Unboxing Cluster Heatmaps

Background: Cluster heatmaps are commonly used in biology and related fields to reveal hierarchical clusters in data matrices. This visualization technique has high data density and reveal clusters better than unordered heatmaps alone. However, cluster heatmaps have known issues making them both time consuming to use and prone to error. We hypothesize that visualization techniques without the rigid grid constraint of cluster heatmaps will perform better at clustering-related tasks. Results: We developed an approach to “unbox” the heatmap values and embed them directly in the hierarchical clustering results, allowing us to use standard hierarchical visualization techniques as alternatives to cluster heatmaps. We then tested our hypothesis by conducting a survey of 45 practitioners to determine how cluster heatmaps are used, prototyping alternatives to cluster heatmaps using pair analytics with a computational biologist, and evaluating those alternatives with hour-long interviews of 5 practitioners and an Amazon Mechanical Turk user study with approximately 200 participants. We found statistically significant performance differences for most clustering-related tasks, and in the number of perceived visual clusters. Visit git.io/vw0t3 for our results. Conclusions: The optimal technique varied by task. However, gapmaps were preferred by the interviewed practitioners and outperformed or performed as well as cluster heatmaps for clustering-related tasks. Gapmaps are similar to cluster heatmaps, but relax the heatmap grid constraints by introducing gaps between rows and/or columns that are not closely clustered. Based on these results, we recommend users adopt gapmaps as an alternative to cluster heatmaps

Genomic biomarker discovery in disease progression and therapy response in bladder cancer utilizing machine learning

Cancer in all its forms of expression is a major cause of death. To identify the genomic reason behind cancer, discovery of biomarkers is needed. In this paper, genomic data of bladder cancer are examined for the purpose of biomarker discovery. Genomic biomarkers are indicators stemming from the study of the genome, either at a very low level based on the genome sequence itself, or more abstractly such as measuring the level of gene expression for different disease groups. The latter method is pivotal for this work, since the available datasets consist of RNA sequencing data, transformed to gene expression levels, as well as data on a multitude of clinical indicators. Based on this, various methods are utilized such as statistical modeling via logistic regression and regularization techniques (elastic-net), clustering, survival analysis through Kaplan–Meier curves, and heatmaps for the experiments leading to biomarker discovery. The experiments have led to the discovery of two gene signatures capable of predicting therapy response and disease progression with considerable accuracy for bladder cancer patients which correlates well with clinical indicators such as Therapy Response and T-Stage at surgery with Disease Progression in a time-to-event manner

Second-generation molecular subgrouping of medulloblastoma: an international meta-analysis of Group 3 and Group 4 subtypes

In 2012, an international consensus paper reported that medulloblastoma comprises four molecular subgroups (WNT, SHH, Group 3, and Group 4), each associated with distinct genomic features and clinical behavior. Independently, multiple recent reports have defined further intra-subgroup heterogeneity in the form of biologically and clinically relevant subtypes. However, owing to differences in patient cohorts and analytical methods, estimates of subtype number and definition have been inconsistent, especially within Group 3 and Group 4. Herein, we aimed to reconcile the definition of Group 3/Group 4 MB subtypes through the analysis of a series of 1501 medulloblastomas with DNA-methylation profiling data, including 852 with matched transcriptome data. Using multiple complementary bioinformatic approaches, we compared the concordance of subtype calls between published cohorts and analytical methods, including assessments of class-definition confidence and reproducibility. While the lowest complexity solutions continued to support the original consensus subgroups of Group 3 and Group 4, our analysis most strongly supported a definition comprising eight robust Group 3/Group 4 subtypes (types I–VIII). Subtype II was consistently identified across all component studies, while all others were supported by multiple class-definition methods. Regardless of analytical technique, increasing cohort size did not further increase the number of identified Group 3/Group 4 subtypes. Summarizing the molecular and clinico-pathological features of these eight subtypes indicated enrichment of specific driver gene alterations and cytogenetic events amongst subtypes, and identified highly disparate survival outcomes, further supporting their biological and clinical relevance. Collectively, this study provides continued support for consensus Groups 3 and 4 while enabling robust derivation of, and categorical accounting for, the extensive intertumoral heterogeneity within Groups 3 and 4, revealed by recent high-resolution subclassification approaches. Furthermore, these findings provide a basis for application of emerging methods (e.g., proteomics/single-cell approaches) which may additionally inform medulloblastoma subclassification. Outputs from this study will help shape definition of the next generation of medulloblastoma clinical protocols and facilitate the application of enhanced molecularly guided risk stratification to improve outcomes and quality of life for patients and their families

Assessing an Abandoned Pyrite Cinder Deposit in Southeast Spain with Electrical Resistivity Tomography: A Case Study

Industrial activities have historically generated significant quantities of by-products, including pyrite cinders, a residue produced during the synthesis of sulphuric acid. This study presents a multidisciplinary approach to characterise an abandoned pyrite cinder deposit. Combining geophysical (electrical resistivity tomography—ERT), geochemical, and statistical methods, we assess the physicochemical properties of the deposit and its environmental implications. Our findings reveal the presence of heavy metals, with lead (7017.5 mg.kg−1) being the most concentrated element on the surface of the deposit, exceeding local legal thresholds by more than 163 times, posing environmental risks and inhibiting vegetation growth. Subsurface characterisation indicates a decreasing concentration trend of metals with depth, alongside variations in pH and electrical conductivity. Clustering analysis identifies groups of similar behaviours between resistivity, the most abundant heavy metals, and other variables, providing valuable insights into the complex interplay within the deposit. Our study underscores the importance of integrated approaches in assessing and managing hazardous waste sites, with implications for environmental remediation strategies

Implications of Below-Ground Allelopathic Interactions of Camelina sativa and Microorganisms for Phosphate Availability and Habitat Maintenance

Toxic breakdown products of young Camelina sativa (L.) Crantz, glucosinolates can eliminate microorganisms in the soil. Since microorganisms are essential for phosphate cycling, only insensitive microorganisms with phosphate-solubilizing activity can improve C. sativa’s phosphate supply. In this study, 33P-labeled phosphate, inductively coupled plasma mass spectrometry and pot experiments unveiled that not only Trichoderma viride and Pseudomonas laurentiana used as phosphate-solubilizing inoculants, but also intrinsic soil microorganisms, including Penicillium aurantiogriseum, and the assemblies of root-colonizing microorganisms solubilized as well phosphate from apatite, trigger off competitive behavior between the organisms. Driving factors in the competitiveness are plant and microbial secondary metabolites, while glucosinolates of Camelina and their breakdown products are regarded as key compounds that inhibit the pathogen P. aurantiogriseum, but also seem to impede root colonization of T. viride. On the other hand, fungal diketopiperazine combined with glucosinolates is fatal to Camelina. The results may contribute to explain the contradictory effects of phosphate-solubilizing microorganisms when used as biofertilizers. Further studies will elucidate impacts of released secondary metabolites on coexisting microorganisms and plants under different environmental conditions

Descodificação da receção dos anúncios publicitários, em diversas plataformas: a abordagem do neuromarketing

Dissertação de mestrado apresentada à Escola Superior de Comunicação Social como parte dos requisitos para obtenção de grau de mestre em Publicidade e Marketing.Os últimos anos têm apresentado um crescimento da publicidade online, quer nas possibilidades de formato e de plataforma quer a nível orçamental. Ainda assim, a sua eficácia é um tema controverso. A possibilidade de ir mais além dos métodos tradicionais, no estudo do comportamento do consumidor, através de ferramentas de Neuromarketing levou a um novo leque de investigações a realizar. Por fim, a popularidade e as características intrínsecas do conteúdo em formato vídeo permitiram definir como principal objetivo, estudar quais os efeitos que, a visualização dos anúncios publicitários (em formato vídeo), em diversas plataformas, tem nos processos psicológicos do recetor. Pretendemos examinar na ótica da atenção, através da utilização de eye tracking, o comportamento dos participantes nas diversas plataformas e o impacto dos diversos elementos das plataformas; analisar o processo mnésico aquando o anúncio de um anúncio e de uma marca desconhecida; observar as variações emocionais nos diversos conteúdos exibidos e, analisar a relação entre a atitude relativamente ao anúncio e a atitude relativamente à marca. Para efetivar o estudo foi idealizada uma triangulação de métodos, composta pelo eye tracking, pelo questionário SAM e por um inquérito aos participantes. Os resultados demonstraram que, de um modo geral, independentemente da plataforma, quando convidados a visualizar o anúncio, a atenção recai na maior parte do tempo para esta área; as emoções positivas sentidas ao longo da reprodução têm peso na atitude criada relativamente ao anúncio que, por sua vez, influencia a atitude relativamente à marca; o storytelling do anúncio em estudo foi claro e eficaz a nível da memória, pelo menos a curto prazo, dado que facilmente os participantes relataram a experiência. Embora os objetivos da investigação tenham sido cumpridos na sua generalidade, permitiram fornecer direções para estudos futuros. Nomeadamente, na replica do estudo num ambiente real, com as plataformas em formato mobile e uma amostra mais representativa e/ou outros grupos de interesse. Ou ainda, alternar a ordem dos anúncios e das plataformas entre os participantes, como também, complementar com outros métodos disponíveis no neuromarketing.ABSTRACT: Recent years have seen an increase in online advertising, format possibilities and platform, to a budget level. Still, its effectiveness is a controversial topic. The possibility of going beyond traditional methods without studying consumer behavior through Neuromarketing tools has led to a new range of investigations to be carried out. Finally, the popularity and intrinsic characteristics of video content allow us to define as main objectives, study the effects and which responses, responses of advertising users (in video format), in various platforms, in the psychological processes of the receiver. Intends to examine from the perspective of attention, through the use of eye tracking, the behavior of participants on different platforms and the impact of various platform elements; analyze the messaging process when announcing an ad and an unknown brand; observe how emotional changes in various content; and analyze a relationship between an ad attitude and a brand attitude. To carry out the study, a triangulation of methods was devised, consisting of eye tracking, the SAM questionnaire and a record to the participants. The results demonstrated that, in general, can be accessed on the platform, when invited to view the announcement, attention received most of the time for this area; how positive emotions felt throughout reproduction weigh on the attitude created toward the ad, which in turn influences an attitude toward the brand; Storytelling of the study ad was clear and effective at the memory level, with a shorter timeframe, as participants easily reported an experiment. Although the research objectives were generally met, they provided instructions for future studies. Namely, a replica of the study in a real environment, with mobile platforms and a more representative sample and / or other interest groups. Alternatively, switch the order of applications and platforms among participants, as well as the other methods available in neuromarketing.N/

Visualizing a Task Performer’s Gaze to Foster Observers’ Performance and Learning : a Systematic Literature Review on Eye Movement Modeling Examples

Eye movement modeling examples (EMMEs) are instructional videos (e.g., tutorials) that visualize another person’s gaze location while they demonstrate how to perform a task. This systematic literature review provides a detailed overview of studies on the effects of EMME to foster observers’ performance and learning and highlights their differences in EMME designs. Through a broad, systematic search on four relevant databases, we identified 72 EMME studies (78 experiments). First, we created an overview of the different study backgrounds. Studies most often taught tasks from the domains of sports/physical education, medicine, aviation, and STEM areas and had different rationales for displaying EMME. Next, we outlined how studies differed in terms of participant characteristics, task types, and the design of the EMME materials, which makes it hard to infer how these differences affect performance and learning. Third, we concluded that the vast majority of the experiments showed at least some positive effects of EMME during learning, on tests directly after learning, and tests after a delay. Finally, our results provide a first indication of which EMME characteristics may positively influence learning. Future research should start to more systematically examine the effects of specific EMME design choices for specific participant populations and task types

Ant Colony Algorithms for the Resolution of Semantic Searches in P2P Networks

Tesis por compendio[EN] The long-lasting trend in the field of computation of stress and resource distribution has found its way into computer networks via the concept of peer-to-peer (P2P) connectivity. P2P is a symmetrical model, where each network node is enabled a comparable range of capacities and resources. It stands in a stark contrast to the classical, strongly asymmetrical client-server approach. P2P, originally considered only a complimentary, server-side structure to the straightforward client-server model, has been shown to have the substantial potential on its own, with multiple, widely known benefits: good fault tolerance and recovery, satisfactory scalability and intrinsic load distribution. However, contrary to client-server, P2P networks require sophisticated solutions on all levels, ranging from network organization, to resource location and managing. In this thesis we address one of the key issues of P2P networks: performing efficient resource searches of semantic nature under realistic, dynamic conditions. There have been numerous solutions to this matter, with evolutionary, stigmergy-based, and simple computational foci, but few attempt to resolve the full range of challenges this problem entails. To name a few: real-life P2P networks are rarely static, nodes disconnect, reconnect and change their content. In addition, a trivial incorporation of semantic searches into well-known algorithms causes significant decrease in search efficiency. In our research we build a solution incrementally, starting with the classic Ant Colony System (ACS) within the Ant Colony Optimization metaheuristic (ACO). ACO is an algorithmic framework used for solving combinatorial optimization problems that fits contractually the problem very well, albeit not providing an immediate solution to any of the aforementioned problems. First, we propose an efficient ACS variant in structured (hypercube structured) P2P networks, by enabling a path-post processing algorithm, which called Tabu Route Optimization (TRO). Next, we proceed to resolve the issue of network dynamism with an ACO-compatible information diffusion approach. Consequently, we attempt to incorporate the semantic component of the searches. This initial approximation to the problem was achieved by allowing ACS to differentiate between search types with the pheromone-per-concept idea. We called the outcome of this merger Routing Concept ACS (RC-ACS). RC-ACS is a robust, static multipheromone implementation of ACS. However, we were able to conclude from it that the pheromone-per-concept approach offers only limited scalability and cannot be considered a global solution. Thus, further progress was made in this respect when we introduced to RC-ACS our novel idea: dynamic pheromone creation, which replaces the static one-to-one assignment. We called the resulting algorithm Angry Ant Framework (AAF). In AAF new pheromone levels are created as needed and during the search, rather than prior to it. The final step was to enable AAF, not only to create pheromone levels, but to reassign them to optimize the pheromone usage. The resulting algorithm is called EntropicAAF and it has been evaluated as one of the top-performing algorithms for P2P semantic searches under all conditions.[ES] La popular tendencia de distribución de carga y recursos en el ámbito de la computación se ha transmitido a las redes computacionales a través del concepto de la conectividad peer-to-peer (P2P). P2P es un modelo simétrico, en el cual a cada nodo de la red se le otorga un rango comparable de capacidades y recursos. Se trata de un fuerte contraste con el clásico y fuertemente asimétrico enfoque cliente-servidor. P2P, originalmente considerado solo como una estructura del lado del servidor complementaria al sencillo modelo cliente-servidor, ha demostrado tener un potencial considerable por sí mismo, con múltiples beneficios ampliamente conocidos: buena tolerancia a fallos y recuperación, escalabilidad satisfactoria y distribución de carga intrínseca. Sin embargo, al contrario que el modelo cliente-servidor, las redes P2P requieren de soluciones sofisticadas a todos los niveles, desde la organización de la red hasta la gestión y localización de recursos. Esta tesis aborda uno de los problemas principales de las redes P2P: la búsqueda eficiente de recursos de naturaleza semántica bajo condiciones dinámicas y realistas. Ha habido numerosas soluciones a este problema basadas en enfoques evolucionarios, estigmérgicos y simples, pero pocas han tratado de resolver el abanico completo de desafíos. En primer lugar, las redes P2P reales son raramente estáticas: los nodos se desconectan, reconectan y cambian de contenido. Además, la incorporación trivial de búsquedas semánticas en algoritmos conocidos causa un decremento significativo de la eficiencia de la búsqueda. En esta investigación se ha construido una solución de manera incremental, comenzando por el clásico Ant Colony System (ACS) basado en la metaheurística de Ant Colony Optimization (ACO). ACO es un framework algorítmico usado para búsquedas en grafos que encaja perfectamente con las condiciones del problema, aunque no provee una solución inmediata a las cuestiones mencionadas anteriormente. En primer lugar, se propone una variante eficiente de ACS para redes P2P estructuradas (con estructura de hipercubo) permitiendo el postprocesamiento de las rutas, al que hemos denominado Tabu Route Optimization (TRO). A continuación, se ha tratado de resolver el problema del dinamismo de la red mediante la difusión de la información a través de una estrategia compatible con ACO. En consecuencia, se ha tratado de incorporar el componente semántico de las búsquedas. Esta aproximación inicial al problema ha sido lograda permitiendo al ACS diferenciar entre tipos de búsquedas através de la idea de pheromone-per-concept. El resultado de esta fusión se ha denominado Routing Concept ACS (RC-ACS). RC-ACS es una implementación multiferomona estática y robusta de ACS. Sin embargo, a partir de esta implementación se ha podido concluir que el enfoque pheromone-per-concept ofrece solo escalabilidad limitada y que no puede ser considerado una solución global. Por lo tanto, para lograr una mejora a este respecto, se ha introducido al RC-ACS una novedosa idea: la creación dinámica de feromonas, que reemplaza la asignación estática uno a uno. En el algoritmo resultante, al que hemos denominado Angry Ant Framework (AAF), los nuevos niveles de feromona se crean conforme se necesitan y durante la búsqueda, en lugar de crearse antes de la misma. La mejora final se ha obtenido al permitir al AAF no solo crear niveles de feromona, sino también reasignarlos para optimizar el uso de la misma. El algoritmo resultante se denomina EntropicAAF y ha sido evaluado como uno de los algoritmos más exitosos para las búsquedas semánticas P2P bajo todas las condiciones.[CA] La popular tendència de distribuir càrrega i recursos en el camp de la computació s'ha estès cap a les xarxes d'ordinadors a través del concepte de connexions d'igual a igual (de l'anglès, peer to peer o P2P). P2P és un model simètric on cada node de la xarxa disposa del mateix nombre de capacitats i recursos. P2P, considerat originàriament només una estructura situada al servidor complementària al model client-servidor simple, ha provat tindre el suficient potencial per ella mateixa, amb múltiples beneficis ben coneguts: una bona tolerància a errades i recuperació, una satisfactòria escalabilitat i una intrínseca distribució de càrrega. No obstant, contràriament al client-servidor, les xarxes P2P requereixen solucions sofisticades a tots els nivells, que varien des de l'organització de la xarxa a la localització de recursos i la seua gestió. En aquesta tesi s'adreça un dels problemes clau de les xarxes P2P: ser capaç de realitzar eficientment cerques de recursos de naturalesa semàntica sota condicions realistes i dinàmiques. Existeixen nombroses solucions a aquest tema basades en la computació simple, evolutiva i també basades en l'estimèrgia (de l'anglès, stigmergy), però pocs esforços s'han realitzat per intentar resoldre l'ampli conjunt de reptes existent. En primer lloc, les xarxes P2P reals són rarament estàtiques: els nodes es connecten, desconnecten i canvien els seus continguts. A més a més, la incorporació trivial de cerques semàntiques als algorismes existents causa una disminució significant de l'eficiència de la cerca. En aquesta recerca s'ha construït una solució incremental, començant pel sistema clàssic de colònia de formigues (de l'anglés, Ant Colony System o ACS) dins de la metaheurística d'optimització de colònies de formigues (de l'anglès, Ant Colony Optimization o ACO). ACO és un entorn algorísmic utilitzat per cercar en grafs i que aborda el problema de forma satisfactòria, tot i que no proveeix d'una solució immediata a cap dels problemes anteriorment mencionats. Primer, s'ha proposat una variant eficient d'ACS en xarxes P2P estructurades (en forma d'hipercub) a través d'un algorisme de processament post-camí el qual s'ha anomenat en anglès Tabu Route Optimization (TRO). A continuació, s'ha procedit a resoldre el problema del dinamisme de les xarxes amb un enfocament de difusió d'informació compatible amb ACO. Com a conseqüència, s'ha intentat incorporar la component semàntica de les cerques. Aquest enfocament inicial al problema s'ha realitzat permetent a ACS diferenciar entre tipus de cerques amb la idea de ''feromona per concepte'', i s'ha anomenat a aquest producte Routing Concept ACS o RC-ACS. RC-ACS és una implementació multi-feromona robusta i estàtica d'ACS. No obstant, s'ha pogut concloure que l'enfocament de feromona per concepte ofereix només una escalabilitat limitada i no pot ser considerada una solució global. En aquest respecte s'ha realitzat progrés posteriorment introduint una nova idea a RC-ACS: la creació dinàmica de feromones, la qual reemplaça a l'assignació un a un de les mateixes. A l'algorisme resultant se l'ha anomenat en anglès Angry Ant Framework (AAF). En AAF es creen nous nivells de feromones a mesura que es necessiten durant la cerca, i no abans d'aquesta. El progrés final s'ha aconseguit quan s'ha permès a AAF, no sols crear nivells de feromones, sinó reassignar-los per optimitzar la utilització de feromones. L'algorisme resultant s'ha anomenat EntropicAAF i ha sigut avaluat com un dels algorismes per a cerques semàntiques P2P amb millors prestacions.Krynicki, KK. (2016). Ant Colony Algorithms for the Resolution of Semantic Searches in P2P Networks [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/61293TESISPremios Extraordinarios de tesis doctoralesCompendi