Miracle-dz/UniFAR-FTUs huggingface dataset:
Overview of the PWMEnrich package

The purpose of this package is to asses the enrichment of already known Position Weight Matrices (PWMs) in a set of DNA sequences. Note that this is not the same as de-novo motif finding which discovers novel motifs, and motif comparison which aligns motifs. The main difference to traditional PWM-based sequence scanning is that PWM hits are considered together in a sequence or DNA region of certain length, instead of being given individual P-values for individual motif hits. One example of such an approach which we re-implement in the package is Clover (Frith et al., 2004). The package is useful both for hypothesis verification, e.g. testing if a ChIP-chip/seq dataset is enriched for a target TF, and for hypothesis generation, e.g. finding novel co-factors (with already existing PWMs) in an already defined regulatory region(s). A variety of algorithms has been implemented to asses enrichment using both motif hit-count based metrics and threshold-free metrics. Enrichments can be normalized to a background (e.g. genomic) distribution and P-values derived.
Geospatial stream query processing using Microsoft SQL Server StreamInsight

Microsoft SQL Server spatial libraries contain several components that handle geometrical and geographical data types. With advances in geo-sensing technologies, there has been an increasing demand for geospatial streaming applications. Microsoft SQL Server StreamInsight (StreamInsight, for brevity) is a platform for developing and deploying streaming applications that run continuous queries over high-rate streaming events. With its extensibility infrastructure, StreamInsight enables developers to integrate their domain expertise within the query pipeline in the form of user defined modules. This demo utilizes the extensibility infrastructure in Microsoft StreamInsight to leverage its continuous query processing capabilities in two directions. The first direction integrates SQL spatial libraries into the continuous query pipeline of StreamInsight. StreamInsight provides a well-defined temporal model over incoming events while SQL spatial libraries cover the spatial properties of events to deliver a solution for spatiotemporal stream query processing. The second direction extends the system with an analytical refinement and prediction layer. This layer analyzes historical data that has been accumulated and summarized over the years to refine, smooth and adjust the current query output as well as predict the output in the near future. The demo scenario is based on transportation data in Los Angeles County.
Web Performance Enhancement of E-business System Using the SSD

In this paper, we proposed web performance enhancement of the e-business system using the SSD (Solid State Drive). In the e-business system, transactions must be strictly ordered, should occur at a fixed point time, and not be lost. We approached to solve e-business problem by using software and hardware techniques such as SSD. X-internet has advantage of C/S and Web applications. Since X-internet technique enables to reduce the loading time of web pages, X-internet is useful to enhance performance of the e-business system. SSD is a storage device that uses DRAM or NAND Flash as primary storage media. Since the SSD stores and accesses data directly to memory chips, which results in storage speeds far greater than conventional magnetic storage devices (HDD). Therefore x-internet techniques can be used to solve confused browsing and poor UI, and SSD can be used to solve I/O bottleneck of the e-business system.
Managers’ Self-Serving Attribution Bias and Corporate Financial Policies

The self-serving attribution bias ("SAB") refers to individuals taking responsibility for good outcomes and blaming others for bad outcomes. Consistent with the existence of managerial SAB, I find that managers tend to use more first-person pronouns (relative to second- and third-person pronouns) in the Management Discussions and Analysis Section of the 10-K filings when firm performance is better. A consequence of SAB is overconfidence (i.e., overestimating the mean and underestimating the variance of future cash flows). Consistent with this argument, managers with more SAB are more likely to issue forward-looking statements and make earnings forecasts, the tone (e.g., positive versus negative) of their forward-looking discussions has smaller variation, and their earnings forecasts tend to be overly optimistic. Firms whose managers have more SAB have higher investment-cash flow sensitivity and experience more negative market reactions around acquisition announcements. These firms also tend to have higher leverage, rely more on long-term debt financing, are more likely to repurchase stocks, and are less likely to issue dividends. Collectively, the evidence suggests that managers have self-serving attribution bias and this bias has implications for corporate policies.
An examination of the effects of a wearable display on informal face-to-face communication

Wearable computers have the potential to support our memory, facilitate our creativity, our communication and augment our physical senses [15] but, like email and cell-phones, they also have the potential to interrupt, displace or downgrade our social interactions. This paper presents the results of a simple laboratory-based study which examines the impact of a xybernaut head-mounted Shimadzu display on conversation between two people. We hypothesized that the wearable, by reducing eye-contact and attention in the wearer would have a detrimental effect. Pairs of friends discussed pre-defined topics under three conditions, no wearable, wearable present but inactive, wearable present and active. Likert scale statements were used to record the wearer's level of attention, concentration, listening, eye contact, naturalness and relaxation, and the impact of the wearable. The presence of the wearable without an active display did not have an effect on the conversation. The quality of the interaction was however impaired in the active wearable condition and eye-contact was effected. This effect may be the result of the nature of the information type, the interface used, the characteristics of its presentation or the novelty of the display to the user. Additional research to identify design implications is discussed.
Optimal Simple Monetary Policy Rules with Nominal Rigidities and Asymmetric Information in the Credit Market∗

This paper evaluates monetary policy rules in a business cycle model with staggered prices, preset nominal wages and asymmetric information in the credit market. Rules are compared in a utility based welfare metric, the effects of the model’s nonlinear dynamics are captured by a quadratic approximation to the policy function. The firms net worth crucially affects the terms of obtaining outside finance. Financial frictions dampen the economies response to shocks and make them highly persistent. When prices are sticky, but wages flexible, these frictions do not matter for monetary policy: The optimal policy is strong inflation targeting. When both wages and prices are sticky, there exists a trade-off between inflation and output. Financial frictions increase the importance of stabilizing output, since they make the output variations more persistent.
Embodied evolution in a morphologically heterogeneous population of robots

Holistic evolution (the concurrent evolution of control structure and morphology) and embodied evolution (the distribution of evolutionary function into asynchronous, autonomous robots operating in a task environment offer a great deal of possibility to the field of evolutionary robotics. Both methodologies have principlistic and practical ramifications, but the most radical—and important—may lie in their confluence. This paper details the motivations behind an experimental work in progress.
Experimental Models to Study the Role of Microbes in Host-Parasite Interactions

Until recently, parasitic infections have been primarily studied as interactions between the parasite and the host, leaving out crucial players: microbes. The recent realization that microbes play key roles in the biology of all living organisms is not only challenging our understanding of host-parasite evolution, but it also provides new clues to develop new therapies and remediation strategies. In this paper we provide a review of promising and advanced experimental organismal systems to examine the dynamic of host-parasite-microbe interactions. We address the benefits of developing new experimental models appropriate to this new research area and identify systems that offer the best promises considering the nature of the interactions among hosts, parasites, and microbes. Based on these systems, we identify key criteria for selecting experimental models to elucidate the fundamental principles of these complex webs of interactions. It appears that no model is ideal and that complementary studies should be performed on different systems in order to understand the driving roles of microbes in host and parasite evolution.
Acyl-CoA Synthetase Isoforms 1, 4, and 5 Are Present in Different Subcellular Membranes in Rat Liver and Can Be Inhibited Independently*

Inhibition studies have suggested that acyl-CoA synthetase (ACS, EC 6.2.1.3) isoforms might regulate the use of acyl-CoAs by different metabolic pathways. In order to determine whether the subcellular locations differed for each of the three ACSs present in liver and whether these isoforms were regulated independently, non-cross-reacting peptide antibodies were raised against ACS1, ACS4, and ACS5. ACS1 was identified in endoplasmic reticulum, mitochondria-associated membrane (MAM), and cytosol, but not in mitochondria. ACS4 was present primarily in MAM, and the 76-kDa ACS5 protein was located in mitochondrial membrane. Consistent with these locations, N-ethylmaleimide, an inhibitor of ACS4, inhibited ACS activity 47% in MAM and 28% in endoplasmic reticulum. Troglitazone, a second ACS4 inhibitor, inhibited ACS activity <10% in microsomes and mitochondria and 45% in MAM. Triacsin C, a competitive inhibitor of both ACS1 and ACS4, inhibited ACS activity similarly in endoplasmic reticulum, MAM, and mitochondria, suggesting that a hitherto unidentified triacsin-sensitive ACS is present in mitochondria. ACS1, ACS4, and ACS5 were regulated independently by fasting and re-feeding. Fasting rats for 48 h resulted in a decrease in ACS4 protein, and an increase in ACS5. Re-feeding normal chow or a high sucrose diet for 24 h after a 48-h fast increased both ACS1 and ACS4 protein expression 1.5–2.0-fold, consistent with inhibition studies. These results suggest that ACS1 and ACS4 may be linked to triacylglycerol synthesis. Taken together, the data suggest that acyl-CoAs may be functionally channeled to specific metabolic pathways through different ACS isoforms in unique subcellular locations.
SKYLINE2GPS: Localization in urban canyons using omni-skylines

This paper investigates the problem of geo-localization in GPS challenged urban canyons using only skylines. Our proposed solution takes a sequence of upward facing omnidirectional images and coarse 3D models of cities to compute the geo-trajectory. The camera is oriented upwards to capture images of the immediate skyline, which is generally unique and serves as a fingerprint for a specific location in a city. Our goal is to estimate global position by matching skylines extracted from omni-directional images to skyline segments from coarse 3D city models. Under day-time and clear sky conditions, we propose a sky-segmentation algorithm using graph cuts for estimating the geo-location. In cases where the skyline gets affected by partial fog, night-time and occlusions from trees, we propose a shortest path algorithm that computes the location without prior sky detection. We show compelling experimental results for hundreds of images taken in New York, Boston and Tokyo under various weather and lighting conditions (daytime, foggy dawn and night-time).
Fast convolution-based methods for computing the signed distance function and its derivatives

We present a fast convolution-based technique for computing an approximate, signed Euclidean distance function at a set of 2D and 3D grid locations. Instead of solving the non-linear static Hamilton-Jacobi equation (|\nabla S|=1), our solution stems from solving for a scalar field \phi in a linear differential equation and then deriving the solution for S from its exponent. In other words, when S and \phi are related by \phi = \exp(-S/\tau) and \phi satisfies a specific linear differential equation corresponding to the extremum of a variational problem, we obtain the Euclidean distance function S = -\tau \log(\phi)in the limit as \tau-->0. This is in sharp contrast to solvers such as the fast marching and fast sweeping methods which directly solve the Hamilton-Jacobi equation by the Godunov upwind discretization scheme. Our linear formulation provides us with a closed-form solution to the approximate Euclidean distance function expressed as a discrete convolution, and hence efficiently computed by the Fast Fourier Transform (FFT). Moreover, the solution circumvents the need for spatial discretization of the derivative operator thereby providing highly accurate results. As \tau-->0, we show the convergence of our results to the true solution and also bound the error for a given value of \tau. The differentiability of our solution allows us to compute - using a set of convolutions - the first and second derivatives of the approximate distance function. In order to determine the sign of the distance function (defined to be positive inside a closed region and negative outside), we compute the winding number in 2D and the topological degree in 3D and again explicitly show that these computations can be performed via fast convolutions.
Direct numerical simulations of the κ-mechanism I. Radial modes in the purely radiative case

Context. We present a purely-radiative hydrodynamical model of the κ-mechanism that sustains radial oscillations in Cepheid variables. Aims. We determine the physical conditions favourable for the κ-mechanism to occur inside a layer, with a configurable conductivityhollow. We complete nonlinear direct numerical simulations (DNS) that initiate from these most favourable conditions. Methods. We compare the results of a linear-stability analysis, applied to radial modes using a spectral solver, and a DNS, which is developed from a high-order finite difference code. Results. We find that by changing the location and shape of the hollow, we can generate well-defined instability strips. For a given position in the layer, the amplitude and width of the hollow appear to be key parameters to vary to attain unstable modes driven by the κ-mechanism. The DNS, starting from the favourable conditions, confirm both the growth rates and the structures of linearly-unstable modes. Nonlinear saturation is produced by intricate couplings between excited fundamental mode and higher damped overtones.
Towards secure model for SCADA systems

Nowadays, Supervisory Control And Data Acquisition (SCADA) systems have huge influences on the human life. They provide a distance remote controlling, monitoring and information gathering of transmission, production and distribution of every automation systems such as electric power, power plants, refineries, rail transportation, waste and water systems, oil and gas. In this paper, different possible threats, risks and vulnerabilities in the SCADA systems are surveyed, and some mitigation strategies to improve the SCADA security systems are proposed.
The deficit at ruin in the stationary renewal risk model

Properties of the distribution of the deficit at ruin in the stationary renewal risk model are studied. A mixture representation for the conditional distribution of the deficit at ruin (given that ruin occurs) is derived, as well as a stochastic decomposition involving the residual lifetime associated with the maximal aggregate loss. When the individual claims have a phase-type distribution, the deficit at ruin is also of phase-type.
Automating the debugging of datacenter applications with ADDA

Debugging data-intensive distributed applications running in datacenters is complex and time-consuming because developers do not have practical ways of deterministically replaying failed executions. The reason why building such tools is hard is that non-determinism that may be tolerable on a single node is exacerbated in large clusters of interacting nodes, and datacenter applications produce terabytes of intermediate data exchanged by nodes, thus making full input recording infeasible. We present ADDA, a replay-debugging system for datacenters that has lower recording and storage overhead than existing systems. ADDA is based on two techniques: First, ADDA provides control plane determinism, leveraging our observation that many typical datacenter applications consist of a separate “control plane” and “data plane”, and most bugs reside in the former. Second, ADDA does not record “data plane” inputs, instead it synthesizes them during replay, starting from the application's external inputs, which are typically persisted in append-only storage for reasons unrelated to debugging. We evaluate ADDA and show that it deterministically replays real-world failures in Hypertable and Memcached.
Contextual and Perceptual Brain Processes Underlying Moral Cognition: A Quantitative Meta-Analysis of Moral Reasoning and Moral Emotions

Background and Objectives Human morality has been investigated using a variety of tasks ranging from judgments of hypothetical dilemmas to viewing morally salient stimuli. These experiments have provided insight into neural correlates of moral judgments and emotions, yet these approaches reveal important differences in moral cognition. Moral reasoning tasks require active deliberation while moral emotion tasks involve the perception of stimuli with moral implications. We examined convergent and divergent brain activity associated with these experimental paradigms taking a quantitative meta-analytic approach. Data Source A systematic search of the literature yielded 40 studies. Studies involving explicit decisions in a moral situation were categorized as active (n = 22); studies evoking moral emotions were categorized as passive (n = 18). We conducted a coordinate-based meta-analysis using the Activation Likelihood Estimation to determine reliable patterns of brain activity. Results & Conclusions Results revealed a convergent pattern of reliable brain activity for both task categories in regions of the default network, consistent with the social and contextual information processes supported by this brain network. Active tasks revealed more reliable activity in the temporoparietal junction, angular gyrus and temporal pole. Active tasks demand deliberative reasoning and may disproportionately involve the retrieval of social knowledge from memory, mental state attribution, and construction of the context through associative processes. In contrast, passive tasks reliably engaged regions associated with visual and emotional information processing, including lingual gyrus and the amygdala. A laterality effect was observed in dorsomedial prefrontal cortex, with active tasks engaging the left, and passive tasks engaging the right. While overlapping activity patterns suggest a shared neural network for both tasks, differential activity suggests that processing of moral input is affected by task demands. The results provide novel insight into distinct features of moral cognition, including the generation of moral context through associative processes and the perceptual detection of moral salience.
‘I really hated school, and couldn’t wait to get out!’: Reflections on ‘a wasted opportunity’ amongst access to HE students.

In constructing a narrative account of our lives, we may recall experiences of schooling with a mixture of resentment and regret, and perhaps a sense of ‘wasted opportunities’. This is particularly true if school has left us with a fragile academic self-esteem, through being labelled ‘a failure’ as a child. For some, this contributes to a desire to ‘make good’ the perceived deficit through re-engagement with formal education as an adult learner. This paper draws upon biographical data from longitudinal research that followed the progress of a group of mature students on a further education Access to Higher Education course. It explores how themes of ‘waste’ especially and ‘desire’ are used in accounting for past, present and (anticipated) future lives and learner identities. It concludes that, despite some commonalities, experiences of adult learners are too individual and personalised to be meaningfully categorised, as some early studies had attempted to do.
Diatoms can be an important exception to temperature–size rules at species and community levels of organization

Climate warming has been linked to an apparent general decrease in body sizes of ectotherms, both across and within taxa, especially in aquatic systems. Smaller body size in warmer geographical regions has also been widely observed. Since body size is a fundamental determinant of many biological attributes, climate‐warming‐related changes in size could ripple across multiple levels of ecological organization. Some recent studies have questioned the ubiquity of temperature–size rules, however, and certain widespread and abundant taxa, such as diatoms, may be important exceptions. We tested the hypothesis that diatoms are smaller at warmer temperatures using a system of geothermally heated streams. There was no consistent relationship between size and temperature at either the population or community level. These field data provide important counterexamples to both James’ and Bergmann's temperature–size rules, respectively, undermining the widely held assumption that warming favours the small. This study provides compelling new evidence that diatoms are an important exception to temperature–size rules for three reasons: (i) we use many more species than prior work; (ii) we examine both community and species levels of organization simultaneously; (iii) we work in a natural system with a wide temperature gradient but minimal variation in other factors, to achieve robust tests of hypotheses without relying on laboratory setups, which have limited realism. In addition, we show that interspecific effects were a bigger contributor to whole‐community size differences, and are probably more ecologically important than more commonly studied intraspecific effects. These findings highlight the need for multispecies approaches in future studies of climate warming and body size.
Cloudlet-based cyber foraging framework for distributed video surveillance provisioning

Continuous monitoring activities in surveillance system generate massive amount of data to be transferred from Internet-of-Things (IoT) devices (i.e., cameras and sensors) to a centralized processing unit for analysis. However, several issues need to be addressed, including data migration over bandwidth limited and high latency communication networks, and the heterogeneous nature of data obtained from the surveillance system. The aim of this paper is to develop a scalable and lightweight intelligent distributed surveillance system that make use of an integrated framework of Internet-of-Things (IoT) and cloud computing. It leverages on the pervasiveness in IoT and ubiquitous property of cloud computing technology. This paper introduces the concept of bringing cloud closer to the IoT in order to address the resource poverty of IoT and the dependency for massive data transmission to distant cloud. For providing real-time on-site object detection, this paper instantiates a cloudlet on resource-rich nearby infrastructure which is connected to the IoT devices for distributed retrieval and processing of critical and sensitive data.