Miracle-dz/UniFAR-FTUs huggingface dataset:
Saving the gene pool : genebanks and the political economy of crop germplasm conservation

In the 1970s, concerns about the erosion of genetic diversity of crops led to the establishment of genebanks, repositories for the conservation of plant genetic material, which raise interesting questions about the ways in which biobanking constructs and shapes bioeconomies. Past theorizations have shown that biobanks are part of new bioeconomies that complicate distinctions between social and economic values, and play essential role by managing the different values and priorities In this thesis, I extend this approach to the conservation and use of crop germplasm. Plant genetic resources for food and agriculture circulate internationally in what I term the ‘germplasm economy’: a complex arrangement that is notable for including a novel multilateral system of mutual facilitated access and benefit sharing. Thus, here I analyse the practices and organisation of genebanks, as a means to explore their role in that economy. Based on an interpretive, discourse analysis of documents and 22 semi-structured, qualitative interviews (with actors involved in gene banking policy and practice in Europe), I argue that genebanks construct the shared pool of plant germplasm by constructing ‘genetic resources’ from germplasm, therefore creating a gene pool that is technically and politically available for sharing in accordance with national and international germplasm policy. In so doing, they manage the different value(s) associated with germplasm in ways that enable and justify the international germplasm economy. Hence, this work corroborates the perspective that biobanks of biological material manage and create the economies that they are part of. Yet, in addition, it suggests that genebanks themselves can be considered resources, and that this understanding is important in constructing the germplasm economy as one predicated on sharing Therefore, it suggests that analyses of biomaterial economies should take into consideration both studies of the bioeconomy and of the political economy of technoscience.
Fast asynchronous byzantine agreement and leader election with full information

We resolve two long-standing open problems in distributed computation by describing polylogarithmic protocols for Byzantine agreement and leader election in the asynchronous full information model with a non-adaptive malicious adversary. All past protocols for asynchronous Byzantine Agreement had been exponential, and no protocol for asynchronous leader election had been known. Our protocols tolerate up to n/6+ε faulty processors, for any positive constant ε. They are Monte Carlo, succeeding with probability 1 - o(1) for Byzantine agreement, and constant probability for leader election. A key technical contribution of our paper is a new approach for emulating Feige's lightest bin protocol, even with adversarial message scheduling.
Leakage-aware multiprocessor scheduling for low power

It is expected that (single chip) multiprocessors will increasingly be deployed to realize high-performance embedded systems. Because in current technologies the dynamic power consumption dominates the static power dissipation, an effective technique to reduce energy consumption is to employ as many processors as possible in order to finish the tasks as early as possible, and to use the remaining time before the deadline (the slack) to apply voltage scaling. We refer to this heuristic as schedule and stretch (S&S). However, since the static power consumption is expected to become more significant, this approach is no longer efficient when leakage current is taken into account. In this paper, we first show for which combinations of leakage current, supply voltage, and clock frequency the static power consumption dominates the dynamic power dissipation. These results imply that, at a certain point, it is no longer advantageous from an energy perspective to employ as many processors as possible. Thereafter, a heuristic is presented to schedule the tasks on a number of processors that minimizes the total energy consumption. Experimental results obtained using a public task graph benchmark set show that our leakage-aware scheduling algorithm reduces the total energy consumption by up to 24% for tight deadlines (1.5times the critical path length) and by up to 67% for loose deadlines (8times the critical path length) compared to S&S
A health map for the local human habitat

At the 2006 UK Public Health Association Conference, held in Telford in March, and the International HIA conference in Cardiff in the same month, there was much interest in a new model of health determinants applied to the planning of human settlements. This ‘health map’ is presented here in its current form for the first time. The authors explain its purpose.
The Anatomy & Dynamics of Vision Advantages

The Strength of Weak Ties and Brokerage Theory rely on the argument that weak bridging ties deliver novel information to brokers. Yet, very little empirical evidence exists to validate this claim. Analyzing an evolving corporate email network, we investigate the dynamic mechanisms that enable the “vision advantage”. Three results emerge. First, we confirm the Diversity-Bandwidth Tradeoff at the heart of the vision advantage: As brokers’ networks becomes more diverse, their channel bandwidth contracts, creating countervailing effects on access to novel information. Second, we uncover the mechanics driving the Diversity-Bandwidth Tradeoff and highlight differences in vision advantages across ties: Strong cohesive ties deliver greater information diversity and more total non-redundant information, while weak bridging ties contribute the greatest uniqueness information which is most different from what other contacts deliver. Third, network stability increases the novelty brokers receive over time, providing the first evidence of the role of network dynamics in vision advantages.
Short-term effects of a disturbed light–dark cycle and environmental enrichment on aggression and stress-related parameters in male mice

In the laboratory setting, environmental factors have a major influence on the well-being of laboratory animals. The present study shows the importance of a semi-natural light–dark cycle. In this experiment one cohort of mice was kept with a continuous lighting for one week. After the first week the artificial light–dark cycle was 12:12 with lights on at 07:00 h. The second cohort of mice was kept with this 12:12 h light–dark cycle from the start. Half of each cohort received environmental enrichment. In order to analyse corticosterone levels, urine samples were collected. To measure agonistic behaviour, the behaviour of the mice was recorded on videotape immediately after cage cleaning. A significant difference in corticosterone levels between cohorts was found during disturbed lighting, but not after lighting conditions were reset to 12:12 h. In the first test week, mice subjected to disturbed lighting also showed a significantly shorter agonistic latency than control mice. This difference had disappeared when in the second test week all mice experienced 12:12 h lighting. No effects of enriched housing were found. This experiment has shown that disturbed lighting for socially-housed male mice caused physiological and behavioural changes indicative of stress, not only leading to much higher levels of corticosterone but also to shorter agonistic latency within the groups.
Assessment of Soil Disturbance Caused by Forest Operations by Means of Portable Laser Scanner and Soil Physical Parameters

Forest operations can cause compaction and rutting, resulting in soil degradation processes. Soil damage is usually assessed through costly and time-consuming manual field measurements. The aim of this study is to investigate the impact of logging operations on soil using traditional ground surveys integrated with laser scanning data acquired by a terrestrial portable laser scanner (PLS). This approach provides an alternative to soil rut manual measurements. Two skid trails, that differed by the numbers of machine passes and slope were sampled. Data collection was performed before and after forest operations. The specific objectives were to: (i) assess soil compaction, and (ii) determine rutting by way of multi-temporal high-resolution digital terrain models (DTM) generated by PLS data. This is the first study to assess changes in soil volume via the PLS. Significant logging impacts were detected using both investigation methods (i.e., physical parameters from traditional surveys and rutting from multi-temporal spatial analysis based on DTM). The PLS method provides a very high sampling density of the soil surface, permitting detailed spatial analysis of terrain changes. Moreover, the pre-processing cost for PLS-generated DTM is low in comparison to the time needed for traditional survey based on manual field measurements. PLS may be a useful instrument for soil sampling in forest monitoring applications.
Caenorhabditis elegans PIAK, a Phospholipid-independent Kinase That Activates the AKT/PKB Survival Kinase*

Phospholipid-dependent kinase 1 (PDK 1) is a 3′-phospholipid-responsive serine/threonine kinase that plays a critical role in cell survival by phosphorylating and activating the anti-apoptotic AKT/PKB kinase. While PDK 1 is clearly an important component of the cell survival machinery, the potential for phospholipid-independent activation of the AKT/PKB survival pathway has not been extensively examined at the molecular level. We have identified a second form of PDK 1 in the nematode Caenorhabditis elegans that we have termed PIAK (phospholipid-independent AKT/PKBkinase). PIAK is highly homologous to C. elegans and mammalian PDK 1 with the exception that the novel kinase lacks a phospholipid binding pleckstrin homology domain. The domain structure of PIAK suggests that it might be a phospholipid-independent kinase, and PIAK phosphorylates mammalian AKT/PKB at the activating Thr308 residue in the presence of the phosphatidylinositol (PI) 3-kinase inhibitors as well as in the absence of growth factors. In addition, PIAK is capable of inducing the phospholipid-independent, AKT/PKB-induced phosphorylation of the AFX-type forkhead transcription factor, resulting in its cytoplasmic localization. Because the nuclear localization of this transcription factor induces an apoptotic state, this PIAK-mediated cytoplasmic sequestration allows for cell survival. Finally, PIAK activity appears to be induced by various inhibitors of cell cycle G1progression. These data suggest an alternate, phosphatidylinositol 3-kinase-independent mechanism for the activation of the AKT/PKB survival pathway that may be utilized during periods of cellular quiescence.
Computer assisted neurophysiology by a distributed JAVA program

We have developed a distributed software package which allows neurophysiologists to have at hand a set of network and graphic tools in order to perform the analysis of data collected from the electrical activity of neurons, studied in the experimental laboratory. This system is built around three major components. First, the experimental data are processed in order to select specific data files from the networked computer and display the spike trains as raster dots. The second part selects one type of analysis (e.g., cross-correlation, out of a set of possible choices) after configuration of some specific parameters. Finally, the third component deals with the results of data analyses, which are selected and displayed on a multi-parameter graphic "ring binder. " We have used the Java programming language to implement this application. This recent object-oriented language offers platform-independent software tools including graphic package and standard network protocols.
Research on Fast 1-D DCT Algorithm Based on Parallel Computing

Discrete cosine transform (DCT) is applied widely in the field of signal processing. But the transform operation is complicated, and a large amount of multiply operation and addition operation affect largely the transform efficiency. To overcome such drawback, a new method based on parallel operation is proposed in the paper. First, a new transform matrix and a sort of new matrix operation principle are defined in the interest of convenient parallel operation. Then, DCT is accomplished by parallel operation tidily based on the new transform matrix and the new matrix operation principle. The theoretical analysis shows that the computation sum of the proposed method to compute DCT only needs one equivalent multiplication and a few equivalent additions, and the operation efficiency relative to other fast algorithm is improved markedly.
Exploring Temporal and Spatial Correlations on Circuit Variables for Enhancing Simulation-based Test Generation

The ever-increasing complexity and size of current circuit designs have made testing and verification major bottlenecks in the design flow of VLSI (Very Large Scale Integrated) circuits. Statistics show that more than 70% of the design effort can be spent on functional verification and manufacturing testing. This percentage is expected to increase in the future if no significant strides in these areas are made. In this dissertation, we target three related problems in simulation-based Design Verification and Testing: Sequential ATPG (Automatic Test Pattern Generation), Unbounded Model Checking (UMC) of safety properties, and low power testing for full-scan sequential circuits. We model these three problems as simulation-based pattern generation problems and exploit novel ATPG algorithms to increase the effectiveness of sequential ATPGs. The main challenge for fault/error detection in sequential circuits is the large number of flip-flops (FFs) in modern designs. Due to the large number and variable length of test sequences required for such circuits, the existing deterministic ATPG algorithms fail to achieve high test coverages. Such algorithms typically work by first unrolling the sequential circuit and then performing frequent backtracking to generate test vectors for fault detection. For the hard-to-detect faults, these schemes either run out of memory or require a huge computational effort. We show that simulationbased ATPGs, on the other hand, scale very well for large circuits as they perform only forward simulation. A fundamental problem associated with simulation-based ATPGs is to avoid exhaustive circuit simulation, which is impractical for large designs in the real world, by choosing high quality test vectors that achieve a high test coverage within a low simulation time. We tackle this primary problem by exploiting different correlation-based heuristics. The intuition behind using correlation-based heuristics is to better guide the pattern generation engine such that the specific objective of either fault detection or property verification in UMC or minimizing power consumption during the testing, is achieved in an efficient manner without resorting to exhaustive simulation. In particular, we model and explore the following correlations: (1) temporal correlations, i.e. correlations on each primary input (PI) in different time frames, and (2) spatial correlations, i.e. correlations among different FFs in the same time frame. We employ temporal correlations in the context of pattern generation of a built-in-self-test (BIST) architecture and we explore spatial correlations to guide a logic-simulation-based sequential ATPG and low power scan test generation. Experimental results on ISCAS and ITC benchmark circuits have shown that those correlations can enhance the simulation to discover more faults or design errors in a significantly shorter time.
Expression Signature Defined by FOXM1–CCNB1 Activation Predicts Disease Recurrence in Non–Muscle-Invasive Bladder Cancer

Purpose: Although standard treatment with transurethral resection and intravesical therapy (IVT) is known to be effective to address the clinical behavior of non–muscle-invasive bladder cancer (NMIBC), many patients fail to respond to the treatment and frequently experience disease recurrence. Here, we aim to identify a prognostic molecular signature that predicts the NMIBC heterogeneity and response to IVT. Experimental Design: We analyzed the genomic profiles of 102 patients with NMIBC to identify a signature associated with disease recurrence. The validity of the signature was verified in three independent patient cohorts (n = 658). Various statistical methods, including a leave-one-out cross-validation and multivariate Cox regression analyses, were applied to identify a signature. We confirmed an association between the signature and tumor aggressiveness with experimental assays using bladder cancer cell lines. Results: Gene expression profiling in 102 patients with NMIBC identified a CCNB1 signature associated with disease recurrence, which was validated in another three independent cohorts of 658 patients. The CCNB1 signature was shown to be an independent risk factor by a multivariate analysis and subset stratification according to stage and grade [HR, 2.93; 95% confidence intervals (CI), 1.302–6.594; P = 0.009]. The subset analysis also revealed that the signature could identify patients who would benefit from IVT. Finally, gene network analyses and experimental assays indicated that NMIBC recurrence could be mediated by FOXM1–CCNB1–Fanconi anemia pathways. Conclusions: The CCNB1 signature represents a promising diagnostic tool to identify patients with NMIBC who have a high risk of recurrence and to predict response to IVT. Clin Cancer Res; 20(12); 3233–43. ©2014 AACR.
Smarter Phones for Healthier Lifestyles: An Adaptive Fitness Game

Mobile phones can persuade users to adopt healthy behaviors such as regular exercise. Monsters & Gold, a context-aware, user-adaptive mobile fitness game, runs on mobile phones to motivate and train users in jogging outdoors. The game dynamically presents virtual monsters, gold, and other items-according to factors such as users' heart rate, age, and exercise phase-to encourage users to speed up or slow down. A first evaluation led to an improved game design; a subsequent evaluation confirmed beneficial effects on training and motivation.
Can't surf, won't surf: The digital divide in mental health

Background New health information technology (HIT) increasingly plays a role in health care as technology becomes cheaper and more widespread. However, there is a danger that those who do not use or have access to technology will not benefit from HIT innovations, thus creating a “digital divide”. Aims To assess the extent to which mental health service users have access to, skills in using and appetite for various technologies. Methods A cross-sectional survey was used to assess technology use and access patterns of 121 people from community mental health services. Data were analysed using logistic regression. Results Technology use and access were very similar to that of the general population with older individuals reporting less familiarity, access and confidence across a range of technologies. Black, minority and ethnic (BME) groups were more likely to access computers outside of their own homes than white individuals. Older participants experiencing psychosis indicated a desire to increase their computer use. Conclusions The findings reported here contrast with recent evidence suggesting that those who do not engage with technology are “self-excluders”. Furthermore, BME groups may need extra support regarding provision of technology in order to engage with HIT.
Information Extraction and the Casual User

The task of information extraction (IE) calls for limited understanding of text, limited by the demands of the user and the domain of inquiry IF. returns specific instances of the concept or relation of interest to the user. Whereas IE systems have, to date, been oriented towards either system experts (e.g., computational linguists) or domain experts (e.g., professionals searching for information within the field of their profession), the availability of large amounts of on-line textual information to the casual user strongly suggests that techniques oriented towards non-experts are needed. We present a review of current user-involvcmcnt tcchniques in IE, and begin to investigate issues of knowledge representation and learning in the development of a mixcd-iuitiativc information extraction system. In particular, we discuss some advantages of dividing the knowledge used by the IE system into a query model, a domain model and a corpus model, to assist casual users in interacting with the system. We also advocate flexibility in determining increments for learning, supporting negotiation between system and user.
Transformation of freshwater and marine caulobacters by electroporation

We performed plasmid electrotransformation of Caulobacter crescentus strains and obtained up to 3 x 10(8) transformants per micrograms of pKT230. The presence and integrity of the paracrystalline protein surface (S) layer influenced electroporation; caulobacters lacking the S layer were electrotransformed 10 times more efficiently than caulobacters possessing the S layers. A procedure yielding 1,500 transformants per micrograms of pKT230 was developed for a marine caulobacter. Electroporation was used in combination with several genetic techniques, including introduction of ligation mixtures, suicide transposon mutagenesis, gene replacement, and plasmid electrotransfer from Escherichia coli to caulobacters.
Artificial Life Applied to Adaptive Information Agents

We propose a model, inspired by recent artificial life theory, applied to the problem of retrieving information from a large, distributed collection of documents such as the World Wide Web. A population of agents is evolved under density dependent selection for the task of locating information for the user. The energy necessary for survival is obtained from both environment and user in exchange for appropriate information. By competing for relevant documents, the agents robustly adapt to their information environment and are allocated to efficiently exploit shared resources. We illustrate the roles played by document locality, adaptive search strategies, and relevance feedback, in the information gathering process.
Performance Inconsistency in Large Scale Data Processing Clusters

A large shared computing platform is usually divided into several virtual clusters of fixed sizes, and each virtual cluster is used by a team. A cluster scheduler dynamically allocates physical servers to the virtual clusters depending on their sizes and current job demands. In this paper, we show that current cluster schedulers, which optimize for instantaneous fairness, cause performance inconsistency among the virtual clusters: Virtual clusters with similar loads see very different performance characteristics. We identify this problem by studying a production trace obtained from a large cluster and performing a simulation study. Our results demonstrate that when using an instantaneous-fairness scheduler, a large VC that contributes more resources during underload periods can not be properly rewarded during its overload periods. These results suggest that not using resource sharing history is the root cause for the performance inconsistency.
Enabling Real-Time Mobile Cloud Computing through Emerging Technologies

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