Handling conflicts of context-aware reminding system in sensorised home

In this paper, we propose a context-aware reminding system to assist dementia elders for their daily activities. We particularly focus on the issue of conflict detecting and handling in the real-world reminding applications. We adopt a planning approach to describe the constraints of reminders, and transform the constraints into temporal constraint graph for reminder conflict detecting. In real-time reminder scheduling, we define three disruptive activities, and present a context-aware reminding strategy to handle the conflicts between pre-planned and disruptive activities. Finally, the system prototype is introduced.     

Accentuating the positive while eliminating the negative of alien tree invasions: a multiple ecosystem services approach to prioritising control efforts

Invasive plants can have both positive and negative impacts on ecosystem services (ES), with decisions on control often being characterised by conflicts over loss of their perceived positive impacts on individual ES following removal. We present an analytical framework to aid in reducing such conflicts by allocating control effort to both minimise negative impacts and to maximise positive impacts on multiple ES. We used spatial models to map the negative impacts of invasive conifers on biodiversity, perceived landscape quality, and water yield and their positive impacts on erosion protection and carbon storage across a major catchment in the South Island of New Zealand. We tested the effect of distribution type (i.e. hotspot vs Gaussian) on trade-offs among these ES. We also tested whether using a non-linear function optimisation algorithm to fit variable weights to individual ES significantly reduced trade-offs. We show that an optimised multiple-ES approach could considerably reduce conflicts around invasive tree management arising from their contrasting impacts on different ecosystem services (i.e. by reducing trade-offs between ES), but cannot remove such conflict altogether. Our results are consistent with studies showing that ES with a hot-spot type distribution are the most vulnerable to trade-offs in multi-ES prioritisation, and hence will be the most likely to cause conflict in invasive tree control decisions. Our approach also shows that giving higher priority to ES with hot-spot distributions could reduce conflicts (by reducing tradeoffs). We argue that, when ES data are available, including estimates of ES impacts should be among the “due diligence” requirements for developing invasive tree control strategies.     

High-throughput protein structural analysis using site-directed fluorescence labeling and the bimane derivative (2-pyridyl)dithiobimane

We present a site-directed fluorescence labeling (SDFL) study of 25 different T4 lysozyme protein samples labeled with the thiol-cleavable fluorophore, (2-pyridyl)dithiobimane (PDT-Bimane). Our results demonstrate PDT-Bimane can be used in cysteine-scanning studies to detect protein secondary structure, and to map proximity between sites in proteins by monitoring tryptophan quenching of bimane fluorescence. In addition, the reducible nature of PDT-Bimane can be exploited to resolve problems often faced in SDFL studies: ensuring specific labeling of cysteine residues, determining the extent of free label contamination, and accurately determining labeling efficiency even at low concentrations. The ability to cleave PDT-Bimane off the protein enables rapid determination of these parameters, and positions it as an ideal fluorophore for automated, high-throughput structural studies of protein folding, the detection of protein-protein interactions, and the monitoring of real-time conformational changes.     

Parks-people conflicts: the case of Gonarezhou National Park and the Chitsa community in south-east Zimbabwe

National parks have been the centre piece of international conservation strategies in developing countries. The expansion in the network of national parks has enabled the conservation of biodiversity and habitats but the acquisition of vast areas into the park system has often been achieved through the displacement of resident local communities. Displaced people are exposed to a variety of impoverishment risks and this stokes up animosity towards parks. The research reported here seeks to understand the key issues involved in the occupation of a section of Gonarezhou National Park by Headman Chitsa’s people. The paper examines how the interplay between the history of displacement and dispossession, demographic pressures, limited economic opportunities, the ‘fast track’ land reform programme and dynastic politics are fomenting the land conflict between Gonarezhou and Chitsa community. Secondary actors with diverse interests have also come into the fold. Official efforts to resolve the conflict using a top-down approach have yielded little success. This culminated in a shift towards the use of traditional mechanisms of resolving a chieftaincy dispute as a step towards addressing the broader parks-people land conflict. Lessons from the case study are, inter alia, that interventions aimed at resolving parks-people conflicts should be alive to local culture, livelihood needs and power dynamics and, to the extent possible, eschew forcible relocations. Finally, we draw attention to the need to address the wider contradiction between policies promoting wildlife conservation and those promoting agriculture. The article is written to share lessons with readers interested in parks-people conflicts.     

Three-point appraisal of genetic linkage maps

This paper develops a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure. The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders. Simulation and two case studies were used to illustrate the method. In the first case study, the diagnostic revealed conflicts in map ordering for short inter-marker distances that were resolved at a distance of 8–12?cM, except for a set of markers at the end of the linkage group. In the second case study, the ordering did not resolve as distances increase, which could be attributed to regions of the map where many individuals were untyped.     

Do Conflict Resolution and Recovery Predict the Survival of Adolescents' Romantic Relationships?

Numerous studies have shown that being able to resolve and recover from conflicts is of key importance for relationship satisfaction and stability in adults. Less is known about the importance of these relationship dynamics in adolescent romantic relationships. Therefore, this study investigated whether conflict resolution and recovery predict breakups in middle adolescent couples. Couples who are able to resolve and recover from conflict were expected to demonstrate a lower probability of breaking up. In total, 80 adolescent couples (M age = 15.48, SD = 1.16) participated in a 4-wave prospective questionnaire and observational study, with one year between measurements. In addition to self-report measures, adolescents were observed in real-time during conflicts with their partners. Multilevel Proportional Hazard analyses revealed that, contrary to the hypothesis, conflict resolution and conflict recovery did not predict the likelihood of breakup. Survival differences were not attributable to conflict resolution or conflict recovery. More research is needed to consider the unique relationship factors of adolescent romantic relationships to determine why some relationships survive while others do not.     

Postconflict behavior in captive western lowland gorillas (Gorilla gorilla gorilla)

Postconflict (PC) behaviors, including reconciliation and consolation, have been observed in many primate and several nonprimate species. Using the PC-matched control (MC) method, PC behavior was examined in two groups (n=13) of captive western lowland gorillas, a species for which no conflict resolution data have been published. Analyses of 223 conflicts showed significantly more affiliation between former opponents after a conflict when compared to control periods, indicating reconciliation. Results also showed significantly more affiliation between the victim and a third-party after a conflict, indicating consolation. Both solicited and unsolicited consolation were observed. The majority of the affiliative interactions observed for both reconciliation and consolation were social proximity, which suggests that unlike most nonhuman primates, proximity, rather than physical contact, may be the main mechanism for resolving conflicts in western lowland gorillas. PC behavior was not uniform throughout the groups, but rather varied according to dyad type.     

A hierarchical approach to aligning collinear regions of genomes

MOTIVATION: As a first approximation, similarity between two long orthologous regions of genomes can be represented by a chain of local similarities. Within such a chain, pairs of successive similarities are collinear (non-conflicting), i.e. segments involved in the nth similarity precede in both sequences segments involved in the (n+1)th similarity. However, when all similarities between two long sequences are considered, usually there are many conflicts between them. Although some conflicts can be avoided by masking transposons or low-complexity sequences, selecting only those similarities that reflect orthology and, thus, belong to the evolutionarily true chain is not trivial. RESULTS: We propose a simple, hierarchical algorithm of finding the true chain of local similarities. Starting from similarities with low P-values, we resolve each pairwise conflict by deleting a similarity with a higher P-value. This greedy approach constructs a chain of similarities faster than when a chain optimal with respect to some global criterion is sought, and makes more sense biologically.     

A Factor Graph Approach to Automated GO Annotation

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.     

Can Economic Incentives Resolve Conservation Conflict: The Case of Wild Deer Management and Habitat Conservation in the Scottish Highlands

Market-based economic incentives are increasingly perceived as a cost-effective approach to biodiversity conservation but empirical evidence to substantiate this claim is lacking. Using both qualitative and quantitative data analysis this paper investigates the potential role of market incentives to increase venison production as a mechanism to resolve conflicts over wild red deer management in the Scottish Highlands. Our analysis suggests the approach is unlikely to be effective because investments in venison production would bring conflict with more important non-pecuniary objectives of landownership such as ‘sporting quality’ and ‘exclusivity’. At a broader level we urge caution when considering the deployment of economic instruments to resolve contemporary conservation conflicts where profit maximisation is not the dominant objective and/or where the target group is extremely wealthy.     

Assessment of transparency indicators across the biomedical literature: How open is open?

Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.

This study uses novel open source automated tools to monitor transparency across all 2.75 million open access articles on PubMed Central, discovering that different disciplines, journals and publishers abide by principles of transparency to varying degrees over time.     

A New Cyclic Scheduling Algorithm for Flexible Manufacturing Systems

Flexible manufacturing system control is an NP-hard problem. A cyclic approach has been demonstrated to be adequate for an infinite scheduling problem because of maximal throughput reachability. However, it is not the only optimization criterion in general. In this article we consider the minimization of the work in process (WIP) as an economical and productivity factor. We propose a new cyclic scheduling algorithm giving the maximal throughput (a hard constraint) while minimizing WIP. This algorithm is based on progressive operations placing. A controlled beam search approach has been developed to determine at each step the schedule of the next operations. After presenting the main principles of the algorithm, we compare our approach to several most known cyclic scheduling algorithms using a significant existing example from the literature.     

Structured motifs search.

In this paper, we describe an algorithm for the localization of structured models, i.e. sequences of (simple) motifs and distance constraints. It basically combines standard pattern matching procedures with a constraint satisfaction solver, and it has the ability, not present in similar tools, to search for partial matches. A significant feature of our approach, especially in terms of efficiency for the application context, is that the (potentially) exponentially many solutions to the considered problem are represented in compact form as a graph. Moreover, the time and space necessary to build the graph are linear in the number of occurrences of the component patterns.     

PCG-Cut: Graph Driven Segmentation of the Prostate Central Gland

Prostate cancer is the most abundant cancer in men, with over 200,000 expected new cases and around 28,000 deaths in 2012 in the US alone. In this study, the segmentation results for the prostate central gland (PCG) in MR scans are presented. The aim of this research study is to apply a graph-based algorithm to automated segmentation (i.e. delineation) of organ limits for the prostate central gland. The ultimate goal is to apply automated segmentation approach to facilitate efficient MR-guided biopsy and radiation treatment planning. The automated segmentation algorithm used is graph-driven based on a spherical template. Therefore, rays are sent through the surface points of a polyhedron to sample the graph’s nodes. After graph construction – which only requires the center of the polyhedron defined by the user and located inside the prostate center gland – the minimal cost closed set on the graph is computed via a polynomial time s-t-cut, which results in the segmentation of the prostate center gland’s boundaries and volume. The algorithm has been realized as a C++ module within the medical research platform MeVisLab and the ground truth of the central gland boundaries were manually extracted by clinical experts (interventional radiologists) with several years of experience in prostate treatment. For evaluation the automated segmentations of the proposed scheme have been compared with the manual segmentations, yielding an average Dice Similarity Coefficient (DSC) of 78.94±10.85%.     

Crossing the taxonomic divide: conflict and its resolution in societies of reproductively totipotent individuals

Reproduction in groups may be unequal, with one or a few individuals monopolizing direct reproduction assisted by nonbreeding helpers. In social insects this has frequently led to a pronounced queen-worker dichotomy and a loss of reproductive totipotency among workers. However, in some invertebrate and all vertebrate societies, all or most individuals remain reproductively totipotent. In these groups, conflicts of interest over reproduction are potentially greatest. Here, we synthesize previous analyses of reproductive conflict, aggression and breeder replacement in haplodiploid societies of totipotent individuals and extend them to cover diploid (vertebrate) examples. We test predictions arising from this approach using the best-studied invertebrate (Dinoponera queenless ants) and vertebrate (naked mole-rat, Heterocephalus glaber) examples, although in principle our analysis applies to all similar groups. We find that premature replacement of a parent breeder by nonbreeders (overthrow) is rare. Dominant coercive control of nonbreeders by the breeder is often unnecessary and honest signalling of breeder vitality can maintain group stability and resolve conflicts over reproduction. We hope that by providing an explicit transfer of social theory between ants and naked mole-rats we will stimulate further cross-taxonomic studies that will greatly broaden our understanding of sociality.     

The train fueling cost minimization problem with fuzzy fuel prices

The train fueling cost minimization problem is to find a scheduling and fueling strategy such that the fueling cost is minimized and no train runs out of fuel. Since fuel prices vary by location and time from month to month, we estimate them by fuzzy variables in this paper. Furthermore, we propose a fuzzy fueling cost minimization model by minimizing the expected fueling cost under the traversing time constraint, maximal allowable speed constraint, tank capacity constraint, and so on. In order to solve the model, we decompose it into a nonlinear scheduling strategy model and a linear fueling strategy model. Based on the Karush–Kuhn–Tucker conditions, we design an iterative algorithm to solve the scheduling strategy model, and furthermore design a numerical algorithm to solve the fuzzy fueling cost minimization model. Finally, some numerical examples are presented for showing the efficiency of the proposed approach on saving fueling cost.     

Metabolic networks are NP-hard to reconstruct

High-throughput data from various omics and sequencing techniques have rendered the automated metabolic network reconstruction a highly relevant problem. Our approach reflects the inherent probabilistic nature of the steps involved in metabolic network reconstruction. Here, the goal is to arrive at networks which combine probabilistic information with the possibility to obtain a small number of disconnected network constituents by reduction of a given preliminary probabilistic metabolic network. We define automated metabolic network reconstruction as an optimization problem on four-partite graph (nodes representing genes, enzymes, reactions, and metabolites) which integrates: (1) probabilistic information obtained from the existing process for metabolic reconstruction from a given genome, (2) connectedness of the raw metabolic network, and (3) clustering of components in the reconstructed metabolic network. The practical implications of our theoretical analysis refer to the quality of reconstructed metabolic networks and shed light on the problem of finding more efficient and effective methods for automated reconstruction. Our main contributions include: a completeness result for the defined problem, polynomial-time approximation algorithm, and an optimal polynomial-time algorithm for trees. Moreover, we exemplify our approach by the reconstruction of the sucrose biosynthesis pathway in Chlamydomonas reinhardtii.     

Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies

We present an RNA-As-Graphs (RAG) based inverse folding algorithm, RAG-IF, to design novel RNA sequences that fold onto target tree graph topologies. The algorithm can be used to enhance our recently reported computational design pipeline (Jain et al., NAR 2018). The RAG approach represents RNA secondary structures as tree and dual graphs, where RNA loops and helices are coarse-grained as vertices and edges, opening the usage of graph theory methods to study, predict, and design RNA structures. Our recently developed computational pipeline for design utilizes graph partitioning (RAG-3D) and atomic fragment assembly (F-RAG) to design sequences to fold onto RNA-like tree graph topologies; the atomic fragments are taken from existing RNA structures that correspond to tree subgraphs. Because F-RAG may not produce the target folds for all designs, automated mutations by RAG-IF algorithm enhance the candidate pool markedly. The crucial residues for mutation are identified by differences between the predicted and the target topology. A genetic algorithm then mutates the selected residues, and the successful sequences are optimized to retain only the minimal or essential mutations. Here we evaluate RAG-IF for 6 RNA-like topologies and generate a large pool of successful candidate sequences with a variety of minimal mutations. We find that RAG-IF adds robustness and efficiency to our RNA design pipeline, making inverse folding motivated by graph topology rather than secondary structure more productive.     

Conflict and post-conflict behavior in a small group of chimpanzees

Chimpanzee research plays a central role in the discussions of conflict negotiation. Reconciliation, or the attraction and affiliation of former opponents following conflict, has been proposed as a central element of conflict negotiation in chimpanzees and various other taxa. In an attempt to expand the database of chimpanzee conflict resolution, conflict and post-conflict behavior were recorded for a small group of socially housed chimpanzees at the Chimpanzee and Human Communication Institute, at Central Washington University. Data were collected over six 6-week periods between 1997 and 2000, for a total of 840 hours of observation, resulting in a substantial post-conflict (PC) and matched control (MC) data set. The data demonstrate this group’s tendencies to maintain visual contact and closer proximity after conflicts. Dyadic corrected conciliatory tendencies ranged between 0 – 37.5% and averaged 17.25% across all dyads. Individual corrected conciliatory tendencies ranged between 5.8 and 32%. The results of this study combined with recent publications on captive and free-ranging chimpanzee post-conflict behavior suggest that variation in post-conflict behavior may be important to our understanding of chimpanzee conflict negotiation, and may also have implications for the design and management of captive chimpanzee enclosures and social groups, respectively.