Design strategies for optimizing holographic optical tweezers setups

We provide a detailed account of the construction of a system of holographic optical tweezers. While much information is available on the design, alignment and calibration of other optical trapping configurations, those based on holography are relatively poorly described. Inclusion of a spatial light modulator in the setup gives rise to particular design trade-offs and constraints, and the system benefits from specific optimization strategies, which we discuss.Comment: 16 pages, 15 figure

The Emerging Chondrocyte Channelome

Chondrocytes are the resident cells of articular cartilage and are responsible for synthesizing a range of collagenous and non-collagenous extracellular matrix macromolecules. Whilst chondrocytes exist at low densities in the tissue (1–10% of the total tissue volume in mature cartilage) they are extremely active cells and are capable of responding to a range of mechanical and biochemical stimuli. These responses are necessary for the maintenance of viable cartilage and may be compromised in inflammatory diseases such as arthritis. Although chondrocytes are non-excitable cells their plasma membrane contains a rich complement of ion channels. This diverse channelome appears to be as complex as one might expect to find in excitable cells although, in the case of chondrocytes, their functions are far less well understood. The ion channels so far identified in chondrocytes include potassium channels (KATP, BK, Kv, and SK), sodium channels (epithelial sodium channels, voltage activated sodium channels), transient receptor potential calcium or non-selective cation channels and chloride channels. In this review we describe this emerging channelome and discuss the possible functions of a range of chondrocyte ion channels

ProkSeq for complete analysis of RNA-Seq data from prokaryotes

Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results

Using Stop Motion Animation to Sketch in Architecture: A practical approach

Widely acknowledged as an archetypal design activity, sketching is typically carried out using little more than pen and paper. Today’s designed artifacts however, are often given qualities that are hard to capture with traditional means of sketching. While pen and paper sketching catches the character of a building, it may not equally well capture how that building changes with the seasons, how people pass through it, how the light moves in between its rooms from sunrise to dawn, and how its façade subtly decays over centuries. Yet, it is often exactly these dynamic and interactive aspects that are emphasised in contemporary design work. So is there a way for designers to be able to sketch also these dynamic processes? Over several years and in different design disciplines, we have been exploring the potential of stop motion animation (SMA) to serve this purpose. SMA is a basic form of animation typically applied to make physical objects appear to be alive. The animator moves objects in small increments between individually photographed frames. When the photographs are combined and played back in continuous sequence, the illusion of movement is created. Although SMA has a long history in filmmaking, the animation technique has received scarce attention in most design fields including product design, architecture, and interaction design. This paper brings SMA into the area of sketching in architecture by reporting on the planning, conduct, result, and evaluation of a workshop course carried out with a group of 50 students at Umeå School of Architecture, Umeå University, Sweden

In pursuit of rigour and accountability in participatory design

The field of Participatory Design (PD) has greatly diversified and we see a broad spectrum of approaches and methodologies emerging. However, to foster its role in designing future interactive technologies, a discussion about accountability and rigour across this spectrum is needed. Rejecting the traditional, positivistic framework, we take inspiration from related fields such as Design Research and Action Research to develop interpretations of these concepts that are rooted in PD׳s own belief system. We argue that unlike in other fields, accountability and rigour are nuanced concepts that are delivered through debate, critique and reflection. A key prerequisite for having such debates is the availability of a language that allows designers, researchers and practitioners to construct solid arguments about the appropriateness of their stances, choices and judgements. To this end, we propose a “tool-to-think-with” that provides such a language by guiding designers, researchers and practitioners through a process of systematic reflection and critical analysis. The tool proposes four lenses to critically reflect on the nature of a PD effort: epistemology, values, stakeholders and outcomes. In a subsequent step, the coherence between the revealed features is analysed and shows whether they pull the project in the same direction or work against each other. Regardless of the flavour of PD, we argue that this coherence of features indicates the level of internal rigour of PD work and that the process of reflection and analysis provides the language to argue for it. We envision our tool to be useful at all stages of PD work: in the planning phase, as part of a reflective practice during the work, and as a means to construct knowledge and advance the field after the fact. We ground our theoretical discussions in a specific PD experience, the ECHOES project, to motivate the tool and to illustrate its workings

Remote effects of acute kidney injury in a porcine model

Background: Acute Kidney Injury (AKI) is a common and serious disease with no specific treatment. An episode of AKI may affect organs distant to the kidney, further increasing the morbidity associated with AKI. The mechanism of organ cross-talk after AKI is unclear. The renal and immune systems of pigs and humans are alike. Using a preclinical animal (porcine) model, we test the hypothesis that early effects of AKI on distant organs is by immune cell infiltration leading to inflammatory cytokine production, extravasation and edema. Study Design: In 29 pigs exposed to either sham-surgery or renal ischemia-reperfusion (control, n=12; AKI, n=17) we assessed remote organ (liver, lung, brain) effects in the short-(from 2 to 48h reperfusion) and longer-term (5 weeks later) using immunofluorescence (for leucocyte infiltration, apoptosis), a cytokine array, tissue elemental analysis (electrolytes), blood hematology and chemistry (e.g. liver enzymes) and PCR (for inflammatory markers). Results: AKI elicited significant, short-term (~24h) increments in enzymes indicative of acute liver damage (e.g. AST:ALT ratio; P=0.02) and influenced tissue biochemistry in some remote organs (e.g. lung tissue [Ca++] increased; P=0.04). These effects largely resolved after 48h and no further histopathology, edema, apoptosis or immune cell infiltration was noted in liver, lung or hippocampus in the short- and longer-term. Conclusions: AKI has subtle biochemical effects on remote organs in the short-term including a transient increment in markers of acute liver damage. These effects resolved by 48h and no further remote organ histopathology, apoptosis, edema or immune cell infiltration was noted

Understanding Engagement with the Privacy Domain Through Design Research.

This paper reports findings from participatory design research aimed at uncovering how technological interventions can engage users in the domain of privacy. Our work was undertaken in the context of a new design concept “Privacy Trends” whose aspiration is to foster technology users’ digital literacy regarding ongoing privacy risks and elucidate how such risks fit within existing social, organizational and political systems, leading to a longer term privacy concern. Our study reveals two challenges for privacy intervention design: the need to develop technology users’ intrinsic motivations with the privacy domain and the importance of framing the concept of privacy within users’ interests. Setting our study within a design context enables us to identify four design opportunities for fostering engagement with the privacy domain through technology design