique using two examples from geology and climate research. The first application concerns a generic model of a nuclear waste repository and the second one an atmospheric simulation over central Europe. Both require complex simulations which involve multiple physical processes. In both cases, the new extended fiber surfaces helps us finding regions of interest like the nuclear waste repository or the power supply of a storm due to their characteristic properties.
Data Comets: Designing a Visualization Tool for Analyzing Autonomous Aerial Vehicle Logs with Grounded Evaluation
Authors: Saffo David , Leventidis Aristotelis , Jain Twinkle , Borkin Michelle A. , Dunne Cody
Published: July 2020

Autonomous unmanned aerial vehicles are complex systems of hardware, software, and human input. Understanding this complexity is key to their development and operation. Information visualizations already exist for exploring flight logs but comprehensive analyses currently require several disparate and custom tools. This design study helps address the pain points faced by autonomous unmanned aerial vehicle developers and operators. We contribute: a spiral development process model for grounded evaluation visualization development focused on progressively broadening target user involvement and refining user goals; a demonstration of the model as part of developing a deployed and adopted visualization system; a data and task abstraction for developers and operators performing post‐flight analysis of autonomous unmanned aerial vehicle logs; the design and implementation of Data Comets, an open‐source and web‐based interactive visualization tool for post‐flight log analysis incorporating temporal, geospatial, and multivariate data; and the results of a summative evaluation of the visualization system and our abstractions based on in‐the‐wild usage. A free copy of this paper and source code are available at osf.io/h4p7g
GTMapLens: Interactive Lens for Geo‐Text Data Browsing on Map
Authors: Ma Chao , Zhao Ye , AL‐Dohuki Shamal , Yang Jing , Ye Xinyue , Kamw Farah , Amiruzzaman Md
Published: July 2020

Data containing geospatial semantics, such as geotagged tweets, travel blogs, and crime reports, associates natural language texts with geographical locations. This paper presents a lens‐based visual interaction technique, GTMapLens, to flexibly browse the geo‐text data on a map. It allows users to perform dynamic focus+context exploration by using movable lenses to browse geographical regions, find locations of interest, and perform comparative and drill‐down studies. Geo‐text data is visualized in a way that users can easily perceive the underlying geospatial semantics along with lens moving. Based on a requirement analysis with a cohort of multidisciplinary domain experts, a set of lens interaction techniques are developed including keywords control, path management, context visualization, and snapshot anchors. They allow users to achieve a guided and controllable exploration of geo‐text data. A hierarchical data model enables the interactive lens operations by accelerated data retrieval from a geo‐text database. Evaluation with real‐world datasets is presented to show the usability and effectiveness of GTMapLens.
Sublinear Time Force Computation for Big Complex Network Visualization
Authors: Meidiana Amyra , Hong Seok‐Hee , Torkel Marnijati , Cai Shijun , Eades Peter
Published: July 2020

In this paper, we present a new framework for sublinear time force computation for visualization of big complex graphs. Our algorithm is based on the sampling of vertices for computing repulsion forces and edge sparsification for attraction force computation. More specifically, for vertex sampling, we present three types of sampling algorithms, including random sampling, geometric sampling, and combinatorial sampling, to reduce the repulsion force computation to sublinear in the number of vertices. We utilize a spectral sparsification approach to reduce the number of attraction force computations to sublinear in the number of edges for dense graphs. We also present a smart initialization method based on radial tree drawing of the BFS spanning tree rooted at the center.

Experiments show that our new sublinear time force computation algorithms run quite fast, while producing good visualization of large and complex networks, with significant improvements in quality metrics such as shape‐based and edge crossing metrics.
Infomages: Embedding Data into Thematic Images
Authors: Coelho D. , Mueller K.
Published: July 2020

Recent studies have indicated that visually embellished charts such as infographics have the ability to engage viewers and positively affect memorability. Fueled by these findings, researchers have proposed a variety of infographic design tools. However, these tools do not cover the entire design space. In this work, we identify a subset of infographics that we call infomages. Infomages are casual visuals of data in which a data chart is embedded into a thematic image such that the content of the image reflects the subject and the designer's interpretation of the data. Creating an effective infomage, however, can require a fair amount of design expertise and is thus out of reach for most people. In order to also afford non‐artists with the means to design convincing infomages, we first study the principled design of existing infomages and identify a set of key chart embedding techniques. Informed by these findings we build a design tool that links web‐scale image search with a set of interactive image processing tools to empower novice users with the ability to design a wide variety of infomages. As the embedding process might introduce some amount of visual distortion of the data our tool also aids users to gauge the amount of this distortion, if any. We experimentally demonstrate the usability of our tool and conclude with a discussion of infomages and our design tool.
Survey on Individual Differences in Visualization
Authors: Liu Zhengliang , Crouser R. Jordan , Ottley Alvitta
Published: July 2020

Developments in data visualization research have enabled visualization systems to achieve great general usability and application across a variety of domains. These advancements have improved not only people's understanding of data, but also the general understanding of people themselves, and how they interact with visualization systems. In particular, researchers have gradually come to recognize the deficiency of having one‐size‐fits‐all visualization interfaces, as well as the significance of individual differences in the use of data visualization systems. Unfortunately, the absence of comprehensive surveys of the existing literature impedes the development of this research. In this paper, we review the research perspectives, as well as the personality traits and cognitive abilities, visualizations, tasks, and measures investigated in the existing literature. We aim to provide a detailed summary of existing scholarship, produce evidence‐based reviews, and spur future inquiry.
The State of the Art in Enhancing Trust in Machine Learning Models with the Use of Visualizations
Authors: Chatzimparmpas A. , Martins R. M. , Jusufi I. , Kucher K. , Rossi F. , Kerren A.
Published: July 2020

Machine learning (ML) models are nowadays used in complex applications in various domains, such as medicine, bioinformatics, and other sciences. Due to their black box nature, however, it may sometimes be hard to understand and trust the results they provide. This has increased the demand for reliable visualization tools related to enhancing trust in ML models, which has become a prominent topic of research in the visualization community over the past decades. To provide an overview and present the frontiers of current research on the topic, we present a State‐of‐the‐Art Report (STAR) on enhancing trust in ML models with the use of interactive visualization. We define and describe the background of the topic, introduce a categorization for visualization techniques that aim to accomplish this goal, and discuss insights and opportunities for future research directions. Among our contributions is a categorization of trust against different facets of interactive ML, expanded and improved from previous research. Our results are investigated from different analytical perspectives: (a) providing a statistical overview, (b) summarizing key findings, (c) performing topic analyses, and (d) exploring the data sets used in the individual papers, all with the support of an interactive web‐based survey browser. We intend this survey to be beneficial for visualization researchers whose interests involve making ML models more trustworthy, as well as researchers and practitioners from other disciplines in their search for effective visualization techniques suitable for solving their tasks with confidence and conveying meaning to their data.