Development of a genetic and molecular toolkit for the oleaginous red yeast Rhodotorula toruloides

Rhodotorula toruloides is an oleaginous yeast with potential use as a biotechnological chassis for both production of industrially and pharmaceutically relevant compounds, and as a drop-in biofuel producer on low-cost substrate. Cells can accumulate lipid droplets to over 70 % weight/weight under certain growth conditions. We here summarise the currently-available genetic and molecular toolkit for the yeast and suggest further avenues for research to enable full utilisation of this yeast. To aid in these objectives, we have constructed lipid droplet-associated GFP-tagged protein Ldp1-GFP and demonstrated how this can be used to quantify individual cell lipid quantity using confocal microscopy. Calnexin-GFP and GFP-Atg8 have also been constructed for live-cell monitoring of the intracellular machinery in lipid droplet synthesis as part of the developing R. toruloides molecular toolkit. Furthermore, the induction profiles of selected heat shock protein promoters have been characterised through a GFP-reporter system. Currently, the only reported inducible promoters in R. toruloides are nutrient-dependent NAR1, ICL1, MET16, CTR3, DAO1, THI4, THI5 and CTR31, and tightly controlling these is not possible in potential use as a biofuel producer using low-cost substrate. Of the promoters highlighted herein (ENO2, TDH3, PGK1, TPI1, SSB1, ACT1 and TDH3), ENO2 is identified as a qualitatively putative heat-shock inducible promoter, further analysis of which may allow the nutrient-dependency limitation to be overcome through exploitation of the native environmental stress response

Application of Musical Computing to Creating a Dynamic Reconfigurable Multilayered Chamber Orchestra Composition

With increasing virtualization and the recognition that today’s virtual computers are faster than hardware computers of 10 years ago, modes of computation are now limited only by the imagination. Pulsed Melodic Affective Processing (PMAP) is an unconventional computation protocol that makes affective computation more human-friendly by making it audible. Data sounds like the emotion it carries. PMAP has been demonstrated in nonmusical applications, e.g. quantum computer entanglement and stock market trading. This article presents a musical application and demonstration of PMAP: a dynamic reconfigurable score for acoustic orchestral performance, in which the orchestra acts as a PMAP half-adder to add two numbers. </jats:p

Application of Intermediate Multi-Agent Systems to Integrated Algorithmic Composition and Expressive Performance of Music

We investigate the properties of a new Multi-Agent Systems (MAS) for computer-aided composition called IPCS (pronounced “ipp-siss”) the Intermediate Performance Composition System which generates expressive performance as part of its compositional process, and produces emergent melodic structures by a novel multi-agent process. IPCS consists of a small-medium size (2 to 16) collection of agents in which each agent can perform monophonic tunes and learn monophonic tunes from other agents. Each agent has an affective state (an “artificial emotional state”) which affects how it performs the music to other agents; e.g. a “happy” agent will perform “happier” music. The agent performance not only involves compositional changes to the music, but also adds smaller changes based on expressive music performance algorithms for humanization. Every agent is initialized with a tune containing the same single note, and over the interaction period longer tunes are built through agent interaction. Agents will only learn tunes performed to them by other agents if the affective content of the tune is similar to their current affective state; learned tunes are concatenated to the end of their current tune. Each agent in the society learns its own growing tune during the interaction process. Agents develop “opinions” of other agents that perform to them, depending on how much the performing agent can help their tunes grow. These opinions affect who they interact with in the future. IPCS is not a mapping from multi-agent interaction onto musical features, but actually utilizes music for the agents to communicate emotions. In spite of the lack of explicit melodic intelligence in IPCS, the system is shown to generate non-trivial melody pitch sequences as a result of emotional communication between agents. The melodies also have a hierarchical structure based on the emergent social structure of the multi-agent system and the hierarchical structure is a result of the emerging agent social interaction structure. The interactive humanizations produce micro-timing and loudness deviations in the melody which are shown to express its hierarchical generative structure without the need for structural analysis software frequently used in computer music humanization

The role of TREM2 protein in skin fibroblast and keratinocyte proliferation and migration

Skin is the first physical barrier of the body as it protects the body from external environment and lets the organism to sense pain, touch and temperature. Therefore, it is important to restore the skin as quicky as possible after damage. This research project aimed to investigate whether the protein Triggering receptor expressed on myeloid cells-2 (TREM2) contributes to skin fibroblast and keratinocyte proliferation and migration that could potentially promote wound healing. The expression of TREM2 in human skin was characterized and the effect of soluble recombinant TREM2 protein in cell proliferation and migration were investigated. It was found that TREM2 is expressed in the dermis and in extracellular matrix of dermis of healthy human skin, but it probably inhibits cell proliferation and has no overall effect on the migration of the cells

Data mining for heart failure : an investigation into the challenges in real life clinical datasets

Clinical data presents a number of challenges including missing data, class imbalance, high dimensionality and non-normal distribution. A motivation for this research is to investigate and analyse the manner in which the challenges affect the performance of algorithms. The challenges were explored with the help of a real life heart failure clinical dataset known as Hull LifeLab, obtained from a live cardiology clinic at the Hull Royal Infirmary Hospital. A Clinical Data Mining Workflow (CDMW) was designed with three intuitive stages, namely, descriptive, predictive and prescriptive. The naming of these stages reflects the nature of the analysis that is possible within each stage; therefore a number of different algorithms are employed. Most algorithms require the data to be distributed in a normal manner. However, the distribution is not explicitly used within the algorithms. Approaches based on Bayes use the properties of the distributions very explicitly, and thus provides valuable insight into the nature of the data.The first stage of the analysis is to investigate if the assumptions made for Bayes hold, e.g. the strong independence assumption and the assumption of a Gaussian distribution. The next stage is to investigate the role of missing values. Results found that imputation does not affect the performance as much as those records which are initially complete. These records are often not outliers, but contain problem variables. A method was developed to identify these. The effect of skews in the data was also investigated within the CDMW. However, it was found that methods based on Bayes were able to handle these, albeit with a small variability in performance. The thesis provides an insight into the reasons why clinical data often causes problems. Even the issue of imbalanced classes is not an issue, for Bayes is independent of this

Програмирање квантних рачунара базираних на употреби логичких кола за потребе рада са музиком

There have been significant attempts previously to use the equations of quantum mechanics for generating sound, and to sonify simulated quantum processes. For new forms of computation to be utilized in computer music, eventually hardware must be utilized. This has rarely happened with quantum computer music. One reason for this is that it is currently not easy to get access to such hardware. A second is that the hardware available requires some understanding of quantum computing theory. Tis paper moves forward the process by utilizing two hardware quantum computation systems: IBMQASM v1.1 and a D-Wave 2X. It also introduces the ideas behind the gate-based IBM system, in a way hopefully more accessible to computerliterate readers. Tis is a presentation of the frst hybrid quantum computer algorithm, involving two hardware machines. Although neither of these algorithms explicitly utilize the promised quantum speed-ups, they are a vitalfrst step in introducing QC to the musical feld. Te article also introduces some key quantum computer algorithms and discusses their possible future contribution to computer music.Досад су забележени значајни покушаји да се једначине квантне механике користе за генерисање звука и да се озвуче симулирани квантни процеси. Али, за нове облике рачунања који би се користили у компјутерској музици, мора се употребити одговарајући хардвер. Ово се досад ретко дешавало са квантном компјутерском музиком, најпре зато што такав хардвер није широко доступан. Други разлог јесте околност да овакав хардвер захтева извесно познавање теорије квантног рачунарства. Овим чланком померамо овај процес унапред помоћу два хардверска квантна рачунарска система: IBMQASM v1.1 и D-Wave 2X. Такође уводимо неке идеје из IBM-овог система заснованог на логичким колима, на начин доступан рачунарски писменим читаоцима. Ово је презентација првог хибридног квантног компјутерског алгоритма, који укључује две хардверске машине. Иако ниједан од ових алгоритама експлицитно не користи обећана квантна убрзања, они представљају виталан први корак у увођењу квантног рачунарства у поље музике. Чланак започињемо кратким прегледом квантног рачунарства и указујемо како се оно може применити на подручју уметности. Следи истраживање претходних пројеката у којима су коришћени стварни или симулирани квантни процеси у музичким делима или извођењима. У следећем одељку се говори о најпознатијој врсти квантних рачунара, заснованих на логичким колима, и описује се хардвер једног од мањих квантних рачунара компаније IBM. Следи кратак увод у теорију квантног рачунарства; ове идеје су потом пројектоване на језик који користе IBM рачунари: IBMQASM. Следећи одељак доноси кратак преглед друге врсте квантног рачунара који се користи: D-Wave. Детаљнији описи мог алгоритма доступни су у другим чланцима на које се позивам. На крају је описан qGen: IBM генерише мелодију, а D-Wave је хармонизује. Фокус је на мелодијском алгоритму, пошто је алгоритам D-Wave описан у поглављу из књиге на коју реферирам. Развијен је “најједноставнији могући“ мелодијски алгоритам, уз који је приложен и одговарајући пример