QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction

In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with simple proof-of-concept examples to target both the genomics research community and quantum application developers in a self-contained manner. The details of the implementation are discussed for the various layers of the quantum full-stack accelerator design. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/prince-ph0en1x/QuASeR.Comment: 24 page

Schmallenberg virus: emergence of an Orthobunyavirus among ruminants in Western Europe

Recently, a novel virus has been identified among ruminants in Western Europe. This virus, the so-called Schmallenberg virus, belongs to the family Bunyaviridae, genus Orthobunyavirus, serogroup Simbu and is closely related to Akabane, Aino and Shamonda virus. In cattle, acute symptoms in the dam and adult animals generally include high fever, milk drop and diarrhea among others. More importantly, infection during gestation may lead to abortion, stillbirth and congenital malformations. As all bunyaviruses, Schmallenberg virus also uses vectors for efficient transmission. Closely related viruses causing similar symptoms, such as Akabane and Akabane-like viruses, are mainly transmitted by Culicoides. It is very likely that Schmallenberg virus is transmitted by similar vectors. This review provides an overview of Bunyaviridae, their epidemiology, symptoms, prevention and control. Special emphasis is put on the Simbu serogroup of the Orthobunyavirus genus pointing out the similarities between them and closely related members

Decoding Third Places

Urban open spaces should give back to the public, creating vital and valuable places within a city. People should want to seek out these spaces to occupy, seeing them not as useless gaps between buildings but areas with their own value and identity. To create this public demand, successful open spaces contain qualities of third places. Third places, a term coined by Ray Oldenburg, describes somewhere familiar that people choose to spend their time outside their first places (their homes) and their second places (their work). Third places bring communities closer together and are open to the public, but not all open spaces are third places. What are the qualities and elements of third places that designers can include in the creation of an open space to establish a cherished and successful component of an urban context? The capstone examines four case studies and consists of observations and photos at each to determine how individual elements contribute to the overall qualities of third places that bring different groups of citizens together and establish a space as a valued part of the community. These four case studies are the City Pump in Rogers, AR, the Cooper Hewitt Museum’s outdoor garden space in New York, NY, the Citygarden in St. Louis, and the 8th Street Market in Bentonville, AR. The observations are compared against the writings of urban designers and theorists including William Whyte, Randolph Hester, and specifically the work of Ray Oldenburg including his constructs of third places to determine if and how their ideas are true in actual precedents. Each case study features key takeaways through written description and graphic diagramming regarding how the different elements create qualities of third places--or if they do at all. The subsequent results have a wide range of applications for the future of public space design. The capstone culminates in the create of a catalog featuring all the case studies, their written descriptions, observations, photos, and elemental diagrams. This breadth of information is a reference for designing other successful open spaces in the future. The results may also point to new or alternative methods for the future research of public third places. The design of open spaces is an important topic for creating more engaging and appealing cities. Without proper consideration, these areas are often uninteresting and wasted space that does little to create attraction to downtown areas. The accommodation of current public needs and desires in conjunction with design moves and decisions that have worked in the past has the potential to create a space that citizens frequently occupy and are proud of. This capstone delves deeper into understanding how such a goal is possible

I just don’t think I have cancer:Why some participants do not follow up with a recommended colonoscopy in colorectal cancer screening

Participants who receive an unfavourable screening result in two-step colorectal cancer screening programmes have a significantly increased risk of colorectal cancer. They are therefore recommended a colonoscopy to examine the colon for the presence of cancer or a precursor to cancer. However, non-follow up of colonoscopy is an issue in almost all invitation based colorectal cancer-screening programmes. This thesis aimed to find out why some participants in the Dutch colorectal cancer-screening programme do not undergo colonoscopy after an unfavourable screening result. Methods used were interviews and a nation-wide questionnaire. Results showed that participants who did not undergo colonoscopy more often feel their risk for colorectal cancer is low; more often have difficulties deciding, and have lower knowledge levels than those who do undergo colonoscopy. A negative colonoscopy advice from someone outside of the medical setting as well as referral to an unfamiliar colonoscopy location were also associated with non-follow up. Participants who do undergo colonoscopy more often believe their general practitioner is supportive of this examination. One third of participants who underwent the recommended colonoscopy (with a favourable outcome) reported high levels of cancer worry. This thesis theorizes that participation in two-step cancer screening may be viewed as a two-step decision by invitees, and that feelings of moral obligation may lead to participation that is less informed than prescribed by the rational choice model. As such, placing emphasis on colorectal cancer screening participation as a 1-step decision and offering guidance to those with decisional difficulties may offer opportunities for further improvement of population based colorectal cancer screening