Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding Spark System Performance for Image Processing in a Heterogeneous Commodity Cluster

In recent years, Apache Spark has seen a widespread adoption in industries and institutions due to its cache mechanism for faster Big Data analytics. However, the speed advantage Spark provides, especially in a heterogeneous cluster environment, is not obtainable out-of-the-box; it requires the right combination of configuration parameters from the myriads of parameters provided by Spark developers. Recognizing this challenge, this thesis undertakes a study to provide insight on Spark performance particularly, regarding the impact of choice parameter settings. These are parameters that are critical to fast job completion and effective utilization of resources. To this end, the study focuses on two specific example applications namely, flowerCounter and imageClustering, for processing still image datasets of Canola plants collected during the Summer of 2016 from selected plot fields using timelapse cameras in a heterogeneous Spark-clustered environments. These applications were of initial interest to the Plant Phenotyping and Imaging Research Centre (PIRC) at the University of Saskatchewan. The PIRC is responsible for developing systems that will aid fast analysis of large-scale seed breeding to ensure global food security. The flowerCounter application estimates the count of flowers from the images while the imageClustering application clusters images based on physical plant attributes. Two clusters are used for the experiments: a 12-node and 3-node cluster (including a master node), with Hadoop Distributed File System (HDFS) as the storage medium for the image datasets. Experiments with the two case study applications demonstrate that increasing the number of tasks does not always speed-up job processing due to increased communication overheads. Findings from other experiments show that numerous tasks with one core per executor and small allocated memory limits parallelism within an executor and result in inefficient use of cluster resources. Executors with large CPU and memory, on the other hand, do not speed-up analytics due to processing delays and threads concurrency. Further experimental results indicate that application processing time depends on input data storage in conjunction with locality levels and executor run time is largely dominated by the disk I/O time especially, the read time cost. With respect to horizontal node scaling, Spark scales with increasing homogeneous computing nodes but the speed-up degrades with heterogeneous nodes. Finally, this study shows that the effectiveness of speculative tasks execution in mitigating the impact of slow nodes varies for the applications.
The Use of the Nematode Caenorhabditis elegans to Evaluate the Adverse Effects of Epoxiconazole Exposure on Spermatogenesis

There is increasing evidence that epoxiconazole exposure can affect reproductive function, but few studies have investigated adverse effects on spermatogenesis. The nematode Caenorhabditis elegans (C. elegans) was used in our study to assess effects of epoxiconazole on spermatogenesis in male nematodes after 48 h of exposure to concentrations of 0.1, 1.0, or 10.0 μg/L. The results demonstrated that epoxiconazole exposure affected spermatogenesis, decreasing the number of total germ cells, mitotic cells, meiotic cells and spermatids, spermatid diameter, and cross-sectional area, and inducing mitotic germ cell proliferation arrest, premature entry into meiosis, and sperm activation inhibition; however, sperm transfer showed no abnormal changes. In addition, the results showed that epoxiconazole activated the transforming growth factor-β (TGFβ) signaling pathway and increased the expression levels of gene daf-1, daf-3, daf-4, daf-5 and daf-7 in nematodes. We therefore propose that epoxiconazole acts by activating the TGFβ signaling pathway, leading to the impairment of spermatogenesis and the consequent decline in male fertility.
Capacity allocation in multilevel virtual networks under uncertainty

This paper concerns the capacity allocation problem in multilevel virtual networks. The utility and cost functions are used to determine network performance in the economic terms. The considered problem is formulated as an optimization issue. This allocation problem (referred to as master problem) is decomposed into series of constrained concave maximization subproblems. The hierarchical procedure, which enables finding the optimal solution of master problem, is presented. Proposed method consists in solving all subproblems and exchanging information concerning obtained results. The analytical solution for a special case is given. Moreover, the uncertainties appearing during virtualization process are also taken into consideration. It is stressed that not whole of the virtual links' capacity is available for further virtualization. In the paper, it is assumed that such an uncertainty may be modeled with uncertain variables (a special case of fuzzy variables) formalism. Two approaches (for determinization knowledge about decision-making and for determinization knowledge about plant) are considered. Simple numerical experiment completes the paper.
Graph Partitioning Problem Applied to Adaptive Mobile Wireless Networks ∗

In a large-scale adaptive mobile wireless network, long-distance message transfer can be routed by introduced mobile servers while nearby mobile units can contact each other through direct constructed communication channels. In order to achieve scalability by direct connection among mobile units and reliability sustained by mobile servers for QoS, a mixed wireless infrastructure incorporating mobile servers and ad hoc communications is investigated. A cluster of mobile units can be modelled as a mobile node. Both mobile nodes and servers are free of movement under the adaptive mobile wireless networks. In this paper, two graph models are introduced to represent mobile node communication requirements as well as mobile server configurations. The dynamically changed topology for mobile nodes and mobile servers together with other constraints (e.g., transmission range, bandwidth) make the assignment of mobile nodes to mobile servers difficult. Such assignment can be formalized as the partition problem, which is proved to be NP-complete to attain optimal solutions. Based on the generated two modelling graphs, polynomial-time algorithms are developed to the partitioning problem such that the communication among different mobile nodes are successfully switched by mobile servers. The experimental environment simulates the dynamically modified network topology of a wireless network consisting of roaming mobile nodes. The simulation results show that the proposed techniques yield good assignments with similar performance as those produced by exhaustive approaches.
Name Matching in Law Enforcement and Counter-Terrorism

Name matching is an important task in law enforcement and counter-terrorism. This paper briefly describes the nature of the name-matching task, enumerates typical name-matching applications, explains the technical challenges posed by namematching, and sets forth several important approaches to these technical challenges. 1. THE NAME-MATCHING TASK Name matching is the task of recognizing when two different strings denote the same person or other named entity. Name matching is an instance of the general task of approximate string matching, a task that also arises in spell correcting [Pet80], database maintenance [NKAJ59], signal processing, text retrieval, data mining, image compression, and many other areas [Nav01]. Approximate string matching is particularly important in computational biology. For example, base-sequence similarity in genomes is an accurate measure of phylogenetic distance [SM97, Gus99]. The general task of name matching is as follows:
A method-based ahead-of-time compiler for Android applications

The execution environment of Android system is based on a virtual machine called Dalvik virtual machine (DVM) in which the execution of an application program is in interpret-mode. To reduce the interpretation overhead of DVM, Google has included a trace-based just-in-time compiler (JITC) in the latest version of Android. Due to limited resources and the requirement for reasonable response time, the JITC is unable to apply deep optimizations to generate high quality code. In this paper, we propose a method-based ahead-of-time compiler (AOTC), called Icing, to speed up the execution of Android applications without the modification of any components of Android framework. The main idea of Icing is to convert the hot methods of an application program from DEX code to C code and uses the GCC compiler to translate the C code to the corresponding native code. With the Java Native Interface (JNI) library, the translated native code can be called by DVM. Both AOTC and JITC have their strength and weakness. In order to combine the strength and avoid the weakness of AOTC and JITC, in Icing, we have proposed a cost model to determine whether a method should be handled by AOTC or JITC during profiling. To evaluate the performance of Icing, four benchmarks used by Google JITC are used as test cases. The performance results show that, with Icing, the execution time of an application is two to three times faster than that without JITC, and 25% to 110% faster than that with JITC.
Exploring and exploiting knowledge in multiple resources

With the huge growth of the Internet and the WWW, several scientific fields have witnessed a proliferation of information available online. Techniques that are able to extract relations and associations that may exist in various resources including structured (ontologies and taxonomies) and unstructured (corpora) to inform search and can offer enhanced recommendations are highly desirable. The aim of this work is to pull together multiple bioinformatics resources with different structures such as ontologies and corpora and develop reasoning methods to extract semantic relations and hidden associations, which do not exist in the original resources. We have designed methods which reason through these resources and contain semantic rules (for instance, identifying sibling relations) that allow us to infer more hidden information between resources and aim to enhance recommendations in situations as described above. Moreover, we have designed a recommender approach for the bioinformatics field that provides recommendations on content (i.e. articles) as a personalised service for users based on information extracted from multiple resources as well as their individual profiles.
An Association Rule Algorithm Based on Quotient Space

Finding the large item set fast is the crucial step in the association rule algorithm. In this paper we apply granular computing and quotient space to frequent item set discovering , by partition the information system to information granule and mapping granule object sets, the algorithm reduced the number of database scanning and reduced object sets required when computing support of candidate item, in this way we improved the efficient of running. For the dataset of small support with high complexity, it is more applicable. The experiment results show: the proposed method is effective.
Discrimination of Linguistic and Non-Linguistic Vocalizations in Spontaneous Speech: Intra- and Inter-Corpus Perspectives

We present a large-scale study on classiﬁcation of linguistic and non-linguistic vocalizations including laughter, vocal noise, hesitation and consent on four corpora amounting to 46h of spontaneous conversational speech. We consider training and testing on speaker-independent subsets of single corpora (intra-corpus) as well as inter-corpus experiments where models built on one or more corpora are evaluated on a disjoint corpus. Our results reveal that while inter-corpus performance is considerably lower than comparable intra-corpus results, this effect can be countered by data agglomeration; furthermore, we observe that inter-corpus classiﬁcation accuracies indicate suitability of corpora for building generalizing models.
Growth rate evolution in improved environments under Prodigal Son dynamics

I use an individual‐based model to investigate the evolution of cell division rates in asexual populations under chronic environmental enrichment. I show that maintaining increased growth rates over hundreds of generations following environmental improvement can be limited by increases in cellular damage associated with more rapid reproduction. In the absence of further evolution to either increase damage tolerance or decrease the cost of repair or rate of damage, environmental improvement does not reliably lead to long‐term increases in reproductive rate in microbes. Here, more rapid cell division rates also increases damage, leading to selection for damage avoidance or repair, and a subsequent decrease in population growth, which I call Prodigal Son dynamics, because the consequences of ‘living fast’ force a return to ancestral growth rates. Understanding the conditions under which environmental enrichment is expected to sustainably increase cell division rates is important in applications that require rapid cell division (e.g. biofuel reactors) or seek to avoid the emergence of rapid cell division rates (controlling biofouling).
Single voltage-gated calcium channel current in rat neocortical layer 5 pyramidal neurons in physiological calcium: voltage ramp fluctuation analysis

Voltage-gated calcium channels (VGCCs) are present in all mammalian central neurons, controlling presynaptic release of transmitter, postsynaptic signalling and synaptic integration. The amplitudes of their single open-channel currents in a physiological concentration of extracellular calcium, however, are not well determined, being too small to resolve directly in patch-clamp recordings. However, measurement of this quantity is essential for estimating numbers of functional VGCCs in the membrane and the size of channel-associated calcium signalling domains, and for understanding the stochastic nature of calcium signalling. Here, we recorded the voltage-gated calcium channel current in nucleated patches from layer 5 pyramidal neurons in rat neocortex, in physiological external calcium (1-2 mM). The pharmacological profile of the current was consistent with R-type or Q-type channels, and a small L-type component. In order to reliably separate the calcium current fluctuations from other background currents for fluctuation analysis, despite their small amplitude and rapid rundown, we developed a method using band-pass filtered current responses to ramp membrane potential stimulation. We validated the accuracy of the method by analysing simulated data. At external calcium concentration of 1 mM, and a membrane potential of -20 to -15 mV, we found that single channel current amplitude was about 0.04 pA, increasing to 0.065 pA at 2 mM external calcium, and 0.12 pA at 5 mM. The relaxation time constant of the fluctuations was in the range 0.2-0.8 ms. The results demonstrate that single channel current amplitude of native voltage-gated calcium channels can be resolved accurately and straightforwardly.
What elements of Leadership have most impact in Integrated Care Teams and Do They Have a Measurable Effect on Patient Outcomes

Background: Current NHS policy is focused on creating regional "Integrated Care Systems" (ICS) across England. The aim of ICS are to cost effectively deliver more integrated and cost-effective health and social care services, eliminating competition and duplication and creating more seamless services. To fully realise these aims, the health and social care workforce, need to work effectively together in integrated teams. A key to maximising the effectiveness of these teams will be to ensure that they have leaders with the appropriate skills. Integrated team leadership (ITL)is still a relatively new concept. This study built on previous work to define integrated team leadership, by exploring its impact of on staff and patients. Study Design: Eleven (11) community based rehabilitation, integrated health and social care teams (CRAICS) were recruited into this research. Team members (253) completed a 360 degree feedback exercise for 11 team leaders, utilising a highly validated leadership questionnaire. They also completed a validated tool to measure team level dynamics. Cross sectional patient outcome data was also collected in the same period, utilising the Therapy Outcome Measures (TOMs) (Enderby et al. 2006) and European Quality of Life indicator, EQ5D (EUROQOL-GROUP, 2006). Results: Data was analysed to answer 3 questions: 1. What is the relationship between effective Leadership, and Team Level Dynamics in integrated health and social care teams? Leadership variables "Person-focused" and "Task-focused" leadership, were found to have a highly significant (0.005) association with and effect upon a wide range of individual staff and Team level dynamics variables. Passive-Avoidant Leadership behaviours were also found to have a highly significant negative association with individual and team level variables. 2. Does leadership in integrated health and social care teams have an observable effect on patient outcomes? Leadership variables were found to have no observable effect on Patient Outcomes. 3. Do team dynamics, in integrated health and social care teams, have an observable affect on patient outcomes? A number of team level variables when combined had highly significant effects on Quality of Life. Effects on Therapy Outcomes were close to significant. Individual level variables had close to significant effect on patient outcomes Conclusions: Leadership in integrated teams has a significant and consistently strong effect on both team and individual staff level dynamics. And there are indications that team level and individual level dynamics have some effect on patient outcomes. Further research is needed to investigate these relationships more fully, perhaps utilising a multilevel statistical model.
Fuzzy AHP–GOAL Programming Approach for a Supplier Selection Problem

This paper presents an integrated evaluation approach for decision support enabling effective supplier selection and ordering processes in textile industry. The integrated evaluation method in this study includes two phases that consist of fuzzy AHP and goal programming approaches. Supplier evaluation and selection is a multi-criterion decision problem which includes both qualitative and quantitative factors. That’s why; firstly, linguistic variables expressed in trapezoidal fuzzy numbers are applied to assess weights and ratings of supplier selection criteria. Then a hierarchy multiple model based on fuzzy set theory is expressed and the geometric mean method of Buckley is used to aggregate pair wise comparisons. Finally, a goal programming model is built using the goals about coefficients of suppliers, total ordering cost, number of wrong deliveries, total delivery cost under the constraints of required minimum and maximum number of orderings and acceptable quality cost levels of each supplier and demand constraint of the product. Paper type: Research Paper Published online: 30 June 2015 Vol. 5, No. 3, pp. 271-285 ISSN 2083-4942 (Print) ISSN 2083-4950 (Online) 272 B. T. Sivrikaya, A. Kaya, E.n Dursun and F. Cebi © 2015 Poznan University of Technology. All rights reserved.
Beneficial and Detrimental Effects of Plasmin(ogen) during Infection and Sepsis in Mice

Plasmin has been proposed to be an important mediator during inflammation/infection. In this study, by using mice lacking genes for plasminogen, tissue-type plasminogen activator (tPA), and urokinase-type PA (uPA), we have investigated the functional roles of active plasmin in infection and sepsis. Two models were used: an infection model by intravenous injection of 1×107 CFU of S. aureus, and a sepsis model by intravenous injection of 1.6×108 CFU of S. aureus. We found that in the infection model, wild-type (WT) mice showed significantly higher survival rates than plasminogen-deficient (plg-/-) mice. However, in the sepsis model, plg-/- or tPA-/-/uPA-/- mice showed the highest survival rate whereas WT and tPA+/-/uPA+/- mice showed the lowest survival rate, and plg+/-, tPA-/-, and uPA-/- mice had an intermediate survival rate. These results indicate that the levels of active plasmin are critical in determining the survival rate in the sepsis, partly through high levels of inflammatory cytokines and enhanced STAT3 activation. We conclude that plasmin is beneficial in infection but promotes the production of inflammatory cytokines in sepsis that may cause tissue destruction, diminished neutrophil function, and an impaired capacity to kill bacteria which eventually causes death of these mice.
Escape to the beach: Pre-retirement in-migrants' narratives of change, place and identity

The pre-retirement cohort encompasses the ages of 50 to 65. Members of this cohort that migrate within New Zealand remains largely ignored in social research. This cohort encompasses people experiencing an emergent mid-life life-stage characterized by increased fluidity between previously distinct phases such as work and retirement. Once relocated, in-migrants seek ways to become endogenous actors in their new locale and construct new identities. A change of habitus is required to successfully navigate the transition from city-dweller to 'local'. One avenue to achieve this is to engage with local volunteer organisations to develop attachment to place, identity and life-meaning. This qualitative research took place in Mercury Bay on the Coromandel Peninsula, New Zealand, with pre-retirees who inmigrated from city locations and sought volunteer roles in local community organisations. My initial exploration looked to understand how social capital is manifest for these individuals in their volunteer roles in their new location. However, findings suggest the existence of a paradox whereby participants' narratives indicate that they unconsciously seek to reproduce the very conditions from which they sought to escape, associated with urban stresses and the demands of new-capitalist workplaces. The paradox is played out in the development of habitus to achieve community embeddedness, although the acquisition of social capital stands in conflict with the existing habitus of workplace efficiency that participants bring with them to effect the changing structure of volunteer groups. This article explores pre-retiree in-migrant narratives of change, place and identity.
Extraction of Radiology Reports using Text mining

In this paper, we propose a text mining system to extract and use the information in radiology reports. The system consists of three main modules: medical finding extractor, report and image retriever. The medical finding extraction module automatically extracts medical findings and associated modifiers to structure radiology reports. The structuring of the free text reports bridges the gap between users and report database, makes the information contained in the reports readily accessible. It also serves as intermediate result to other components of the system. The retrieval module analyzes user's query and returns the reports and images that match the query. The overall evaluation results are satisfactory, though more thorough testing and evaluation are needed. Our future work includes improving the current system performance and implementing the radiology report generation system using statistical machine translation approach, for which we have designed the general architecture. Keywords-component; Text Mining, Radiology reports