bluuebunny/crossref_metadata_2025_split huggingface dataset:
CDKN2A exon 1B deletion predisposing to melanoma and neural system tumour syndrome
Authors: Wong Samantha L. , Martiniuc Daniela , Kiuru Maija 
Published: July 2022

Abstract
CDKN2A at chromosome positon 9p21 is a tumour suppressor gene encoding the cell cycle regulators p16 and p14ARF. While melanoma is associated with variants affecting both transcripts, families with mutations involving the p14ARF-specific exon 1B may be predisposed to central nervous system tumours. We describe a family with a deletion of exon 1B in CDKN2A, who had multiple cutaneous melanomas, neural tumours and various malignancies.
ModelWise: Interactive Model Comparison for Model Diagnosis, Improvement and Selection
Authors: Meng Linhao , van den Elzen Stef , Vilanova Anna 
Published: July 2022

AbstractModel comparison is an important process to facilitate model diagnosis, improvement, and selection when multiple models are developed for a classification task. It involves careful comparison concerning model performance and interpretation. Current visual analytics solutions often ignore the feature selection process. They either do not support detailed analysis of multiple multi‐class classifiers or rely on feature analysis alone to interpret model results. Understanding how different models make classification decisions, especially classification disagreements of the same instances, requires a deeper model understanding. We present ModelWise, a visual analytics method to compare multiple multi‐class classifiers in terms of model performance, feature space, and model explanation. ModelWise adapts visualizations with rich interactions to support multiple workflows to achieve model diagnosis, improvement, and selection. It considers feature subspaces generated for use in different models and improves model understanding by model explanation. We demonstrate the usability of ModelWise with two case studies, one with a small exemplar dataset and another developed with a machine learning expert with real‐world perioperative data.
Optimizing Grid Layouts for Level‐of‐Detail Exploration of Large Data Collections
Authors: Frey S. 
Published: July 2022

AbstractThis paper introduces an optimization approach for generating grid layouts from large data collections such that they are amenable to level‐of‐detail presentation and exploration. Classic (flat) grid layouts visually do not scale to large collections, yielding overwhelming numbers of tiny member representations. The proposed local search‐based progressive optimization scheme generates hierarchical grids: leaves correspond to one grid cell and represent one member, while inner nodes cover a quadratic range of cells and convey an aggregate of contained members. The scheme is solely based on pairwise distances and jointly optimizes for homogeneity within inner nodes and across grid neighbors. The generated grids allow to present and flexibly explore the whole data collection with arbitrary local granularity. Diverse use cases featuring large data collections exemplify the application: stock market predictions from a Black‐Scholes model, channel structures in soil from Markov chain Monte Carlo, and image collections with feature vectors from neural network classification models. The paper presents feedback by a domain scientist, compares against previous approaches, and demonstrates visual and computational scalability to a million members, surpassing classic grid layout techniques by orders of magnitude.
Branch Decomposition‐Independent Edit Distances for Merge Trees
Authors: Wetzels Florian , Leitte Heike , Garth Christoph 
Published: July 2022

AbstractEdit distances between merge trees of scalar fields have many applications in scientific visualization, such as ensemble analysis, feature tracking or symmetry detection. In this paper, we propose branch mappings, a novel approach to the construction of edit mappings for merge trees. Classic edit mappings match nodes or edges of two trees onto each other, and therefore have to either rely on branch decompositions of both trees or have to use auxiliary node properties to determine a matching. In contrast, branch mappings employ branch properties instead of node similarity information, and are independent of predetermined branch decompositions. Especially for topological features, which are typically based on branch properties, this allows a more intuitive distance measure which is also less susceptible to instabilities from small‐scale perturbations. For trees with 𝒪(n) nodes, we describe an 𝒪(n4) algorithm for computing optimal branch mappings, which is faster than the only other branch decomposition‐independent method in the literature by more than a linear factor. Furthermore, we compare the results of our method on synthetic and real‐world examples to demonstrate its practicality and utility.
A Typology of Guidance Tasks in Mixed‐Initiative Visual Analytics Environments
Authors: Pérez‐Messina I. , Ceneda D. , El‐Assady M. , Miksch S. , Sperrle F. 
Published: July 2022

AbstractGuidance has been proposed as a conceptual framework to understand how mixed‐initiative visual analytics approaches can actively support users as they solve analytical tasks. While user tasks received a fair share of attention, it is still not completely clear how they could be supported with guidance and how such support could influence the progress of the task itself. Our observation is that there is a research gap in understanding the effect of guidance on the analytical discourse, in particular, for the knowledge generation in mixed‐initiative approaches. As a consequence, guidance in a visual analytics environment is usually indistinguishable from common visualization features, making user responses challenging to predict and measure. To address these issues, we take a system perspective to propose the notion of guidance tasks and we present it as a typology closely aligned to established user task typologies. We derived the proposed typology directly from a model of guidance in the knowledge generation process and illustrate its implications for guidance design. By discussing three case studies, we show how our typology can be applied to analyze existing guidance systems. We argue that without a clear consideration of the system perspective, the analysis of tasks in mixed‐initiative approaches is incomplete. Finally, by analyzing matchings of user and guidance tasks, we describe how guidance tasks could either help the user conclude the analysis or change its course.
A Grammar‐Based Approach for Applying Visualization Taxonomies to Interaction Logs
Authors: Gathani Sneha , Monadjemi Shayan , Ottley Alvitta , Battle Leilani 
Published: July 2022

AbstractResearchers collect large amounts of user interaction data with the goal of mapping user's workflows and behaviors to their high‐level motivations, intuitions, and goals. Although the visual analytics community has proposed numerous taxonomies to facilitate this mapping process, no formal methods exist for systematically applying these existing theories to user interaction logs. This paper seeks to bridge the gap between visualization task taxonomies and interaction log data by making the taxonomies more actionable for interaction log analysis. To achieve this, we leverage structural parallels between how people express themselves through interactions and language by reformulating existing theories as regular grammars. We represent interactions as terminals within a regular grammar, similar to the role of individual words in a language, and patterns of interactions or non‐terminals as regular expressions over these terminals to capture common language patterns. To demonstrate our approach, we generate regular grammars for seven existing visualization taxonomies and develop code to apply them to three public interaction log datasets. In analyzing these regular grammars, we find that the taxonomies at the low‐level (i.e., terminals) show mixed results in expressing multiple interaction log datasets, and taxonomies at the high‐level (i.e., regular expressions) have limited expressiveness, due to primarily two challenges: inconsistencies in interaction log dataset granularity and structure, and under‐expressiveness of certain terminals. Based on our findings, we suggest new research directions for the visualization community to augment existing taxonomies, develop new ones, and build better interaction log recording processes to facilitate the data‐driven development of user behavior taxonomies.
Vessel Maps: A Survey of Map‐Like Visualizations of the Cardiovascular System
Authors: Eulzer P. , Meuschke M. , Mistelbauer G. , Lawonn K. 
Published: July 2022

AbstractMap‐like visualizations of patient‐specific cardiovascular structures have been applied in numerous medical application contexts. The term map‐like alludes to the characteristics these depictions share with cartographic maps: they show the spatial relations of data attributes from a single perspective, they abstract the underlying data to inCrease legibility, and they facilitate tasks centered around overview, navigation, and comparison. A vast landscape of techniques exists to derive such maps from heterogeneous data spaces. Yet, they all target similar purposes within disease diagnostics, treatment, or research and they face coinciding challenges in mapping the spatial component of a treelike structure to a legible layout. In this report, we present a framing to unify these approaches. On the one hand, we provide a classification of the existing literature according to the data spaces such maps can be derived from. On the other hand, we view the approaches in light of the manifold requirements medical practitioners and researchers have in their efforts to combat the ever‐growing burden of cardiovascular disease. Based on these two perspectives, we offer recommendations for the design of map‐like visualizations of the cardiovascular system.
Assessing taxonomic, functional and phylogenetic diversity of giant clams across the Indo‐Pacific for conservation prioritization
Authors: Tan Edwin Y. W. , Neo Mei Lin , Huang Danwei 
Published: July 2022

AbstractAimGiant clams are iconic bivalves known to serve numerous ecological roles contributing to the functioning of coral reef ecosystems. In the next decade, giant clams will continue to face critical anthropogenic pressures from over‐exploitation for their meat and shells, the aquarium trade and global warming that threaten the persistence of their species. Here, we assess the relationships between different biodiversity components to inform conservation prioritization and management.LocationIndo‐Pacific marine realm.MethodsWe quantified taxonomic, functional and phylogenetic diversity measures throughout 25 marine provinces and assessed their relationships for all 12 giant clam species in the subfamily Tridacninae. These biodiversity measures were used to identify potentially threatened species that contribute disproportionately to trait and evolutionary diversity and to highlight areas for global conservation prioritization of giant clam species.ResultsAnalyses show positive correlations among species richness (SR), functional diversity (FD) and phylogenetic diversity (PD), with the strongest relationship between FD and PD. However, spatial patterns of higher‐than‐expected FD and PD are incongruent with SR patterns, indicating that SR omits information associated with functional and phylogenetic diversity. Among the giant clam species, Tridacna gigas and Hippopus spp. have the greatest functional and evolutionary diversity contributions within assemblies, respectively. Spatial analyses reveal that the Bay of Bengal, Andaman and numerous parts of the eastern Indo‐Pacific potentially hold higher‐than‐expected FD and PD levels relative to their SR and thus warrant more attention with respect to conserving the diversity of giant clams.ConclusionsOur findings underscore the importance of integrating functional trait contributions and evolutionary diversity into conservation planning to better differentiate giant clam assemblages, as it remains challenging to implement dedicated conservation given the limited resources. This study provides comprehensive biodiversity information for managers to initiate measures that holistically capture species' ecological and evolutionary standings across global reef ecosystems.
Risk of reinfection and disease afterSARS‐CoV‐2 primary infection: Meta‐analysis
Authors: Flacco Maria Elena , Acuti Martellucci Cecilia , Baccolini Valentina , De Vito Corrado , Renzi Erika , Villari Paolo , Manzoli Lamberto 
Published: July 2022

AbstractIntroductionA precise estimate of the frequency and severity of SARS‐CoV‐2 reinfections would be critical to optimize restriction and vaccination policies for the hundreds of millions previously infected subjects. We performed a meta‐analysis to evaluate the risk of reinfection and COVID‐19 following primary infection.MethodsWe searched MedLine, Scopus and preprint repositories for cohort studies evaluating the onset of new infections among baseline SARS‐CoV‐2‐positive subjects. Random‐effect meta‐analyses of proportions were stratified by gender, exposure risk, vaccination status, viral strain, time between episodes, and reinfection definition.ResultsNinety‐one studies, enrolling 15,034,624 subjects, were included. Overall, 158,478 reinfections were recorded, corresponding to a pooled rate of 0.97% (95% CI: 0.71%–1.27%), with no substantial differences by definition criteria, exposure risk or gender. Reinfection rates were still 0.66% after ≥12 months from first infection, and the risk was substantially lower among vaccinated subjects (0.32% vs. 0.74% for unvaccinated individuals). During the first 3 months of Omicron wave, the reinfection rates reached 3.31%. Overall rates of severe/lethal COVID‐19 were very low (2–7 per 10,000 subjects according to definition criteria) and were not affected by strain predominance.ConclusionsA strong natural immunity follows the primary infection and may last for more than one year, suggesting that the risk and health care needs of recovered subjects might be limited. Although the reinfection rates considerably increased during the Omicron wave, the risk of a secondary severe or lethal disease remained very low. The risk–benefit profile of multiple vaccine doses for this subset of population needs to be carefully evaluated.
Novel insights into the pathogenic impact of diabetes on the gastrointestinal tract
Authors: Portincasa Piero , Bonfrate Leonilde , Wang David Q.‐H. , Frühbeck Gema , Garruti Gabriella , Di Ciaula Agostino 
Published: July 2022

AbstractType 2 and type 1 diabetes are common endocrine disorders with a progressively increasing incidence worldwide. These chronic, systemic diseases have multiorgan implications, and the whole gastrointestinal (GI) tract represents a frequent target in terms of symptom appearance and interdependent pathophysiological mechanisms. Metabolic alterations linked with diabetic complications, neuropathy and disrupted hormone homeostasis can lead to upper and/or lower GI symptoms in up to 75% of diabetic patients, with multifactorial involvement of the oesophagus, stomach, upper and lower intestine, and of the gallbladder. On the other hand, altered gastrointestinal motility and/or secretions are able to affect glucose and lipid homeostasis in the short and long term. Finally, diabetes has been linked with increased cancer risk at different levels of the GI tract. The presence of GI symptoms and a comprehensive assessment of GI function should be carefully considered in the management of diabetic patients to avoid further complications and to ameliorate the quality of life. Additionally, the presence of gastrointestinal dysfunction should be adequately managed to improve metabolic homeostasis, the efficacy of antidiabetic treatments and secondary prevention strategies.
α‐Glyceryl‐phosphoryl‐ethanolamine protects human hippocampal neurons from ageing‐induced cellular alterations
Authors: Zappelli Elisa , Daniele Simona , Ceccarelli Lorenzo , Vergassola Matteo , Ragni Lorella , Mangano Giorgina , Martini Claudia 
Published: July 2022

AbstractBrain ageing has been related to a decrease in cellular metabolism, to an accumulation of misfolded proteins and to an alteration of the lipid membrane composition. These alterations act as contributive aspects of age‐related memory decline by reducing membrane excitability and neurotransmitter release. In this sense, precursors of phospholipids (PLs) can restore the physiological composition of cellular membranes and ameliorate the cellular defects associated with brain ageing. In particular, phosphatidylcholine (PC) and phosphatidylethanolamine (PE) have been shown to restore mitochondrial function, reduce the accumulation of amyloid beta (Aβ) and, at the same time, provide the amount of acetylcholine needed to reduce memory deficit. Among PL precursors, alpha‐glycerylphosphorylethanolamine (GPE) has shown to protect astrocytes from Aβ injuries and to slow‐down ageing of human neural stem cells. GPE has been evaluated in aged human hippocampal neurons, which are implicated in learning and memory, and constitute a good in vitro model to investigate the beneficial properties of GPE. In order to mimic cellular ageing, the cells have been maintained 21 days in vitro and challenged with GPE. Results of the present paper showed GPE ability to increase PE and PC content, glucose uptake and the activity of the chain respiratory complex I and of the GSK‐3β pathway. Moreover, the nootropic compound showed an increase in the transcriptional/protein levels of neurotrophic and well‐being related genes. Finally, GPE counteracted the accumulation of ageing‐related misfolded proteins (a‐synuclein and tau). Overall, our data underline promising effects of GPE in counteracting cellular alterations related to brain ageing and cognitive decline.
Movement disorders in valine métabolism diseases caused by HIBCH and ECHS1 deficiencies
Authors: François‐Heude Marie‐Céline , Lebigot Elise , Roze Emmanuel , Warde Marie Thérèse Abi , Cances Claude , Damaj Lena , Espil Caroline , Fluss Joel , de Lonlay Pascale , Kern Ilse , Lenaers Guy , Munnich Arnold , Meyer Pierre , Spitz Marie‐Aude , Torre Stéphanie , Doummar Diane , Touati Guy , Leboucq Nicolas , Roubertie Agathe 
Published: July 2022

AbstractBackground and purposeHIBCH and ECHS1 genes encode two enzymes implicated in the critical steps of valine catabolism, 3‐hydroxyisobutyryl‐coenzyme A (CoA) hydrolase (HIBCH) and short‐chainenoyl‐CoA hydratase (ECHS1), respectively. HIBCH deficiency (HIBCHD) and ECHS1 deficiency (ECHS1D) generate rare metabolic dysfunctions, often revealed by neurological symptoms. The aim of this study was to describe movement disorders spectrum in patients with pathogenic variants in ECHS1 and HIBC.MethodsWe reviewed a series of 18 patients (HIBCHD: 5; ECHS1D: 13) as well as 105 patients from the literature. We analysed the detailed phenotype of HIBCHD (38 patients) and ECHS1D (85 patients), focusing on MDs.ResultsThe two diseases have a very similar neurological phenotype, with an early onset before 10 years of age for three clinical presentations: neonatal onset, Leigh‐like syndrome (progressive onset or acute neurological decompensation), and isolated paroxysmal dyskinesia. Permanent or paroxysmal MDs were recorded in 61% of HIBCHD patients and 72% of ECHS1D patients. Patients had a variable combination of either isolated or combined MD, and dystonia was the main MD. These continuous MDs included dystonia, chorea, parkinsonism, athetosis, myoclonus, tremors, and abnormal eye movements. Patients with paroxysmal dyskinesia (HIBCHD: 4; ECHS1D: 9) usually had pure paroxysmal dystonia with normal clinical examination and no major impairment in psychomotor development. No correlation could be identified between clinical pattern (especially MD) and genetic pathogenic variants.ConclusionsMovement disorders, including abnormal ocular movements, are a hallmark of HIBCHD and ECHS1D. MDs are not uniform; dystonia is the most frequent, and various types of MD are combined in single patient.
Trigeminal neuropathy in two horses following trauma to the infraorbital and mental nerves
Authors: Ogden Nadine , Thomas Hannah , Carslake Harry , Kane‐Smyth Justine 
Published: July 2022

SummaryThis case series describes two cases of a head injury resulting in a traumatic neuropathy of the infraorbital nerve and the mental nerve, respectively. Both cases presented with head‐shaking behaviour and assumed facial dysaesthesia. This is a cause of head‐shaking not previously described in horses. One horse (Case 1) had a small wound at the level of the infraorbital foramen and was diagnosed with a bony fragment adjacent to the infraorbital nerve using computed tomography (CT) and ultrasonography. Treatment consisted of surgical removal of the fragment, systemic anti‐inflammatories and multimodal analgesia. The second case (Case 2) was diagnosed with a nondisplaced comminuted fracture of the right hemi‐mandible using CT. The fracture line, along with multiple small fragments, was overlying the mental nerve as the nerve exits the mental foramen. The horse was treated with multimodal analgesia, and the fracture healed without requiring stabilisation. Clinical signs took several months to resolve in both cases. There were no reported signs of dysaesthesia or head‐shaking 6 months (Case 1) and 4 months (Case 2) following diagnosis. Long‐term follow‐up is still required to assess these horses. Traumatic neuropathy should be considered as a differential diagnosis in horses presenting with head‐shaking behaviour.
A single centre, open label, pilot study evaluating the effect of intra‐articular hyaluronic acid injection on pain and functionality when injected into the ankle (tibio‐talar and sub‐talar) joint in patients with haemophilic arthropathy
Authors: Taylor Stephanie , David Joel , Partington Karen , Pemberton Sam , Mangles Sarah , Wells Anna , Curry Nicola 
Published: July 2022

AbstractAimsAnkle arthropathy commonly affects persons with haemophilia (PWH). Joint damage causes loss of movement, pain and reduced function. Current treatments are limited. Viscosupplementation has been used to treat other patient groups with joint damage. Viscosupplements serve to augment or act as a substitute for synovial fluid and may ameliorate the effects of cartilage loss by cushioning joints and reducing pain. This study evaluated intra‐articular Ostenil Plus™ (HA) for ankle arthropathy in PWH. Reduction in pain was the primary outcome.MethodsA single centre open label pilot study. PWH and significant ankle arthropathy, according to MRI scores, were recruited. Participants received intra‐articular HA injections at baseline and 6 months. Follow up assessments were completed three‐monthly for 1 year. Pain was assessed by the Visual Analogue Scale (VAS). Participant perceptions of overall changes to pain, function and quality of life were sought.ResultsTwenty‐four participants were recruited, three withdrew. Twenty‐six joints were injected. Twenty participants had severe haemophilia. Mean age 35 years. Participants reported significant reduction in pain over the study. VAS baseline: 5.62; 6 month 3.92; 12‐month 3.42, P < .0001. Joint function improved together with ankle HJHS. No change was seen for EQ‐5D‐5L. Sixteen participants reported reductions in ankle pain and stiffness and greater confidence in undertaking physical activities. No significant adverse reactions were reported.ConclusionOstenil Plus™ treatment improves pain, function and patient perception of functional ability in PWH and ankle arthropathy. This study supports the use of HA as a safe treatment in PWH.