htsint: a Python library for sequencing pipelines that combines data through gene set generation

Background: Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. Results: We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for 'enrichment' or conditional differences using one of a number of commonly available packages. Conclusion: The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint

The Effect of Imagined Interactions on Secret Revelation and Health

This study examined the influence of imagined interactions on the decision to reveal secrets and some health outcomes. Recent research has only begun to investigate how individuals decide to reveal or conceal secrets. It is accepted that people base decisions to reveal on predictions of expected outcomes of revealing/concealing (Caughlin, Afifi, Carpetner-Theune, & Miller, 2005). Imagined interactions, the imagined cognitive rehearsal of potential conversations, are proposed to serve as a mechanism for making predictions, which influences the decision to reveal. Particularly, imagined interactions where hypothesized to influence one’s expected outcomes and increase one’s confidence in feeling like they can communicate the secret effectively. Other research suggests that imagined revelation also influences health outcomes (Rodriguez & Kelly, 2006). It was hypothesized that imagining a negative reaction on the part of a confidant would result in more illness in the future. Two separate questionnaires, separated by two months, were used to assess these hypotheses. Participants first described a secret they were keeping from an individual and how they imagined telling that secret to that person. At the second data collection, participants reported whether the secret had been revealed, how that revelation took place, and experienced affective and physical health over the last two months. Results indicated that imagined interactions predict secret revelation. Participants who imagined frequent, positive, specific, rehearsed, and self-understanding conversations were more likely to reveal their secrets, had more positive expected outcomes, and were more confident in their ability to communicate the secret. Additionally, people who had positive secrets and infrequent, positive, and cathartic imagined interactions experienced less physical illness and more negative affect in the two months after the initial questionnaire. These findings offer new insight into how people decide to disclose secrets, and how the imagination, irrespective of revelation, can influence health

Survival of the Persuasible: An Evolutionary Approach to Interpersonal Influence

This dissertation used evolutionary theory to explain the persuasive effects of source characteristics on message targets. It was argued that targets are differentially persuaded by sources who possess certain phenotypic characteristics because such responses increased reproductive success over the course of human history and were therefore evolutionarily adaptive. Attitude and attributions toward the source and message were hypothesized to be affected by a three-way interaction between source characteristic, the source's communicated intention of goodwill, and participant dominance. In addition, a structural model was used to test whether source and message attributions mediated the effect of source characteristics on attitude. Four experiments were conducted to test different phenotypic cues: facial symmetry (Experiment 1, N = 287), facial sexual dimorphism (Experiment 2, N = 278), voice pitch (Experiment 3, N = 286), and facial similarity (Experiment 4, N = 100). These phenotypic manipulations were crossed with message manipulations in which the source framed the advocated action as either benefitting the source or the message targets. Participants were randomly assigned to between-subjects experimental conditions in which they read or listened to a series of persuasive messages attributed to different sources. Results provided weak support for the hypothesized interaction. Significant two- and three-way interactions were found, but these interactions did not fully support predictions and lacked consistency across experiments. Further, structural equation models demonstrated few and inconsistent effects of source characteristics on attitude or attributions toward the source and message. Despite these findings, the significant results provide some reason to believe that targets' susceptibility to influence may have some evolutionary underpinnings. Implications, limitations, and directions for future research are discussed

Designing Parametric Matter

This paper presents a series of design experiments that seek to move beyond today’s computer-aided design and computer-aided manufacture (CAD/CAM) technologies and investigates alternative material practices based on programmable self-assembly. When using CAD software, 3D designs can be rendered extremely flexible and adaptable such that changes to an objects size, colour, transparency, topology, or geometry can be made quickly and easily. However, once digital designs are converted into physical objects via typical CAM technologies, this capability for adaptation usually dissolves as objects are typically fabricated using inert materials and no consideration of a material’s computational abilities. The series of design experiments discussed in this paper help to rethink and re-imagine the possibilities of design and making with adaptive fabrication processes. The design experiments explore mineral accretion and generative paint recipes. Mineral accretion is predominantly controlled via a process of electrolysis to produce adaptable crystal structures that are grown on cathode scaffolds within a volume of seawater. The generative paint experiments expand on the mineral accretion work to explore how material self-assembly can be guided using less restrictive scaffolds. The experiments reveal how ‘contrast’ can be exploited within the design process as a means of guiding and monitoring material scale self-assembly. Through reflection of these material experiments, this paper seeks to provoke discussion about the role of design within future manufacturing systems, and the possible physical properties of future designed objects

Incidental Malrotation in Adolescent Diagnosed with Appendicitis

17-year-old male patient with a history of autism presenting with right lower quadrant pain that started in the morning. The appendix was not able to be visualized by ultrasonography. An abdominal and pelvic CT with contrast showed a dilated appendix with surrounding inflammation. Malrotation was not identified on CT Scan. Patient was transferred to a nearby Children’s Hospital for laparoscopic appendectomy. During the procedure, the pediatric surgeon noted that initially, neither the appendix nor cecum was present in the right lower quadrant. This case represents an uncommon finding for a patient in the adolescent age group

Alteplase Used in a Child with an Acute Ischemic Stroke

Stroke, also known as cerebrovascular accident (CVA), is a neurological injury caused by inadequate brain perfusion due to either ischemia or hemorrhage. There is an abundance of literature on the management of ischemic strokes in adults and this has led to well-defined diagnostic and treatment guidelines. However, the management of pediatric ischemic strokes is currently based on clinical experience of experts, recommendations of consensus guidelines, case studies and extrapolation from adult clinical trials. In this case report, a pediatric patient suffering from an ischemic stroke is successfully treated with IV alteplase (tPA)

The Use of Airborne LiDAR in Assessing Coastal Erosion in the Southeastern USA

Changes in sea level along the coastal southeastern United States (U.S.) influence the dynamic coastal response. In particular, the Southeast Coastal Network (SECN) of the National Park Service (NPS) has exhibited evidence of fluctuations in sea level which caused coastal erosion. Airborne LiDAR acquired from NOAA for Fort Matanzas National Monument, Fort Pulaski National Monument, Charles Pinckney National Historic Site, and Cape Lookout National Seashore were analyzed to identify changes in both elevation and the spatial volume of unconsolidated sedimentary material in the coastal southeast over time. Areas that exhibited an increase (deposited material) or decrease (eroded material) in elevation were mapped across the study area from 2006 to 2018. Results indicate a quasi-cyclic process where unconsolidated sediment distribution and the morphodynamic equilibrium changes with time. The coastal zones are steadily oscillating between the process of erosion and deposition affecting the coastal geomorphological dynamic. The use of LiDAR for evaluating coastal sustainability and resiliency due to this environmental phenomenon is clear