Lost in Translation

The chapter examines the role of practice-related research in the arts, humanities, and social sciences. It will extend existing debates regarding the academic rigour of such methodologies as arts-based research and consider their impact on future research culture, using Zen arts as an example of a subject of study within such a methodological framing. It also discusses complimentary methods used by Zen arts researchers such as ethnography to examine why qualitative techniques are not only useful but imperative in the study of such fields. While practice is the key to Zen arts research, neither of the practice-related method types, practice-led or practice-based, currently defined describes how such practice or the writing function in PhD investigations, where together such components are the subject of investigation as well as the method of research and presentation. The chapter thus suggests an additional category of PRR, “practice-reflexive,” when describing such research whose focus is on the distinction of (or the lack thereof) the written exegesis and the notional artefact.

Identification of CD8+ T cell epitopes through proteasome cleavage site predictions

Background We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model to discriminate CD8+ T cell epitopes. Results We first assembled an epitope dataset consisting of 844 unique virus-specific CD8+ T cell epitopes and their source proteins. We then analyzed cleavage predictions by PCPS immunoproteasome cleavage model on this dataset and compared them with those provided by a related method implemented by NetChop web server. PCPS was clearly superior to NetChop in term of sensitivity (0.89 vs. 0.79) but somewhat inferior with regard to specificity (0.55 vs. 0.60). Judging by the Mathew’s Correlation Coefficient, PCPS predictions were overall superior to those provided by NetChop (0.46 vs. 0.39). We next analyzed the power of C-terminal cleavage predictions provided by the same PCPS model to discriminate CD8+ T cell epitopes, finding that they could be discriminated from random peptides with an accuracy of 0.74. Following these results, we tuned the PCPS web server to predict CD8+ T cell epitopes and predicted the entire SARS-CoV-2 epitope space. Conclusions We report an improved version of PCPS named iPCPS for predicting proteasome cleavage sites and peptides with CD8+ T cell epitope features. iPCPS is available for free public use at https://imed.med.ucm.es/Tools/pcps/.

Fast and Flexible Estimation of Effective Migration Surfaces

An important feature in spatial population genetic data is often “isolation-by-distance,” where genetic differentiation tends to increase as individuals become more geographically distant. Recently, Petkova et al. (2016) developed a statistical method called Estimating Effective Migration Surfaces (EEMS) for visualizing spatially heterogeneous isolation-by-distance on a geographic map. While EEMS is a powerful tool for depicting spatial population structure, it can suffer from slow runtimes. Here we develop a related method called Fast Estimation of Effective Migration Surfaces (FEEMS). FEEMS uses a Gaussian Markov Random Field in a penalized likelihood framework that allows for efficient optimization and output of effective migration surfaces. Further, the efficient optimization facilitates the inference of migration parameters per edge in the graph, rather than per node (as in EEMS). When tested with coalescent simulations, FEEMS accurately recovers effective migration surfaces with complex gene-flow histories, including those with anisotropy. Applications of FEEMS to population genetic data from North American gray wolves shows it to perform comparably to EEMS, but with solutions obtained orders of magnitude faster. Overall, FEEMS expands the ability of users to quickly visualize and interpret spatial structure in their data.

FIRM COMPETITIVENESS OF MANUFACTURING INDUSTRY

The study of firm competitiveness allows to make an objective assessment of the economic results and the possibilities for increasing the level of competitiveness by highlighting the sources of competitive advantage of the respective company in the conditions of expanding competition in the domestic and international markets. This will allow for effective strategies to be developed and will reveal new opportunities for good long-term results. The aim of the paper is to apply a firm-level competitiveness approach and model for the Manufacturing sector identifying the main sources of competitive advantage that determine it. Biserial Correlation and Optimal Binning are used as a related method in this study for assessing firm competitiveness.

A landscape embroiled: experience of nature through experience of art

The article sets out with the theory of “aesthetics of reality” (created by Maria Gołaszewska) and its related method of transferring artistic structures onto non-artistic reality. The resulting construct, which is dubbed a para-artistic structure, becomes the theoretical basis for the aesthetic experience of nature. The so-called “formalization”—a procedure which consists in inserting nature into artistic frameworks—makes natural phenomena acquire a pretense of artwork. Nature as a picture becomes a landscape, while terms connected with the aesthetics of nature gain artistic qualities, enabling use of such notions as picturesque or kitsch. The methodological proposal by Gołaszewska is subsequently compared with the critical perspective of environmental aesthetics.

Madelung’s deformity: capitate-related versus ulna-related measurement methods

Several investigators have defined measurements for Madelung’s deformity based on the distal radius or on the longitudinal ulnar axis to avoid the distorted distal radius and its lunate fossa. However, errors may occur in severe cases because of ulnar deformity and displacement. We quantified seven established measurements for Madelung’s deformity relying on the central axis of the capitate. The inter- and intrarater reliability of the capitate-related and the ulna-related techniques were compared. We observed a higher inter- and intrarater reliability for the capitate-related method than for the ulna-related method. Better agreement was also observed for measurements of distance than for measurements of angles. However, the palmar tilt angle measurement method was neither reliable nor reproducible. The capitate-related technique can help to accurately determine the severity of Madelung’s deformity, assist in surgical planning and identify the prognosis. Level of evidence: III

New methodology and instrument for determination of the isothermal drying rate of cotton and polypropylene fabrics at constant air velocity

The most important parameters characterizing thermal comfort of garments are thermal resistance and water vapour permeability. Contrary to common garments, protective and sport garments (dresses) are often used in wet state (due to the absorbed sweat), which affects their comfort properties. That is why testing of both mentioned parameters in recent became important, along with the determination of the drying rate and drying time of sport dresses and underwear. However, current method of the drying rate mostly does not enable reliable measurement of this parameter, mostly due to non-isothermal conditions during the measurement and unknown velocity of the drying rate. In the article, a new method and instrument determination of the isothermal drying rate and drying time of sport dresses and underwear are presented, which is executed under at constant velocity of the parallel air flow. The reliability of the instrument and related method was verified by determination of the drying rate of selected woven fabrics.