Comparative analysis of five protein-protein interaction corpora

Conclusions: Our comparative analysis uncovers key similarities and differences between the diverse PPI corpora, thus taking an important step towards standardization. In the course of this study we have created a major practical contribution in converting the corpora into a shared format. The conversion software is freely available at http://mars.cs.utu.fi/PPICorpora.</p

Benchmarking Digital-Analog Quantum Computation

Digital-Analog Quantum Computation (DAQC) has recently been proposed as an alternative to the standard paradigm of digital quantum computation. DAQC creates entanglement through a continuous or analog evolution of the whole device, rather than by applying two-qubit gates. This manuscript describes an in-depth analysis of DAQC by extending its implementation to arbitrary connectivities and by performing the first systematic study of its scaling properties. We specify the analysis for three examples of quantum algorithms, showing that except for a few specific cases, DAQC is in fact disadvantageous with respect to the digital case.Comment: 16+5 pages, 11 figure

Family Partner: Study protocol for a pilot randomised study of a home-visitation intervention in Norway

Abstract Aim: Every year, about 5% of children in Norway experience severe child maltreatment and need support from the child welfare services. However, research-supported interventions for this group are lacking. The current study piloted an intensive home-visitation intervention, Family Partner, which aims to reduce child maltreatment among at-risk parents by improving parental skills, agency and trust in the welfare services, and children’s well-being. The randomised controlled trial piloted in this study examines the acceptability of the Family Partner intervention for staff and families and evaluates its feasibility for a full-scale randomised controlled trial. Methods: This protocol outlines a prospective, parallel, pilot randomised trial of the Family Partner intervention in three Norwegian municipal child welfare services. The participants are families with children under 12 years of age, where the parents are identified as having challenges. Families in the treatment group receive the Family Partner intervention, while families in the control group receive ordinary child welfare services. Data are collected at baseline, and at 3, 6, 12 and 18 months after recruitment. The pilot study monitor retention and adherence to inform the feasibility of a future full-scale randomised study. To assess the acceptability of the trial and intervention, a subsample of the participating families, as well as the family partners and representatives of the child welfare services in each municipality, are invited to complete qualitative interviews. Conclusions: The results will guide the design of a fully powered randomised controlled trial of the Family Partner intervention compared with ordinary child welfare services. Trial registration: ClinicalTrials.gov identifier: NCT04957394; Pilot Trial of Family Partner: a Child Maltreatment Prevention Intervention (FAMPART); registered on 12 July 2021

Co-Design quantum simulation of nanoscale NMR

Quantum computers have the potential to efficiently simulate the dynamics of nanoscale NMR systems. In this work, we demonstrate that a noisy intermediate-scale quantum computer can be used to simulate and predict nanoscale NMR resonances. In order to minimize the required gate fidelities, we propose a superconducting application-specific Co-Design quantum processor that reduces the number of SWAP gates by over 90% for chips with more than 20 qubits. The processor consists of transmon qubits capacitively coupled via tunable couplers to a central co-planar waveguide resonator with a quantum circuit refrigerator (QCR) for fast resonator reset. The QCR implements the nonunitary quantum operations required to simulate nuclear hyperpolarization scenarios.The authors would like to thank Caspar Ockeloen-Korppi, Alessandro Landra, and Johannes Heinsoo for their help in de- veloping the idea of the star-architecture chip, Jani Tuorila for his support in developing the gate theory, Amin Hosseinkhani and Tianhan Liu for reviewing the manuscript, and Hen- rikki Mäkynen and Hoang-Mai Nguyen for graphic design. J.C. additionally acknowledges the Ramón y Cajal program (RYC2018-025197-I). We further acknowledge support from Atos with the Quantum Learning Machine (QLM). Finally, the authors acknowledge financial support to BMBF through the Q-Exa Project No. FZK: 13N16062

The role of ocelli in cockroach optomotor performance

Insect ocelli are relatively simple eyes that have been assigned various functions not related to pictorial vision. In some species they function as sensors of ambient light intensity, from which information is relayed to various parts of the nervous system, e.g., for the control of circadian rhythms. In this work we have investigated the possibility that the ocellar light stimulation changes the properties of the optomotor performance of the cockroach Periplaneta americana. We used a virtual reality environment where a panoramic moving image is presented to the cockroach while its movements are recorded with a trackball. Previously we have shown that the optomotor reaction of the cockroach persists down to the intensity of moonless night sky, equivalent to less than 0.1 photons/s being absorbed by each compound eye photoreceptor. By occluding the compound eyes, the ocelli, or both, we show that the ocellar stimulation can change the intensity dependence of the optomotor reaction, indicating involvement of the ocellar visual system in the information processing of movement. We also measured the cuticular transmission, which, although relatively large, is unlikely to contribute profoundly to ocellar function, but may be significant in determining the mean activity level of completely blinded cockroaches

Entrepreneurs’ age, institutions, and social value creation goals: a multi-country study

This study explores the relationship between an entrepreneur's age and his/her social value creation goals. Building on the lifespan developmental psychology literature and institutional theory, we hypothesize a U-shaped relationship between entrepreneurs’ age and their choice to create social value through their ventures, such that younger and older entrepreneurs create more social value with their businesses while middle age entrepreneurs are relatively more economically and less socially oriented with their ventures. We further hypothesize that the quality of a country’s formal institutions in terms of economic, social, and political freedom steepen the U-shaped relationship between entrepreneurs’ age and their choice to pursue social value creation as supportive institutional environments allow entrepreneurs to follow their age-based preferences. We confirm our predictions using multilevel mixed-effects linear regressions on a sample of over 15,000 entrepreneurs (aged between 18 and 64 years) in 45 countries from Global Entrepreneurship Monitor data. The findings are robust to several alternative specifications. Based on our findings, we discuss implications for theory and practice, and we propose future research directions

Comparative analysis of five protein-protein interaction corpora

<p>Abstract</p> <p>Background</p> <p>Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate.</p> <p>Results</p> <p>We present the first comparative evaluation of the diverse PPI corpora, performing quantitative evaluation using two separate information extraction methods as well as detailed statistical and qualitative analyses of their properties. For the evaluation, we unify the corpus PPI annotations to a shared level of information, consisting of undirected, untyped binary interactions of non-static types with no identification of the words specifying the interaction, no negations, and no interaction certainty.</p> <p>We find that the F-score performance of a state-of-the-art PPI extraction method varies on average 19 percentage units and in some cases over 30 percentage units between the different evaluated corpora. The differences stemming from the choice of corpus can thus be substantially larger than differences between the performance of PPI extraction methods, which suggests definite limits on the ability to compare methods evaluated on different resources. We analyse a number of potential sources for these differences and identify factors explaining approximately half of the variance. We further suggest ways in which the difficulty of the PPI extraction tasks codified by different corpora can be determined to advance comparability. Our analysis also identifies points of agreement and disagreement in PPI corpus annotation that are rarely explicitly stated by the authors of the corpora.</p> <p>Conclusions</p> <p>Our comparative analysis uncovers key similarities and differences between the diverse PPI corpora, thus taking an important step towards standardization. In the course of this study we have created a major practical contribution in converting the corpora into a shared format. The conversion software is freely available at <url>http://mars.cs.utu.fi/PPICorpora</url>.</p

Towards a New Paradigm for Intuitive Theatrical Lighting Control

A simplified model of a lighting process applied in theatrical productions is one that involves two key players. The first is that of the lighting designer, to produce a set of intentions and plans for the scenes that define the show. The second, the lighting technician, has the job of translating these designs into practice using control equipment, luminaires, and other technical instruments. The lighting design often becomes a ‘working document’ subject to change and adaptation as the physical reality of the design becomes apparent, and the input of other stakeholders is considered. This process can be a valuable creative tool, and also a difficult technical hurdle to overcome, depending on a varied number of factors. A common frustration with this process is that either the complexity of the task, or difficulty in communication can make it difficult for the final creative vision to be effectively realised. Strains may also arise in the case of small, often touring, theatre companies where the lighting designer and technician may be the same person, and frequently one of the performers as well. Considering the design aspect, there can be challenges in ensuring efficacy of lighting plans between venues in touring productions, with 2D lighting sketches or even 3D computer simulations confined to the paper or screen. From a technical perspective, the role of the lighting technician in theatres and performance situations has included the operation of lighting control equipment during shows. The equipment has evolved over time but has, until recently, been grounded upon the basis of faders and the mixing desk. It is argued that this paradigm has failed to keep pace with the change in other interactive technologies. The on-going research described in this paper explores existing and upcoming technologies in the field, whilst also seeking to understand the roles and communication workflows of those involved in theatrical lighting to find the best areas to seek improvement, adopting principles of user-centred design. The intention of this research is to develop a new paradigm, and manifestation of it, using a control method for lighting or projection that allows a more intuitive form of operation in theatre productions, which will be scalable and flexible

How market structure drives commodity prices

We introduce an agent-based model, in which agents set their prices to maximize profit. At steady state the market self-organizes into three groups: excess producers, consumers and balanced agents, with prices determined by their own resource level and a couple of macroscopic parameters that emerge naturally from the analysis, akin to mean-field parameters in statistical mechanics. When resources are scarce prices rise sharply below a turning point that marks the disappearance of excess producers. To compare the model with real empirical data, we study the relationship between commodity prices and stock-to-use ratios in a range of commodities such as agricultural products and metals. By introducing an elasticity parameter to mitigate noise and long-term changes in commodities data, we confirm the trend of rising prices, provide evidence for turning points, and indicate yield points for less essential commodities