A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years

Background: The long-term availability of online Web services is of utmost importance to ensure reproducibility of analytical results. However, because of lack of maintenance following acceptance, many servers become unavailable after a short period of time. Our aim was to monitor the accessibility and the decay rate of published Web services as well as to determine the factors underlying trends changes. Methods: We searched PubMed to identify publications containing Web server-related terms published between 1994 and 2017. Automatic and manual screening was used to check the status of each Web service. Kruskall-Wallis, Mann-Whitney and Chi-square tests were used to evaluate various parameters, including availability, accessibility, platform, origin of authors, citation, journal impact factor and publication year. Results: We identified 3649 publications in 375 journals of which 2522 (69%) were currently active. Over 95% of sites were running in the first 2 years, but this rate dropped to 84% in the third year and gradually sank afterwards (P < 1e-16). The mean half-life of Web services is 10.39 years. Working Web services were published in journals with higher impact factors (P = 4.8e-04). Services published before the year 2000 received minimal attention. The citation of offline services was less than for those online (P = 0.022). The majority of Web services provide analytical tools, and the proportion of databases is slowly decreasing. Conclusions. Almost one-third of Web services published to date went out of service. We recommend continued support of Web-based services to increase the reproducibility of published results

Using Web Archives to Enrich the Live Web Experience Through Storytelling

Much of our cultural discourse occurs primarily on the Web. Thus, Web preservation is a fundamental precondition for multiple disciplines. Archiving Web pages into themed collections is a method for ensuring these resources are available for posterity. Services such as Archive-It exists to allow institutions to develop, curate, and preserve collections of Web resources. Understanding the contents and boundaries of these archived collections is a challenge for most people, resulting in the paradox of the larger the collection, the harder it is to understand. Meanwhile, as the sheer volume of data grows on the Web, storytelling is becoming a popular technique in social media for selecting Web resources to support a particular narrative or story . In this dissertation, we address the problem of understanding the archived collections through proposing the Dark and Stormy Archive (DSA) framework, in which we integrate storytelling social media and Web archives. In the DSA framework, we identify, evaluate, and select candidate Web pages from archived collections that summarize the holdings of these collections, arrange them in chronological order, and then visualize these pages using tools that users already are familiar with, such as Storify. To inform our work of generating stories from archived collections, we start by building a baseline for the structural characteristics of popular (i.e., receiving the most views) human-generated stories through investigating stories from Storify. Furthermore, we checked the entire population of Archive-It collections for better understanding the characteristics of the collections we intend to summarize. We then filter off-topic pages from the collections the using different methods to detect when an archived page in a collection has gone off-topic. We created a gold standard dataset from three Archive-It collections to evaluate the proposed methods at different thresholds. From the gold standard dataset, we identified five behaviors for the TimeMaps (a list of archived copies of a page) based on the page’s aboutness. Based on a dynamic slicing algorithm, we divide the collection and cluster the pages in each slice. We then select the best representative page from each cluster based on different quality metrics (e.g., the replay quality, and the quality of the generated snippet from the page). At the end, we put the selected pages in chronological order and visualize them using Storify. For evaluating the DSA framework, we obtained a ground truth dataset of hand-crafted stories from Archive-It collections generated by expert archivists. We used Amazon’s Mechanical Turk to evaluate the automatically generated stories against the stories that were created by domain experts. The results show that the automatically generated stories by the DSA are indistinguishable from those created by human subject domain experts, while at the same time both kinds of stories (automatic and human) are easily distinguished from randomly generated storie

Effectiveness of Telemedicine in Diabetes Management: A Retrospective Study in an Urban Medically Underserved Population Area (UMUPA).

The purpose of this research is to assess the efficacy of employing telemedicine (TM) technology compared to traditional face-to-face (F2F) visits as an alternative healthcare delivery service for managing diabetes in populations residing in urban medically underserved areas (UMUPA). Researchers investigating public health and healthcare systems fully grasp the enormous challenges encountered by vulnerable populations as a result of healthcare access barriers.1 Prior to the COVID-19 pandemic, F2F visits were most often utilized for healthcare delivery service, which frequently posed barriers for vulnerable populations. When marginalized people, encounter healthcare access barriers, a cascade of events generally occur leading to forestalling or avoiding healthcare services entirely, complicating disease management, resulting in negative health outcomes. This was a novel study examining the hemoglobin A1c (HbA1c) values of 111 patients with uncontrolled type 2 diabetes mellitus (T2DM) and 81 patients with prediabetes. Retrospective electronic patient health records (PHR) from a medical clinic were examined from January 1st, 2019, to June 30th, 2021. The results indicate that lowering HbA1c values for T2DM patients through utilizing TM is similar to outcomes from traditional visits, suggesting that TM may be an alternative mode of healthcare delivery for vulnerable populations. Results for patients with prediabetes were not statistically significant. Patients with uncontrolled diabetes and prediabetes shared a number of similar characteristics; they were predominantly Black, non-Hispanic, females, with a median age of 57 years; and resided in locations with inadequate access to healthcare services in an UMUPA. The majority of patients with uncontrolled diabetes who reside in an UMUPA completed appointments utilized TM technology, lending credence to its potential as an alternative healthcare delivery service for underserved populations. TM technology supports PH and the healthcare system with a viable, alternative strategy for expanding healthcare access where chronic illness and disease pose a significant threat to the health and wellbeing of vulnerable groups. Optimal treatment for patients with diabetes necessitates a proactive, coordinated, systems-thinking team approach. This research supports PH’s endeavors in tackling the long-standing healthcare access barrier challenges in underserved populations

Improving Collection Understanding for Web Archives with Storytelling: Shining Light Into Dark and Stormy Archives

Collections are the tools that people use to make sense of an ever-increasing number of archived web pages. As collections themselves grow, we need tools to make sense of them. Tools that work on the general web, like search engines, are not a good fit for these collections because search engines do not currently represent multiple document versions well. Web archive collections are vast, some containing hundreds of thousands of documents. Thousands of collections exist, many of which cover the same topic. Few collections include standardized metadata. Too many documents from too many collections with insufficient metadata makes collection understanding an expensive proposition. This dissertation establishes a five-process model to assist with web archive collection understanding. This model aims to produce a social media story – a visualization with which most web users are familiar. Each social media story contains surrogates which are summaries of individual documents. These surrogates, when presented together, summarize the topic of the story. After applying our storytelling model, they summarize the topic of a web archive collection. We develop and test a framework to select the best exemplars that represent a collection. We establish that algorithms produced from these primitives select exemplars that are otherwise undiscoverable using conventional search engine methods. We generate story metadata to improve the information scent of a story so users can understand it better. After an analysis showing that existing platforms perform poorly for web archives and a user study establishing the best surrogate type, we generate document metadata for the exemplars with machine learning. We then visualize the story and document metadata together and distribute it to satisfy the information needs of multiple personas who benefit from our model. Our tools serve as a reference implementation of our Dark and Stormy Archives storytelling model. Hypercane selects exemplars and generates story metadata. MementoEmbed generates document metadata. Raintale visualizes and distributes the story based on the story metadata and the document metadata of these exemplars. By providing understanding immediately, our stories save users the time and effort of reading thousands of documents and, most importantly, help them understand web archive collections

Restoring and valuing global kelp forest ecosystems

Kelp forests cover ~30% of the world’s coastline and are the largest biogenic marine habitat on earth. Across their distribution, kelp forests are essential for the healthy functioning of marine ecosystems and consequently underpin many of the benefits coastal societies receive from the ocean. Concurrently, rising sea temperatures, overgrazing by marine herbivores, sedimentation, and water pollution have caused kelp forests populations to decline in most regions across the world. Effectively managing the response to these declines will be pivotal to maintaining healthy marine ecosystems and ensuring the benefits they provide are equitably distributed to coastal societies. In Chapter 1, I review how the marine management paradigm has shifted from protection to restoration as well as the consequences of this shift. Chapter 2 introduces the field of kelp forest restoration and provides a quantitative and qualitative review of 300 years of kelp forest restoration, exploring the genesis of restoration efforts, the lessons we have learned about restoration, and how we can develop the field for the future. Chapter 3 is a direct answer to the question faced while completing Chapter 2. This chapter details the need for a standardized marine restoration reporting framework, the benefits that it would provide, the challenges presented by creating one, and the solutions to these problems. Similarly, Chapter 4 is a response to the gaps discovered in Chapter 2. Chapter 4 explores how we can use naturally occurring positive species interactions and synergies with human activities to not only increase the benefits from ecosystem restoration but increase the probability that restoration is successful. The decision to restore an ecosystem or not is informed by the values and priorities of the society living in or managing that ecosystem. Chapter 5 quantifies the fisheries production, nutrient cycling, and carbon sequestration potential of five key genera of globally distributed kelp forests. I conclude the thesis by reviewing the lessons learned and the steps required to advance the field kelp forest restoration and conservation

Development of Computational Techniques for Identification of Regulatory DNA Motif

Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motif (motif) plays a fundamental role in researching transcriptional regulatory mechanism in cells and helping construct regulatory networks for biological investigation. Chromatin immunoprecipitation combined with sequencing (ChIP-seq) and lambda exonuclease digestion followed by high-throughput sequencing (ChIP-exo) enables researchers to identify TFBS on a genome-scale with improved resolution. Several algorithms have been developed to perform motif identification, employing widely different methods and often giving divergent results. In addition, these existing methods still suffer from prediction accuracy. Thesis focuses on the development of improved regulatory DNA motif identification techniques. We designed an integrated framework, WTSA, that can reliably combine the experimental signals from ChIP-exo data in base pair (bp) resolution to predict the statistically significant DNA motifs. The algorithm improves the prediction accuracy and extends the scope of applicability of the existing methods. We have applied the framework to Escherichia coli k12 genome and evaluated WTSA prediction performance through comparison with seven existing programs. The performance evaluation indicated that WTSA provides reliable predictive power for regulatory motifs using ChIP-exo data. An important application of DNA motif identification is to identify transcriptional regulatory mechanisms. The rapid development of single-cell RNA-Sequencing (scRNAseq) technologies provides an unprecedented opportunity to discover the gene transcriptional regulation at the single-cell level. In the scRNA-seq analyses, a critical step is to identify the cell-type-specific regulons (CTS-Rs), each of which is a group of genes co-regulated by the same transcription regulator in a specific cell type. We developed a web server, IRIS3 (Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq), to solve this problem by the integration of data preprocessing, cell type prediction, gene module identification, and cis-regulatory motif analyses. Compared with other packages, IRIS3 predicts more efficiently and provides more accurate regulon from scRNA-seq data. These CTS-Rs can substantially improve the elucidation of heterogeneous regulatory mechanisms among various cell types and allow reliable constructions of global transcriptional regulation networks encoded in a specific cell type. Also presented in this thesis is DESSO (DEep Sequence and Shape mOtif (DESSO), using deep neural networks and the binomial distribution model to identify DNA motifs, DESSO outperformed existing tools, including DeepBind, in 690 human ENCODE ChIP-Sequencing datasets. DESSO also further expanded motif identification power by integrating the detection of DNA shape features

Economic and Social Consequences of the COVID-19 Pandemic in Energy Sector

The purpose of the Special Issue was to collect the results of research and experience on the consequences of the COVID-19 pandemic for the energy sector and the energy market, broadly understood, that were visible after a year. In particular, the impact of COVID-19 on the energy sector in the EU, including Poland, and the US was examined. The topics concerned various issues, e.g., the situation of energy companies, including those listed on the stock exchange, mining companies, and those dealing with renewable energy. The topics related to the development of electromobility, managerial competences, energy expenditure of local government units, sustainable development of energy, and energy poverty during a pandemic were also discussed

Deriving statistical inference from the application of artificial neural networks to clinical metabolomics data

Metabolomics data are complex with a high degree of multicollinearity. As such, multivariate linear projection methods, such as partial least squares discriminant analysis (PLS-DA) have become standard. Non-linear projections methods, typified by Artificial Neural Networks (ANNs) may be more appropriate to model potential nonlinear latent covariance; however, they are not widely used due to difficulty in deriving statistical inference, and thus biological interpretation. Herein, we illustrate the utility of ANNs for clinical metabolomics using publicly available data sets and develop an open framework for deriving and visualising statistical inference from ANNs equivalent to standard PLS-DA methods

Tracking in the wild: exploring the everyday use of physical activity trackers

As the rates of chronical diseases, such as obesity, cardiovascular disease and diabetes continue to increase, the development of tools that support people in achieving healthier habits is becoming ever more important. Personal tracking systems, such as activity trackers, have emerged as a promising class of tools to support people in managing their everyday health. However, for this promise to be fulfilled, these systems need to be well designed, not only in terms of how they implement specific behavior change techniques, but also in how they integrate into people’s daily lives and address their daily needs. My dissertations provides evidence that accounting for people’s daily practices and needs can help to design activity tracking systems that help people get more value from their tracking practices. To understand how people derive value from their activity tracking practices, I have conducted two inquiries into people’s daily uses of activity tracking systems. In a fist attempt, I led a 10-month study of the adoption of Habito, our own activity tracking mobile app. Habito logged not only users’ physical activity, but also their interactions with the app. This data was used to acquire an estimate of the adoption rate of Habito, and understanding of how adoption is affected by users’ ‘readiness’, i.e., their attitude towards behavior change. In a follow-up study, I turned to the use of video methods and direct, in-situ observations of users’ interactions to understand what motivates people to engage with these tools in their everyday life, and how the surrounding environment shapes their use. These studies revealed some of the complexities of tracking, while extending some of the underlying ideas of behavior change. Among key results: (1) people’s use of activity trackers was found to be predominantly impulsive, where they simultaneously reflect, learn and change their behaviors as they collect data; (2) people’s use of trackers is deeply entangled with their daily routines and practices, and; (3) people use of trackers often is not in line with the traditional vision of these tools as mediators of change – trackers are also commonly used to simply learn about behaviors and engage in moments of self-discovery. Examining how to design activity tracking interfaces that best support people’s different needs , my dissertation further describes an inquiry into the design space of behavioral feedback interfaces. Through a iterative process of synthesis and analysis of research on activity tracking, I devise six design qualities for creating feedback that supports people in their interactions with physical activity data. Through the development and field deployment of four concepts in a field study, I show the potential of these displays for highlighting opportunities for action and learning.À medida que a prevalência de doenças crónicas como a obesidade, doenças cardiovasculares e diabetes continua a aumentar, o desenvolvimento de ferramentas que suportam pessoas a atingir mudanças de comportamento tem-se tornado essencial. Ferramentas de monitorização de comportamentos, tais como monitores de atividade física, têm surgido com a promessa de encorajar um dia a dia mais saudável. Contudo, para que essa promessa seja cumprida, torna-se essencial que estas ferramentas sejam bem concebidas, não só na forma como implementam determinadas estratégias de mudança de comportamento, mas também na forma como são integradas no dia-a-dia das pessoas. A minha dissertação demonstra a importância de considerar as necessidades e práticas diárias dos utilizadores destas ferramentas, de forma a ajudá-las a tirar melhor proveito da sua monitorização de atividade física. De modo a entender como é que os utilizadores destas ferramentas derivam valor das suas práticas de monitorização, a minha dissertação começa por explorar as práticas diárias associadas ao uso de monitores de atividade física. A minha dissertação contribui com duas investigações ao uso diário destas ferramentas. Primeiro, é apresentada uma investigação da adoção de Habito, uma aplicação para monitorização de atividade física. Habito não só registou as instâncias de atividade física dos seus utilizadores, mas também as suas interações com a própria aplicação. Estes dados foram utilizados para adquirir uma taxa de adopção de Habito e entender como é que essa adopção é afetada pela “prontidão” dos utilizadores, i.e., a sua atitude em relação à mudança de comportamento. Num segundo estudo, recorrendo a métodos de vídeo e observações diretas e in-situ da utilização de monitores de atividade física, explorei as motivações associadas ao uso diário destas ferramentas. Estes estudos expandiram algumas das ideias subjacentes ao uso das ferramentas para mudanças de comportamento. Entre resultados principais: (1) o uso de monitores de atividade física é predominantemente impulsivo, onde pessoas refletem, aprendem e alteram os seus comportamentos à medida que recolhem dados sobe estes mesmos comportamentos; (2) o uso de monitores de atividade física está profundamente interligado com as rotinas e práticas dos seus utilizadores, e; (3) o uso de monitores de atividade física nem sempre está ligado a mudanças de comportamento – estas ferramentas também são utilizadas para divertimento e aprendizagem. A minha dissertação contribui ainda com uma exploração do design de interfaces para a monitorização de atividade física. Através de um processo iterativo de síntese e análise de literatura, seis qualidades para a criação de interfaces são derivadas. Através de um estudo de campo, a minha dissertação demonstro o potencial dessas interfaces para ajudar pessoas a aprender e gerir a sua saúde diária